The DOI matches its Crossref record; 40 of the 40 references it cites were found in a registry or an index; 12 of the 18 sources its claims cite were checked for support.
Molecular insights into human phosphatidylserine synthase 2 and its regulation of SREBP pathways
Open accessAbstract
Homologous proteins share similar sequences, enabling them to work together in cells to support normal physiological functions. Phosphatidylserine synthases 1 and 2 (PSS1 and PSS2) are homologous enzymes that catalyze the synthesis of phosphatidylserine (PS) from different substrates. PSS2 shows a preference for phosphatidylethanolamine (PE) as its substrate, whereas PSS1 can utilize either PE or phosphatidylcholine. Previous studies showed that inhibiting PSS1 promotes SREBP-2 cleavage. Interestingly, despite their homology, our findings reveal that PSS2 exerts an opposing effect on the cleavage of both SREBP-1 and SREBP-2. We resolved the cryo-electron microscopy (cryo-EM) structure of human PSS2 at 3.3 Å resolution. Structural comparison of the catalytic cavities between PSS1 and PSS2 along with molecular dynamics simulations uncovers the molecular details behind the substrate preference of PSS2 for PE. The lipidomic analysis showed that PSS2 deficiency leads to PE accumulation in the endoplasmic reticulum, which has been shown to inhibit the cleavage of sterol regulatory element-binding proteins (SREBPs) in mice. Thus, our findings reveal the intricate network of intracellular phospholipid metabolism and underscore the distinct regulatory roles of homologous proteins in cellular activities.
Overview
AI snapshot
Written from the paper’s full text.
TL;DR
PSS2 deficiency in CHO-K1 cells suppresses SREBP-1 and SREBP-2 cleavage by elevating ER phosphatidylethanolamine (PE), unlike PSS1 deficiency, which lowers PS and activates SREBP2. The 3.3 Å cryo-EM structure of human PSS2 reveals a smaller catalytic cavity that restricts substrate use to PE rather than PC.
Key findings
- In Ptdss2−/− CHO-K1 cells, SREBP-1 and SREBP-2 cleavage was suppressed, including significantly reduced nuclear SREBP-1 and suppressed SREBP-2 cleavage; downstream SREBP pathway genes were also suppressed.
- Ptdss2−/− cells showed no notable change in total PS versus WT, whereas Ptdss1−/− cells had considerably lower PS, indicating PSS1 is the major PS contributor in WT CHO-K1 cells. PSS2 mRNA was ~30% of PSS1 mRNA in WT CHO-K1 cells.
- ER PE levels were substantially elevated in Ptdss2−/− cells and decreased in Ptdss1−/− cells versus WT, supporting the model that accumulated ER PE inhibits SREBP cleavage.
- The human PSS2 cryo-EM structure at 3.3 Å with C2 symmetry shows a homodimer with 10 transmembrane helices per monomer, a PE density in the catalytic cavity, Ca2+ coordinated by Glu225, Glu228, Glu240, and Asp249, and two PS molecules in the cytosolic pocket. Substrate specificity is explained by a smaller catalytic cavity: F196 and F332 face inward in PSS2, while corresponding PSS1 residues F168 and F305 face away; MD simulations showed PC head-to-catalytic-histidine distances of ~3.5–4 Å versus >6 Å for PE.
Methods
- WT, Ptdss1−/−, and Ptdss2−/− CHO-K1 cells generated by CRISPR-Cas9 were analyzed by RT-PCR, LC-MS/MS lipidomics, ER isolation via density gradient centrifugation, western blotting for SREBP processing, and quantitative real-time PCR.
- Recombinant human PSS2 was expressed in HEK-293S GnTI− cells using baculovirus, purified via Flag affinity and size-exclusion chromatography, assayed for serine-exchange activity with POPE and L-serine, and imaged by cryo-EM at 3.3 Å; models were built using AlphaFold2 coordinates, COOT, PHENIX, and MolProbity.
- Molecular dynamics simulations used CHARMM36 parameters and NAMD, with 100 ns production runs, to measure distances between PE/PC head groups and catalytic residues.
Limitations
- The paper does not include an explicit limitations section.
- Evident from the text: cryo-EM resolution limited model building, leaving residues 1–57 and 437–487 of PSS2 unbuilt; serine was tentatively modeled into the catalytic cavity; substrate-specificity conclusions rely partly on MD simulations over a 100 ns timescale.
- The text states that the mechanism by which PSS1 activity, but not PSS2, regulates Asters-mediated cholesterol transport remains to be explored in future studies.
Model-written summary. Check it against the paper before relying on it.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
12 of 18 cited sources checked · 0 supported · 1 flagged · accuracy not yet measured
- Interpretationreasoning
The suppression of SREBP-1 and SREBP-2 cleavage by PSS2 deficiency is caused by elevated PE levels in the endoplasmic reticulum.
“we show that PSS2 deficiency instead suppresses both SREBP-1 and SREBP-2 cleavage by elevating phosphatidylethanolamine (PE) levels in the endoplasmic reticulum.”
- Also stated in: § Discussion · hedged
“in the absence of PSS2, the accumulated PE in the ER would inhibit SREBP1 and SREBP2 cleavage.”
Quote in the paperSubstantial claim1 of 1 sources checked- cites [16] S. Rong, DGAT2 inhibition blocks SREBP-1 cleavage and improves hepatic steatosis by increasing phosphatidylethanolamine in the ER. Cell Metab. 36, 617– 629.e7 (2024). 38340721 PMC10939742 source
In Results, under “PE enrichment suppresses SREBP-1 cleavage” (page unavailable), the paper says PE enrichment reduced nuclear SREBP-1 but did not significantly change nuclear SREBP-2. It studies DGAT2 inhibition, not PSS2 deficiency. Thus its finding is contrary to the attributed claim that elevated ER PE suppresses cleavage of both isoforms through PSS2 deficiency. (LLM, conf=0.90)
Checked by a reasoning model — may be wrong.
Experimental — accuracy not yet measured
- Also stated in: § Discussion · hedged
- Findingown data
Ptdss1 knockout reduces total PS levels in CHO-K1 cells.
“The lipidomic analysis showed that the total amount of PS was considerably lower in Ptdss1−/− cells, consistent with a previous finding (15).”
Quote in the paperSubstantial claim1 of 1 sources checked- cites [15] D. Arikketh, R. Nelson, J. E. Vance, Defining the importance of phosphatidylserine synthase-1 (PSS1): Unexpected viability of PSS1-deficient mice. J. Biol. Chem. 283, 12888– 12897 (2008). 18343815 source
The discussion of CHO mutants (section labeled Abstract in our copy; page unavailable) reports that PSS1-deficient CHO cells had 35–66% less PS. It does not identify those cells as CHO-K1 or establish that their PSS1 deficiency was a Ptdss1 knockout, so those specifics are not supported. (LLM, conf=0.85)
Experimental — accuracy not yet measured
- Premiseown data
The two mammalian phosphatidylserine synthases PSS1 and PSS2 have opposing roles in lipid regulation.
“the two mammalian phosphatidylserine synthases, Phosphatidylserine synthases 1 and 2 (PSS1 and PSS2), have opposing roles in lipid regulation.”
Quote in the paperSubstantial claim3 of 3 sources checked- cites [10] T. Long, Molecular insights into human phosphatidylserine synthase 1 reveal its inhibition promotes LDL uptake. Cell 187, 5665– 5678.e18 (2024). 39208797 PMC11455612 source
The Introduction identifies PSS1 and PSS2 as the two mammalian phosphatidylserine synthases and describes different substrate preferences. The Results link PSS1 to cholesterol regulation, but our copy does not establish that PSS2 has an opposing role in lipid regulation. (LLM, conf=0.84)
Experimental — accuracy not yet measured - cites [11] M. N. Trinh, Interplay between Asters/GRAMD1s and phosphatidylserine in intermembrane transport of LDL cholesterol. Proc. Natl. Acad. Sci. U.S.A. 119, e2120411119 (2022). 34992143 PMC8764668 source
The Abstract identifies PTDSS1 (PSS1) as a major phosphatidylserine-synthesizing enzyme in mammalian cells, and the Results link its loss to reduced cholesterol esterification. The passages do not describe PSS2 or compare the synthases, so they do not support the claimed opposing roles. (LLM, conf=0.85)
Experimental — accuracy not yet measured - cites [12] J. Sandhu, Aster proteins facilitate nonvesicular plasma membrane to ER cholesterol transport in mammalian cells. Cell 175, 514– 529.e20 (2018). 30220461 PMC6469685 source
The Discussion (page unavailable) says the Aster GRAM domain binds phosphatidylserine, but it does not discuss phosphatidylserine synthases. Searches for PSS1, PSS2, and phosphatidylserine synthase found no passage comparing their roles in lipid regulation. (LLM, conf=0.78)
Experimental — accuracy not yet measured
- Findingown data
Ptdss2 knockout increases PE levels in the endoplasmic reticulum.
“elevating phosphatidylethanolamine (PE) levels in the endoplasmic reticulum”
- Also stated in: § Results · plain
“PE levels were substantially elevated in Ptdss2−/− cells and decreased in Ptdss1−/− cells (Fig. 2C), supporting our hypothesis.”
- Also stated in: § Abstract · plain
“Here, we found Ptdss2 knockout in CHO-K1 cells increased PE levels in the ER and is inclined to inhibit the cleavage of SREBPs.”
Quote in the paperSubstantial claim - Also stated in: § Results · plain
- Findingown data
PSS2 mRNA level is approximately 30% that of PSS1 in wild-type CHO-K1 cells.
“the messenger RNA (mRNA) level of PSS2 is ~30% that of PSS1 in wild-type (WT) CHO-K1 cells (Fig. 1A).”
Quote in the paperNot a substantial claim
- Findingown data
Ptdss1 knockout slightly increases Ptdss2 mRNA levels in CHO-K1 cells.
“knocking out Ptdss1 in CHO-K1 cells leads to a slight increase in the mRNA levels of Ptdss2.”
Quote in the paperNot a substantial claim - Findingown data
PE levels in the endoplasmic reticulum are decreased in Ptdss1−/− cells compared to wild-type cells.
“PE levels were substantially elevated in Ptdss2−/− cells and decreased in Ptdss1−/− cells (Fig. 2C)”
Quote in the paperSubstantial claim - Findingown data
PSS2 deficiency does not affect PS synthesis in CHO-K1 cells.
“there is no notable change in the amount of PS in Ptdss2−/− cells compared to that in WT cells”
- Also stated in: § Results · plain
“abolishing PSS2 does not affect the PS synthesis in CHO-K1 cells”
Quote in the paperSubstantial claim - Also stated in: § Results · plain
- Findingown data
Ptdss2 knockout does not alter Ptdss1 mRNA levels in CHO-K1 cells.
“knocking out Ptdss2 in CHO-K1 cells did not alter the Ptdss1 mRNA levels (Fig. 1A).”
Quote in the paperNot a substantial claim - Findingown data
The catalytic cavity of PSS2 is much smaller than that of PSS1.
“The catalytic cavity of PSS2 is much smaller than that of PSS1, since F196 and F332 face into the cavity but the corresponding residues (F168 and F305) in PSS1 face away from each other enlarging the cavity to accommodate PC (Fig. 3H).”
Quote in the paperSubstantial claim - Findingreasoning
Loss of PSS2 leads to repression of both SREBP pathways.
“Loss of PSS2 leads to repression of both pathways.”
Quote in the paperSubstantial claim - Findingown data
Two PS molecules were found in the cytosolic pocket of PSS2.
“two PS molecules were found in the cytosolic pocket of PSS2 (Fig. 3A and SI Appendix, Fig. S2)”
Quote in the paperSubstantial claim - Findingown data
The calcium ion in the PSS2 catalytic cavity is coordinated by residues Glu225, Glu228, Glu240, and Asp249.
“Inside the catalytic cavity, the calcium ion is coordinated by residues Glu225, Glu228, Glu240, and Asp249 (Fig. 3B).”
Quote in the paperNot a substantial claim - Findingown data
A PE density is found between the luminal halves of TM4 and TM8 in the cryo-EM map of PSS2.
“A PE density was found between the luminal halves of TM4 and TM8 in the cryo-EM map of PSS2 (Fig. 3B and SI Appendix, Fig. S2).”
Quote in the paperNot a substantial claim - Findingown data
The PC head group is positioned closer to F196, F224, and F332 in the catalytic core compared to PE.
“the PC head group is positioned closer to F196, F224, and F332 in the catalytic core compared to PE (Fig. 3I).”
Quote in the paperSubstantial claim - Findingreasoning
The corresponding residue in PSS1 is W297, which pulls TM5 away from TM7 via hydrophobic contacts.
“the corresponding residue in PSS1 is W297, which pulls TM5 away from TM7 via hydrophobic contacts.”
Quote in the paperSubstantial claim - Findingown data
Residue F324 in TM7 has a hydrophobic contact with I220 in TM5.
“Residue F324 in TM7 has a hydrophobic contact with I220 in TM5.”
Quote in the paperSubstantial claim - Findingown data
TMs 4 to 8 form the catalytic cavity in the luminal leaflet, which opens to both the lipid bilayer and the lumen.
“TMs 4 to 8 form the catalytic cavity in the luminal leaflet, which opens to both the lipid bilayer and the lumen.”
Quote in the paperSubstantial claim - Interpretationown data
PSS1 is a major contributor of PS in wild-type CHO-K1 cells.
“demonstrating that PSS1 is a major contributor of PS in WT CHO-K1 cells (Fig. 1B).”
Quote in the paperSubstantial claim - Interpretationown data
PC introduces steric hindrance with residues in the catalytic core due to its bulky head group, potentially disrupting interactions between the phospholipid substrate, catalytic histidine, and serine and inhibiting the reaction.
“It is likely that PC introduces steric hindrance with the residues in the catalytic core due to its bulky head group.”
- Also stated in: § Results · hedged
“These potential steric interferences may disrupt interactions between the phospholipid substrate, the catalytic histidine, and serine, ultimately inhibiting the reaction.”
Quote in the paperSubstantial claim - Also stated in: § Results · hedged
- Interpretationown data
PSS2's substrate specificity restricts it to using PE.
“Our biophysical studies reveal the structural basis for PSS2’s substrate specificity, which restricts it to using PE.”
- Also stated in: § Abstract · plain
“PSS1 can also utilize phosphatidylcholine (PC) as its substrate, whereas PSS2 cannot (3).”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [3] S. Tomohiro, A. Kawaguti, Y. Kawabe, S. Kitada, O. Kuge, Purification and characterization of human phosphatidylserine synthases 1 and 2. Biochem. J. 418, 421– 429 (2009). 19014349 source
- Also stated in: § Abstract · plain
- Interpretationreasoning
In the absence of PSS2, accumulated PE in the endoplasmic reticulum would inhibit SREBP1 and SREBP2 cleavage.
“in the absence of PSS2, the accumulated PE in the ER would inhibit SREBP1 and SREBP2 cleavage.”
Quote in the paperSubstantial claim - Interpretationreasoning
PSS2 may consume considerable amounts of PE for PS synthesis.
“we propose that PSS2 may consume considerable amounts of PE for PS synthesis.”
Quote in the paperSubstantial claim - Interpretationreasoning
PSS2 plays a critical role in modulating the concentration of PE in the endoplasmic reticulum to regulate SREBP1 and SREBP2 pathways.
“we report that PSS2 plays a critical role in modulating the concentration of PE in the ER to regulate SREBP1 and SREBP2 pathways.”
Quote in the paperSubstantial claim
- It may state two separate claims as one. 12
- Probably not a substantial claim. 4
It may state two separate claims as one.
Findingown dataSREBP1 and SREBP2 gene expression is increased in Ptdss1−/− cells.
“we observed an increase in Srebp1 and Srebp2 gene expression from the Ptdss1−/− cells (10)”
Quote in the paperSubstantial claim1 of 1 sources checked- cites [10] T. Long, Molecular insights into human phosphatidylserine synthase 1 reveal its inhibition promotes LDL uptake. Cell 187, 5665– 5678.e18 (2024). 39208797 PMC11455612 source
The Results section (‘PSS1 inhibitor activates SREBP pathway and stimulates LDL uptake’; page unavailable) reports SREBP-2 cleavage in Ptdss1−/− cells, not increased Srebp1 or Srebp2 gene expression. The quantitative real-time PCR methods list primers for LDLR, but not either Srebp gene. Searches for Srebp1 and Srebp2 expression found no passage establishing the claimed increase. (LLM, conf=0.77)
Experimental — accuracy not yet measured
Probably not a substantial claim.
PremisecitationAn increase in PE levels in the endoplasmic reticulum can inhibit SREBP cleavage.
“an increase in PE levels in the ER can inhibit SREBP cleavage (16).”
Quote in the paperSubstantial claim1 of 1 sources checked- cites [16] S. Rong, DGAT2 inhibition blocks SREBP-1 cleavage and improves hepatic steatosis by increasing phosphatidylethanolamine in the ER. Cell Metab. 36, 617– 629.e7 (2024). 38340721 PMC10939742 source
The Results section, “PE enrichment suppresses SREBP-1 cleavage,” reports that increased ER PE blocks SREBP-1 processing. It also says the effect was specific to SREBP-1, not SREBP-2, so the claim’s unqualified reference to SREBP cleavage is broader than the finding. (LLM, conf=0.90)
Experimental — accuracy not yet measured
Probably not a substantial claim. The paper’s conclusions may not depend on it.
PremisecitationPSS1 and PSS2 use PE as a substrate to produce PS in the endoplasmic reticulum.
“PSS1 and PSS2 (gene names: Ptdss1 and Ptdss2, respectively) use phosphatidylethanolamine (PE) as a substrate to produce PS in the endoplasmic reticulum (ER) (2, 3).”
Quote in the paperNot a substantial claim1 of 2 sources checked- cites [2] J. E. Vance, Historical perspective: Phosphatidylserine and phosphatidylethanolamine from the 1800s to the present. J. Lipid Res. 59, 923– 944 (2018). 29661786 PMC5983396 source
Our copy says PS synthase-2 uses PE to make PS and places the active sites of both synthases on the cytosolic face of the ER. It does not support the claim that PSS1 also uses PE; the passage describing PSS1 instead distinguishes PC exchange from PSS2’s PE-to-PS activity. The supplied passages are labeled Abstract and have no page numbers. (LLM, conf=0.88)
Experimental — accuracy not yet measured - cites [3] S. Tomohiro, A. Kawaguti, Y. Kawabe, S. Kitada, O. Kuge, Purification and characterization of human phosphatidylserine synthases 1 and 2. Biochem. J. 418, 421– 429 (2009). 19014349 source
Probably not a substantial claim. The paper’s conclusions may not depend on it.
PremisecitationPtdss2 knockout does not impair LDL-derived cholesterol trafficking from the plasma membrane to the endoplasmic reticulum.
“unlike that in Ptdss1−/− cells, Ptdss2 knockout does not impair LDL-derived cholesterol trafficking from the PM to the ER (11).”
Quote in the paperNot a substantial claim1 of 1 sources checked- cites [11] M. N. Trinh, Interplay between Asters/GRAMD1s and phosphatidylserine in intermembrane transport of LDL cholesterol. Proc. Natl. Acad. Sci. U.S.A. 119, e2120411119 (2022). 34992143 PMC8764668 source
The Results report impaired LDL-cholesterol delivery to the ER in Ptdss1−/− cells, supporting the comparison in the citing sentence. The passages from our copy and a search for PTDSS2 do not address Ptdss2 knockout, so they do not support the claim that its loss leaves trafficking unimpaired. (LLM, conf=0.82)
Experimental — accuracy not yet measured
It may state two separate claims as one.
PremisecitationPSS1 inhibition or deficiency reduces PS levels, thereby blocking Aster-mediated cholesterol transport to activate the SREBP2 pathway.
“While PSS1 inhibition or deficiency reduces phosphatidylserine (PS) levels, thereby blocking Aster-mediated cholesterol transport to activate the SREBP2 pathway”
- Also stated in: § Abstract · plain
“inhibition of PSS1 can activate the SREBP2 pathway and influence cholesterol metabolism (10). This function is primarily achieved by a reduction in PSS1-mediated PS synthesis, which in turn prevents the transport of cholesterol by Asters proteins from the plasma membrane to the ER (11, 12).”
Quote in the paperSubstantial claim3 of 3 sources checked- cites [10] T. Long, Molecular insights into human phosphatidylserine synthase 1 reveal its inhibition promotes LDL uptake. Cell 187, 5665– 5678.e18 (2024). 39208797 PMC11455612 source
The Results section (‘PSS1 inhibitor activates SREBP pathway and stimulates LDL uptake’; page unavailable) says PS is indispensable for Aster-mediated cholesterol transport, reports that PSS1 depletion lowers intracellular PS and activates SREBP-2, and shows that a PSS1 inhibitor activates SREBP-2. It does not establish that inhibitor treatment lowers cellular PS or that Aster-mediated transport is blocked as the demonstrated causal step linking PSS1 inhibition to SREBP-2 activation. (LLM, conf=0.83)
Experimental — accuracy not yet measured - cites [11] M. N. Trinh, Interplay between Asters/GRAMD1s and phosphatidylserine in intermembrane transport of LDL cholesterol. Proc. Natl. Acad. Sci. U.S.A. 119, e2120411119 (2022). 34992143 PMC8764668 source
The Abstract reports that PTDSS1 deficiency reduces PS by 90% and impairs cholesterol transport to the ER; the Results report that LDL then suppresses SREBP-2 processing much less effectively. But the Discussion says Asters still contribute to transport in PS-deficient cells, so their transport is not completely blocked. The supplied passages address PTDSS1 deficiency, not inhibition. (LLM, conf=0.88)
Experimental — accuracy not yet measured - cites [12] J. Sandhu, Aster proteins facilitate nonvesicular plasma membrane to ER cholesterol transport in mammalian cells. Cell 175, 514– 529.e20 (2018). 30220461 PMC6469685 source
The Discussion says Asters bind phosphatidylserine, and the Results (‘Aster-B Promotes PM to ER Cholesterol Transport’; page unavailable) show that reducing Aster function increases SREBP-2 processing. Our copy does not report PSS1 inhibition or deficiency, reduced PS levels from PSS1 loss, or that such a reduction blocks Aster-mediated transport and activates SREBP-2. (LLM, conf=0.86)
Experimental — accuracy not yet measured
- Also stated in: § Abstract · plain
It may state two separate claims as one.
Findingown dataDownstream genes in the SREBP pathway are suppressed in Ptdss2−/− cells, but other genes such as Scap are not.
“the expression of downstream genes in the SREBP pathway, but not the other genes (e.g., Scap), was also suppressed (Fig. 1F).”
Quote in the paperSubstantial claimIt may state two separate claims as one.
Findingown dataPSS2 deficiency suppresses both SREBP-1 and SREBP-2 cleavage.
“we show that PSS2 deficiency instead suppresses both SREBP-1 and SREBP-2 cleavage by elevating phosphatidylethanolamine (PE) levels in the endoplasmic reticulum.”
- Also stated in: § Results · plain
“SREBP-2 cleavage was suppressed in the Ptdss2−/− cells as well (Fig. 1E).”
- Also stated in: § Results · plain
“the nuclear form (N) of SREBP-1 is significantly suppressed (Fig. 1E).”
Quote in the paperSubstantial claim- Also stated in: § Results · plain
It may state two separate claims as one.
Findingown dataSREBP1 and SREBP2 gene expression is suppressed in Ptdss2−/− cells.
“the expression of SREBP genes in Ptdss2−/− cells was suppressed (Fig. 1C).”
Quote in the paperSubstantial claimIt may state two separate claims as one.
Findingown dataF196 and F332 face into the PSS2 catalytic cavity, while corresponding residues F168 and F305 in PSS1 face away from each other, enlarging the cavity to accommodate PC.
“F196 and F332 face into the cavity but the corresponding residues (F168 and F305) in PSS1 face away from each other enlarging the cavity to accommodate PC (Fig. 3H).”
Quote in the paperSubstantial claimIt may state two separate claims as one.
Findingown dataPSS2 forms a homodimer, with each monomer containing 10 transmembrane helices.
“two PSS2 molecules form a homodimer, with each monomer containing 10 transmembrane helices (TMs).”
Quote in the paperNot a substantial claimIt may state two separate claims as one.
Findingown dataHuman PSS2 structure was determined by cryo-EM at 3.3 Å resolution with C2 symmetry.
“We determined the structure of human PSS2 by cryo-EM at 3.3 Å resolution with C2 symmetry.”
Quote in the paperSubstantial claimIt may state two separate claims as one.
Findingown dataMD simulations show that the distance between the catalytic histidine and the PC head methyl group remains approximately 3.5 to 4 Å, whereas the corresponding distance for the PE head group exceeds 6 Å.
“the distance between the Nε2/Nδ1 of the catalytic histidine and the methyl group of the PC head remains ~3.5 to 4 Å, whereas the corresponding distance for the PE head group exceeds 6 Å (Fig. 3I).”
Quote in the paperSubstantial claimIt may state two separate claims as one.
Findingown dataRecombinant PSS2 has catalytic activity, whereas the catalytically dead mutant PSS2H200A does not.
“recombinant PSS2 but not its catalytically dead mutant PSS2H200A presented reasonable activity”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [3] S. Tomohiro, A. Kawaguti, Y. Kawabe, S. Kitada, O. Kuge, Purification and characterization of human phosphatidylserine synthases 1 and 2. Biochem. J. 418, 421– 429 (2009). 19014349 source
It may state two separate claims as one.
PremisecitationPSS2 is an endoplasmic reticulum-associated enzyme that utilizes PE as a substrate.
“As an ER-associated enzyme that utilizes PE as a substrate”
Quote in the paperSubstantial claim0 of 2 sources checked- cites [2] J. E. Vance, Historical perspective: Phosphatidylserine and phosphatidylethanolamine from the 1800s to the present. J. Lipid Res. 59, 923– 944 (2018). 29661786 PMC5983396 source
Checked before — its earlier verdict is held back until a new check runs.
- cites [3] S. Tomohiro, A. Kawaguti, Y. Kawabe, S. Kitada, O. Kuge, Purification and characterization of human phosphatidylserine synthases 1 and 2. Biochem. J. 418, 421– 429 (2009). 19014349 source
Probably not a substantial claim. The paper’s conclusions may not depend on it.
Premiseown dataHuman PSS1 and PSS2 are well conserved with approximately 40% amino acid sequence identity.
“human PSS1 and PSS2 are well conserved with an amino acid sequence identify of ~40% (SI Appendix, Fig. S1)”
Quote in the paperNot a substantial claimIt may state two separate claims as one.
PremisecitationPSS1 can utilize PC as a substrate, whereas PSS2 cannot.
“PSS1 can also utilize phosphatidylcholine (PC) as its substrate, whereas PSS2 cannot (3).”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [3] S. Tomohiro, A. Kawaguti, Y. Kawabe, S. Kitada, O. Kuge, Purification and characterization of human phosphatidylserine synthases 1 and 2. Biochem. J. 418, 421– 429 (2009). 19014349 source
The authors state this as an assumption.
PSS2 employs its catalytic histidine H200 to deprotonate the hydroxyl group of serine, allowing it to attack the ester bond of PE to generate PS.
“we speculate that PSS2 may employ its catalytic histidine (H200) to deprotonate the hydroxyl-group of serine allowing it to attack the ester bond of PE to generate PS (Fig. 3F).”
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
Each contradiction between two passages listed here was confirmed by an independent check.
PHENIX refinement cites a Dali server reference
MinorThe Methods cite reference 22 for PHENIX refinement, but reference 22 is titled "Dali server," not PHENIX.
“The models were refined in real space using PHENIX (22).”
“22. L. Holm, P. Rosenstrom, Dali server: Conservation mapping in 3D. Nucleic Acids Res. 38, W545– W549 (2010). 20457744 PMC2896194”
POPE concentration differs between the activity assay descriptions
MinorThe Results describe the recombinant PSS2 assay as using 200 mM POPE, whereas the Methods describe the serine-exchange assay under the same incubation conditions as using 200 μM POPE-a 1,000-fold difference.
“We incubated equal concentrations of PSS2 with 200 mM POPE and 2 mM L-serine at 37 °C for 90 min before the LC-MS analysis.”
“First, 200 μM POPE (Avanti) liposomes were prepared by sonication in a buffer containing 50 mM HEPES, pH 7.5, and 5 mM CaCl2. Serine-exchange activity was measured by supplementation of 500 nM PSS2 or PSS2H200A into liposomes and 2 mM serine. Assays were performed in a 100 μL volume for 90 min at 37 °C”
Five-part membrane ratio lists only four components
MinorThe membrane composition specifies five ratio terms but names only four lipid components, leaving one term without a stated component.
“The membrane composition consists of a 10: 4: 2: 1: 1 mixture”
“3-palmitoyl-2-oleoyl-D-glycero-1-phosphatidylcholine: 3-palmitoyl-2-oleoyl-D-glycero-1-PE (POPE): 1-Palmitoyl-2-Oleoyl-inositol: 3-palmitoyl-2-oleoyl-D-glycero-1-pqhosphatidylserine.”
Citations
Cites
VMD: visual molecular dynamics
Humphrey, W., Dalke, A., & Schulten, K. (1996) · Journal of Molecular Graphics · doi:10.1016/0263-7855(96)00018-5 · Cited by 66,952
Comparison of simple potential functions for simulating liquid water
Jorgensen, W. L., Chandrasekhar, J., Madura, J., Impey, R., & Klein, M. (1983) · The Journal of Chemical Physics · doi:10.1063/1.445869 · Cited by 38,397
Coot : model-building tools for molecular graphics
Emsley, P., & Cowtan, K. (2004) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444904019158 · Cited by 30,571
A smooth particle mesh Ewald method
Essmann, U., Perera, L., Berkowitz, M., Darden, T., Lee, H.-C., & Pedersen, L. (1995) · The Journal of Chemical Physics · doi:10.1063/1.470117 · Cited by 21,378
Scalable molecular dynamics with NAMD
Phillips, J. C., Braun, R., Wang, W., Gumbart, J., Tajkhorshid, E., Villa, E., Chipot, C., Skeel, R. D., Kalé, L., & Schulten, K. (2005) · Journal of Computational Chemistry · doi:10.1002/jcc.20289 · Cited by 16,914
All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins
MacKerell, A. D., Bashford, D., Bellott, M., Dunbrack, R. L., Evanseck, J. D., Field, M. J., Fischer, S., Gao, J., Guo, H., Ha, S., et al. (1998) · The Journal of Physical Chemistry B · doi:10.1021/jp973084f · Cited by 14,429
MolProbity : all-atom structure validation for macromolecular crystallography
Chen, V. B., Arendall, W. B., Headd, J. J., Keedy, D. A., Immormino, R. M., Kapral, G. J., Murray, L. W., Richardson, J. S., & Richardson, D. C. (2010) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444909042073 · Cited by 14,115
CHARMM: A program for macromolecular energy, minimization, and dynamics calculations
Brooks, B., Bruccoleri, R., Olafson, B. D., States, D., Swaminathan, S., & Karplus, M. (1983) · Journal of Computational Chemistry · doi:10.1002/jcc.540040211 · Cited by 13,736
cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination
Punjani, A., Rubinstein, J. L., Fleet, D. J., & Brubaker, M. A. (2017) · Nature Methods · doi:10.1038/nmeth.4169 · Cited by 11,626
UCSF ChimeraX : Structure visualization for researchers, educators, and developers
Pettersen, E. F., Goddard, T. D., Huang, C. C., Meng, E. C., Couch, G. S., Croll, T. I., Morris, J. H., & Ferrin, T. E. (2020) · Protein Science · doi:10.1002/pro.3943 · Cited by 9,521
CHARMM‐GUI: A web‐based graphical user interface for CHARMM
Jo, S., Kim, T., Iyer, V. G., & Im, W. (2008) · Journal of Computational Chemistry · doi:10.1002/jcc.20945 · Cited by 9,284
Vanommeslaeghe, K., Hatcher, E., Acharya, C., Kundu, S. C., Zhong, S., Shim, J. Y., Darian, E., Guvench, O., Lopes, P. E. M., Vorobyov, I. V., et al. (2009) · Journal of Computational Chemistry · doi:10.1002/jcc.21367 · Cited by 7,637
Dali server: conservation mapping in 3D
Holm, L., & Rosenstr�m, P. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq366 · Cited by 3,640
Lipid extraction by methyl-tert-butyl ether for high-throughput lipidomics
Matyash, V., Liebisch, G., Kurzchalia, T. V., Shevchenko, A., & Schwudke, D. (2008) · Journal of Lipid Research · doi:10.1194/jlr.d700041-jlr200 · Cited by 2,633
A ubiquitin-like system mediates protein lipidation
Ichimura, Y., Kirisako, T., Takao, T., Satomi, Y., Shimonishi, Y., Ishihara, N., Mizushima, N., Tanida, I., Kominami, E., Ohsumi, M., et al. (2000) · Nature · doi:10.1038/35044114 · Cited by 2,138
Very fast empirical prediction and rationalization of protein pK a values
Li, H., Robertson, A. D., & Jensen, J. H. (2005) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.20660 · Cited by 2,089
SPHIRE-crYOLO is a fast and accurate fully automated particle picker for cryo-EM
Wagner, T., Merino, F., Stabrin, M., Moriya, T., Antoni, C., Apelbaum, A., Hagel, P., Sitsel, O., Raisch, T., Prumbaum, D., et al. (2019) · Communications Biology · doi:10.1038/s42003-019-0437-z · Cited by 1,249
OPM: Orientations of Proteins in Membranes database
Lomize, M. A., Lomize, A. L., Pogozheva, I. D., & Mosberg, H. I. (2006) · Bioinformatics · doi:10.1093/bioinformatics/btk023 · Cited by 1,180
Membrane Phosphatidylserine Regulates Surface Charge and Protein Localization
Yeung, T., Gilbert, G. E., Shi, J., Silvius, J. R., Kapùs, A., & Grinstein, S. (2008) · Science · doi:10.1126/science.1152066 · Cited by 1,109
Phospholipid Synthesis and Transport in Mammalian Cells
Vance, J. E. (2014) · Traffic · doi:10.1111/tra.12230 · Cited by 795
Radhakrishnan, A., Goldstein, J. L., McDonald, J. G., & Brown, M. S. (2008) · Cell Metabolism · doi:10.1016/j.cmet.2008.10.008 · Cited by 534
Self-citationSandhu, J., Li, S., Fairall, L., Pfisterer, S. G., Gurnett, J. E., Xiao, X., Weston, T. A., Vashi, D., Ferrari, A., Orozco, J. L., et al. (2018) · Cell · doi:10.1016/j.cell.2018.08.033 · Cited by 287
Trinh, M. N., Brown, M. S., Goldstein, J. L., Han, J., Vale, G., McDonald, J. G., Seemann, J., Mendell, J. T., & Lu, F. (2020) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2010682117 · Cited by 129
Self-citationMechanisms and inhibition of Porcupine-mediated Wnt acylation
Liu, Y., Qi, X., Donnelly, L., Elghobashi-Meinhardt, N., Long, T., Zhou, R. W., Sun, Y., Wang, B., & Li, X. (2022) · Nature · doi:10.1038/s41586-022-04952-2 · Cited by 128
Self-citationLight modulates glucose metabolism by a retina-hypothalamus-brown adipose tissue axis
Meng, J.-J., Shen, J., Li, G., Ouyang, C., Hu, J., Li, Z., Zhao, H., Shi, Y., Zhang, M., Liu, R., et al. (2023) · Cell · doi:10.1016/j.cell.2022.12.024 · Cited by 122
Sousa, S. B., Jenkins, D., Chanudet, E., Tasseva, G., Ishida, M., Anderson, G., Docker, J., Ryten, M., Sa, J., Saraiva, J. M., et al. (2014) · Nature Genetics · doi:10.1038/ng.2829 · Cited by 115
Vance, J. E. (2018) · Journal of Lipid Research · doi:10.1194/jlr.r084004 · Cited by 113
Rong, S., Xia, M., Vale, G., Wang, S., Kim, C.-W., Li, S., McDonald, J. G., Radhakrishnan, A., & Horton, J. D. (2024) · Cell Metabolism · doi:10.1016/j.cmet.2024.01.011 · Cited by 102
Self-citationDefining the Importance of Phosphatidylserine Synthase 2 in Mice
Bergö, M. O., Gavino, B. J., Steenbergen, R., Sturbois, B., Parlow, A. F., Sanan, D. A., Skarnes, W. C., Vance, J. E., & Young, S. G. (2002) · Journal of Biological Chemistry · doi:10.1074/jbc.m207734200 · Cited by 99
Defining the Importance of Phosphatidylserine Synthase-1 (PSS1)
Arikketh, D., Nelson, R., & Vance, J. E. (2008) · Journal of Biological Chemistry · doi:10.1074/jbc.m800714200 · Cited by 93
Role of Phosphatidylethanolamine in the Biogenesis of Mitochondrial Outer Membrane Proteins
Becker, T., Horvath, S. E., Böttinger, L., Gebert, N., Daum, G., & Pfanner, N. (2013) · Journal of Biological Chemistry · doi:10.1074/jbc.m112.442392 · Cited by 85
Structural basis for itraconazole-mediated NPC1 inhibition
Long, T., Qi, X., Hassan, A., Liang, Q., Brabander, J. K. D., & Li, X. (2020) · Nature Communications · doi:10.1038/s41467-019-13917-5 · Cited by 72
Self-citationPurification and characterization of human phosphatidylserine synthases 1 and 2
Tomohiro, S., Kawaguti, A., Kawabe, Y., Kitada, S., & Kuge, O. (2009) · Biochemical Journal · doi:10.1042/bj20081597 · Cited by 69
Structure and Expression of the Murine Phosphatidylserine Synthase-1 Gene
Sturbois, B., Stone, S. J., Sreenivas, A., & Vance, J. E. (2001) · Journal of Biological Chemistry · doi:10.1074/jbc.m009776200 · Cited by 46
Trinh, M. N., Brown, M. S., Seemann, J., Vale, G., McDonald, J. G., Goldstein, J. L., & Lu, F. (2022) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2120411119 · Cited by 42
Self-citationMolecular basis of Wnt biogenesis, secretion, and Wnt7-specific signaling
Qi, X., Hu, Q., Elghobashi-Meinhardt, N., Long, T., Chen, H., & Li, X. (2023) · Cell · doi:10.1016/j.cell.2023.09.021 · Cited by 40
Self-citationLong, T., Li, D., Vale, G., Jiang, Y., Schmiege, P., Yang, Z. J., McDonald, J. G., & Li, X. (2024) · Cell · doi:10.1016/j.cell.2024.08.004 · Cited by 31
Self-citationStructural basis for catalytic mechanism of human phosphatidylserine synthase 1
Ning, Y., Xu, R., Yu, J., & Ge, J. (2025) · Cell Discovery · doi:10.1038/s41421-025-00775-3 · Cited by 4
Cryo-EM structure of human PSS2
Li, D. Y., & Li, X. (2025) · Worldwide Protein Data Bank · doi:10.2210/pdb9n0x/pdb · Cited by 1
Self-citationCryo-EM structure of human MON1A-CCZ1-RAB7A: 9lol
Li, X., Li, D., Tang, D., Wang, J., & Qi, S. (2025) · Worldwide Protein Data Bank · doi:10.2210/pdb9lol/pdb
Self-citation
Flagged first, then by citations
Research works printed but not linked: 1
- D. Li X. Li Cryo-EM structure of human PSS2. RCSB Protein Data Bank. https://www.rcsb.org/structure/9N0X. Deposited 24 January 2025. · DOI
Cited by
Sorted by citations
Qiao, Z., Liu, T., Hu, X.-F., Ni, W., Jiang, B., & Lu, C. (2026) · Environmental Pollution · doi:10.1016/j.envpol.2026.129044 · Cited by 1
Zhang, W., Qu, H.-R., Du, X.-S., Sun, S., Chen, P., Deng, Z.-H., Pan, Q., Luo, F.-L., Wu, H.-Y., Song, C., et al. (2026) · Cellular Oncology · doi:10.1007/s13402-026-01163-z
Fabbre, A., & Drin, G. (2026) · Biochemical Society Transactions · doi:10.1042/bst20250365
Hu, Y., Cui, Y., Xu, Z., Wu, D., & Yu, X. (2026) · International Journal of Molecular Sciences · doi:10.3390/ijms27146226
Mechanisms of substrate recognition and catalysis in a mammalian phosphatidylserine synthase 2
Wang, L., Zhang, Z., Yang, H., Laganowsky, A. D., & Zhou, M. (2026) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2607382123
Tri-Organelle Contact Sites Integrate Metabolic Function in Health and Disease
Mukunda, S. G., Khan, M. M., Marshall, A., Hinton, A., & Katti, P. (2026) · Contact · doi:10.1177/25152564261496636
Metadata
- Authors
- Li, D., Chen, H., Vale, G., Elghobashi-Meinhardt, N., Hatton, A., Rong, S., McDonald, J. G., & Li, X.
- Affiliations
- The University of Texas Southwestern Medical Center (US)
- Center for Human Nutrition, University of Texas Southwestern Medical Center
- School of Chemistry, University College Dublin
- Corresponding author
- Li, Xiaochun
- ORCID
- Venue
- Proceedings of the National Academy of Sciences
- Publisher
- National Academy of Sciences
- Published
- 2025-05-15
- Volume
- 122
- Issue
- 20
- Pages
- e2501177122-e2501177122
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- PMC
- PMC12107096
- OpenAlex
- W4410398755
- Cited by
- 6
- References
- 39
- Citations by year
- 2026: 6
- FWCI
- 1.92
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Proceedings of the National Academy of Sciences (publishedVersion, cc-by-nc-nd)
- Europe PMC (PubMed Central) (publishedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- PubMed Central (publishedVersion, cc-by-nc-nd)
- Funders
- HHS | NIH | National Institute of General Medical Sciences (R35GM149533)
- Welch Foundation (I-1957)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Biochemistry › Lipid metabolism and biosynthesis
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Cancer, Lipids, and Metabolism
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Sphingolipid Metabolism and Signaling
- Keywords
- SREBP1, SREBP2, phosphatidylethanolamine, substrate preference, phospholipid metabolism, endoplasmic reticulum, homologous enzymes, protein structure, lipidomics
- MeSH terms
- Animals, Endoplasmic Reticulum, Humans, Phosphatidylethanolamines, CDPdiacylglycerol-Serine O-Phosphatidyltransferase, Phosphatidylserines, Substrate Specificity, Cryoelectron Microscopy, Mice, Sterol Regulatory Element Binding Protein 1, Sterol Regulatory Element Binding Protein 2, Molecular Dynamics Simulation
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
A language model drew the claims from the paper on 2026-11-09, under version 3 of the claim definition (model deepseek-v4.1-flash, prompt extract-v3).
A second model labelled each claim on 2026-11-09 (model jev-1.13-20260917, definition revision gold-guideline-v0.2).
Cited sources are checked with a language model’s help (gpt-6-sol).
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review