CoChat
Sign Up
Cited by 128

The DOI matches its Crossref record; 6 of the 6 references it cites were found in a registry or an index.

Structure of HHARI, a RING-IBR-RING Ubiquitin Ligase: Autoinhibition of an Ariadne-Family E3 and Insights into Ligation Mechanism

Duda, David M., Olszewski, Jennifer L., Schuermann, Jonathan P., Kurinov, Igor, Miller, Darcie J., Nourse, Amanda, Alpi, Arno F., Schulman, Brenda A.·2013·Structure
DOI 10.1016/j.str.2013.04.019PMC PMC3747818
Open this paper in CoChat — free account

Overview

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1016/j.str.2013.04.019

Cites

6 of 6 references verified0 citation errors · 0 not checkable

Statistics

Verification

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

  • USP8 deubiquitinating activity is specific toward parkin, as it was much less efficient at deubiquitinating other E3s, including HHARI.

    “The DUB activity of USP8 appeared to be specific toward parkin, as it was much less efficient at deubiquitinating other E3s, including HHARI, an RBR family E3 Ub-ligase structurally very similar to parkin (Fig 3D) (Duda et al, 2013;Trempe et al, 2013).”

    From USP8 regulates mitophagy by removing K6‐linked ubiquitin conjugates from parkin (2014) · cites this paper as Duda et al, 2013

    The Results identify HHARI as an RBR E3 ligase related to parkin through its RBR domain. The paper does not report USP8 activity or compare its deubiquitination of parkin and HHARI, so it does not support the specificity finding. (LLM, conf=0.86)

    Experimental — accuracy not yet measured

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Citations

Cites

Flagged first, then by citations

Research works printed but not linked: 59

  1. Aguilera, 2000, Ariadne-1: a vital Drosophila gene is required in development and defines a new conserved family of ring-finger proteins, Genetics, 155, 1231, 10.1093/genetics/155.3.1231 · DOI
  2. Anderson, 2012, Five mechanisms of manipulation by bacterial effectors: a ubiquitous theme, PLoS Pathog., 8, e1002823, 10.1371/journal.ppat.1002823 · DOI
  3. Ardley, 2001, Features of the parkin/ariadne-like ubiquitin ligase, HHARI, that regulate its interaction with the ubiquitin-conjugating enzyme, Ubch7, J. Biol. Chem., 276, 19640, 10.1074/jbc.M011028200 · DOI
  4. Beasley, 2007, Structure of the Parkin in-between-ring domain provides insights for E3-ligase dysfunction in autosomal recessive Parkinson’s disease, Proc. Natl. Acad. Sci. USA, 104, 3095, 10.1073/pnas.0610548104 · DOI
  5. Calabrese, 2011, A RING E3-substrate complex poised for ubiquitin-like protein transfer: structural insights into cullin-RING ligases, Nat. Struct. Mol. Biol., 18, 947, 10.1038/nsmb.2086 · DOI
  6. Capili, 2004, Structure of the C-terminal RING finger from a RING-IBR-RING/TRIAD motif reveals a novel zinc-binding domain distinct from a RING, J. Mol. Biol., 340, 1117, 10.1016/j.jmb.2004.05.035 · DOI
  7. Chacko, 2012, Severe diffraction anisotropy, rotational pseudosymmetry and twinning complicate the refinement of a pentameric coiled-coil structure of NSP4 of rotavirus, Acta Crystallogr. D Biol. Crystallogr., 68, 1541, 10.1107/S090744491203836X · DOI
  8. Chaugule, 2011, Autoregulation of Parkin activity through its ubiquitin-like domain, EMBO J., 30, 2853, 10.1038/emboj.2011.204 · DOI · Paper page
  9. Diao, 2008, Crystal structure of SopA, a Salmonella effector protein mimicking a eukaryotic ubiquitin ligase, Nat. Struct. Mol. Biol., 15, 65, 10.1038/nsmb1346 · DOI
  10. Dou, 2012, Structural basis for autoinhibition and phosphorylation-dependent activation of c-Cbl, Nat. Struct. Mol. Biol., 19, 184, 10.1038/nsmb.2231 · DOI
  11. Dou, 2012, BIRC7-E2 ubiquitin conjugate structure reveals the mechanism of ubiquitin transfer by a RING dimer, Nat. Struct. Mol. Biol., 19, 876, 10.1038/nsmb.2379 · DOI · Paper page
  12. Dove, 2012, RING-between-RINGs—keeping the safety on loaded guns, EMBO J., 31, 3792, 10.1038/emboj.2012.260 · DOI
  13. Du, 2002, Pairs of dipeptides synergistically activate the binding of substrate by ubiquitin ligase through dissociation of its autoinhibitory domain, Proc. Natl. Acad. Sci. USA, 99, 14110, 10.1073/pnas.172527399 · DOI
  14. Dueber, 2011, Antagonists induce a conformational change in cIAP1 that promotes autoubiquitination, Science, 334, 376, 10.1126/science.1207862 · DOI
  15. Emsley, 2004, Coot: model-building tools for molecular graphics, Acta Crystallogr. D Biol. Crystallogr., 60, 2126, 10.1107/S0907444904019158 · DOI · Paper page
  16. Gallagher, 2006, Activation of the E3 ubiquitin ligase Itch through a phosphorylation-induced conformational change, Proc. Natl. Acad. Sci. USA, 103, 1717, 10.1073/pnas.0510664103 · DOI · Paper page
  17. Hamilton, 2001, Structure of a conjugating enzyme-ubiquitin thiolester intermediate reveals a novel role for the ubiquitin tail, Structure, 9, 897, 10.1016/S0969-2126(01)00657-8 · DOI
  18. Huang, 1999, Structure of an E6AP-UbcH7 complex: insights into ubiquitination by the E2-E3 enzyme cascade, Science, 286, 1321, 10.1126/science.286.5443.1321 · DOI
  19. Huang, 2004, A unique E1-E2 interaction required for optimal conjugation of the ubiquitin-like protein NEDD8, Nat. Struct. Mol. Biol., 11, 927, 10.1038/nsmb826 · DOI
  20. Huibregtse, 1995, A family of proteins structurally and functionally related to the E6-AP ubiquitin-protein ligase, Proc. Natl. Acad. Sci. USA, 92, 2563, 10.1073/pnas.92.7.2563 · DOI
  21. Kamadurai, 2009, Insights into ubiquitin transfer cascades from a structure of a UbcH5B approximately ubiquitin-HECT(NEDD4L) complex, Mol. Cell, 36, 1095, 10.1016/j.molcel.2009.11.010 · DOI
  22. Kirisako, 2006, A ubiquitin ligase complex assembles linear polyubiquitin chains, EMBO J., 25, 4877, 10.1038/sj.emboj.7601360 · DOI
  23. Kitada, 1998, Mutations in the parkin gene cause autosomal recessive juvenile parkinsonism, Nature, 392, 605, 10.1038/33416 · DOI · Paper page
  24. Kobashigawa, 2011, Autoinhibition and phosphorylation-induced activation mechanisms of human cancer and autoimmune disease-related E3 protein Cbl-b, Proc. Natl. Acad. Sci. USA, 108, 20579, 10.1073/pnas.1110712108 · DOI
  25. Kondapalli, 2012, PINK1 is activated by mitochondrial membrane potential depolarization and stimulates Parkin E3 ligase activity by phosphorylating serine 65, Open Biol., 2, 120080, 10.1098/rsob.120080 · DOI · Paper page
  26. Lazarou, 2012, Role of PINK1 binding to the TOM complex and alternate intracellular membranes in recruitment and activation of the E3 ligase Parkin, Dev. Cell, 22, 320, 10.1016/j.devcel.2011.12.014 · DOI · Paper page
  27. Lazarou, 2013, PINK1 drives Parkin self-association and HECT-like E3 activity upstream of mitochondrial binding, J. Cell Biol., 200, 163, 10.1083/jcb.201210111 · DOI · Paper page
  28. Lin, 2012, Crystal structures of two bacterial HECT-like E3 ligases in complex with a human E2 reveal atomic details of pathogen-host interactions, Proc. Natl. Acad. Sci. USA, 109, 1925, 10.1073/pnas.1115025109 · DOI
  29. Lin, 2013, ARIH2 is essential for embryogenesis, and its hematopoietic deficiency causes lethal activation of the immune system, Nat. Immunol., 14, 27, 10.1038/ni.2478 · DOI
  30. Lopez, 2011, CARD-mediated autoinhibition of cIAP1’s E3 ligase activity suppresses cell proliferation and migration, Mol. Cell, 42, 569, 10.1016/j.molcel.2011.04.008 · DOI
  31. Lougheed, 2001, Structure of melanoma inhibitory activity protein, a member of a recently identified family of secreted proteins, Proc. Natl. Acad. Sci. USA, 98, 5515, 10.1073/pnas.091601698 · DOI
  32. Marín, 2009, RBR ubiquitin ligases: Diversification and streamlining in animal lineages, J. Mol. Evol., 69, 54, 10.1007/s00239-009-9252-3 · DOI
  33. Marín, 2002, Comparative genomics of the RBR family, including the Parkinson’s disease-related gene parkin and the genes of the ariadne subfamily, Mol. Biol. Evol., 19, 2039, 10.1093/oxfordjournals.molbev.a004029 · DOI
  34. Matthews, 1968, Solvent content of protein crystals, J. Mol. Biol., 33, 491, 10.1016/0022-2836(68)90205-2 · DOI
  35. Moynihan, 1999, The ubiquitin-conjugating enzymes UbcH7 and UbcH8 interact with RING finger/IBR motif-containing domains of HHARI and H7-AP1, J. Biol. Chem., 274, 30963, 10.1074/jbc.274.43.30963 · DOI
  36. Nuytemans, 2010, Genetic etiology of Parkinson disease associated with mutations in the SNCA, PARK2, PINK1, PARK7, and LRRK2 genes: a mutation update, Hum. Mutat., 31, 763, 10.1002/humu.21277 · DOI
  37. Quezada, 2009, A family of Salmonella virulence factors functions as a distinct class of autoregulated E3 ubiquitin ligases, Proc. Natl. Acad. Sci. USA, 106, 4864, 10.1073/pnas.0811058106 · DOI
  38. Reverter, 2005, Insights into E3 ligase activity revealed by a SUMO-RanGAP1-Ubc9-Nup358 complex, Nature, 435, 687, 10.1038/nature03588 · DOI
  39. Saha, 2011, Essential role for ubiquitin-ubiquitin-conjugating enzyme interaction in ubiquitin discharge from Cdc34 to substrate, Mol. Cell, 42, 75, 10.1016/j.molcel.2011.03.016 · DOI
  40. Sarraf, 2013, Landscape of the PARKIN-dependent ubiquitylome in response to mitochondrial depolarization, Nature, 496, 372, 10.1038/nature12043 · DOI · Paper page
  41. Scheffner, 1995, Protein ubiquitination involving an E1-E2-E3 enzyme ubiquitin thioester cascade, Nature, 373, 81, 10.1038/373081a0 · DOI
  42. Sha, 2010, Phosphorylation of parkin by Parkinson disease-linked kinase PINK1 activates parkin E3 ligase function and NF-kappaB signaling, Hum. Mol. Genet., 19, 352, 10.1093/hmg/ddp501 · DOI
  43. Sheldrick, 1997, SHELXL: high-resolution refinement, 319, 10.1016/S0076-6879(97)77018-6 · DOI
  44. Singer, 2008, Structure of the Shigella T3SS effector IpaH defines a new class of E3 ubiquitin ligases, Nat. Struct. Mol. Biol., 15, 1293, 10.1038/nsmb.1511 · DOI
  45. Singh, 2012, Novel E3 ubiquitin ligases that regulate histone protein levels in the budding yeast Saccharomyces cerevisiae, PLoS ONE, 7, e36295, 10.1371/journal.pone.0036295 · DOI
  46. Smit, 2012, The E3 ligase HOIP specifies linear ubiquitin chain assembly through its RING-IBR-RING domain and the unique LDD extension, EMBO J., 31, 3833, 10.1038/emboj.2012.217 · DOI
  47. Stieglitz, 2012, LUBAC synthesizes linear ubiquitin chains via a thioester intermediate, EMBO Rep., 13, 840, 10.1038/embor.2012.105 · DOI
  48. Strong, 2006, Toward the structural genomics of complexes: crystal structure of a PE/PPE protein complex from Mycobacterium tuberculosis, Proc. Natl. Acad. Sci. USA, 103, 8060, 10.1073/pnas.0602606103 · DOI
  49. Tokunaga, 2012, LUBAC, a novel ubiquitin ligase for linear ubiquitination, is crucial for inflammation and immune responses, Microbes Infect., 14, 563, 10.1016/j.micinf.2012.01.011 · DOI
  50. Verdecia, 2003, Conformational flexibility underlies ubiquitin ligation mediated by the WWP1 HECT domain E3 ligase, Mol. Cell, 11, 249, 10.1016/S1097-2765(02)00774-8 · DOI
  51. Wenzel, 2012, Following Ariadne’s thread: a new perspective on RBR ubiquitin ligases, BMC Biol., 10, 24, 10.1186/1741-7007-10-24 · DOI
  52. Wenzel, 2011, UBCH7 reactivity profile reveals parkin and HHARI to be RING/HECT hybrids, Nature, 474, 105, 10.1038/nature09966 · DOI
  53. Wickliffe, 2011, The mechanism of linkage-specific ubiquitin chain elongation by a single-subunit E2, Cell, 144, 769, 10.1016/j.cell.2011.01.035 · DOI
  54. Wiesner, 2007, Autoinhibition of the HECT-type ubiquitin ligase Smurf2 through its C2 domain, Cell, 130, 651, 10.1016/j.cell.2007.06.050 · DOI
  55. Yamoah, 2008, Autoinhibitory regulation of SCF-mediated ubiquitination by human cullin 1’s C-terminal tail, Proc. Natl. Acad. Sci. USA, 105, 12230, 10.1073/pnas.0806155105 · DOI
  56. Zagotta, 2003, Structural basis for modulation and agonist specificity of HCN pacemaker channels, Nature, 425, 200, 10.1038/nature01922 · DOI
  57. Zheng, 2000, Structure of a c-Cbl-UbcH7 complex: RING domain function in ubiquitin-protein ligases, Cell, 102, 533, 10.1016/S0092-8674(00)00057-X · DOI · Paper page
  58. Zhu, 2008, Structure of a Shigella effector reveals a new class of ubiquitin ligases, Nat. Struct. Mol. Biol., 15, 1302, 10.1038/nsmb.1517 · DOI
  59. Zwart, 2005, Characterization of X-ray ata sets, CCP4 Newsletter, 42

Cited by

Sorted by citations

Metadata

Authors
Duda, D. M., Olszewski, J. L., Schuermann, J. P., Kurinov, I., Miller, D. J., Nourse, A., Alpi, A. F., & Schulman, B. A.
Venue
Structure
Publisher
Elsevier BV
Published
2013-06
Volume
21
Issue
6
Pages
1030-1041
ISSN
0969-2126
DOI
10.1016/j.str.2013.04.019
PMC
PMC3747818
Cited by
128
References
6
Language
en
Licence

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.

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