A new pattern for helix–turn–helix recognition revealed by the PU.l ETS–domain–DNA complex
Abstract
The Ets family of transcription factors, of which there are now about 35 members regulate gene expression during growth and development. They share a conserved domain of around 85 amino acids which binds as a monomer to the DNA sequence 5'-C/AGGAA/T-3'. We have determined the crystal structure of an ETS domain complexed with DNA, at 2.3-A resolution. The domain is similar to alpha + beta (winged) 'helix-turn-helix' proteins and interacts with a ten-base-pair region of duplex DNA which takes up a uniform curve of 8 degrees. The domain contacts the DNA by a novel loop-helix-loop architecture. Four of amino acids that directly interact with the DNA are highly conserved: two arginines from the recognition helix lying in the major groove, one lysine from the 'wing' that binds upstream of the core GGAA sequence, and another lysine, from the 'turn' of the 'helix-turn-helix' motif, which binds downstream and on the opposite strand.
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The crystal structure of PU.1 DBD bound to DNA shows that the N-terminus of PU.1 faces the binding site for Pip.
“The crystal structure of the PU.1 DBD bound to DNA shows that the N-terminus of PU.1 faces the binding site for Pip (Kodandapani et al., 1996).”
From Assembly requirements of PU.1–Pip (IRF‐4) activator complexes: inhibiting function in vivo using fused dimers (1999) · cites this paper as Kodandapani et al., 1996
In the PU.1 DBD-DNA co-crystal structure, the N-terminus of PU.1 is adjacent to the predicted Pip binding site.
“in the PU.1 DBD-DNA co-crystal structure, the N-terminus of PU.1 is adjacent to the predicted binding site of Pip.”
From Assembly requirements of PU.1–Pip (IRF‐4) activator complexes: inhibiting function in vivo using fused dimers (1999) · cites this paper as Kodandapani et al., 1996
The PU.1-DNA co-crystal structure shows numerous protein-DNA backbone contacts.
“This last suggestion is supported by the numerous protein-DNA backbone contacts observed in the PU.1-DNA co-crystal structure”
From Assembly requirements of PU.1–Pip (IRF‐4) activator complexes: inhibiting function in vivo using fused dimers (1999) · cites this paper as Kodandapani et al., 1996
In the crystal structure of the PU.1-ETS domain-DNA complex, the ETS domain has a tight globular structure of three α-helices and a four-stranded anti-parallel β-sheet.
“In the crystal structure of PU.1-ETS domain-DNA complex, Kodandpani et al. showed that the ETS domain assumes a tight globular structure formed by three α-helices and a four-stranded anti-parallel β-sheet.”
From PU.1 and partners: regulation of haematopoietic stem cell fate in normal and malignant haematopoiesis (2009) · cites this paper as [47]
The PU.1 ETS domain binds the 5′-GGAA-3′ core in the major groove via the α3-recognition helix, while two loops contact the phosphate backbone in the minor groove.
“It binds to the 5′-GGAA-3′ core sequence in the major groove via the α3-recognition helix, whereas the two loops on both sides contact the phosphate backbone in the minor groove.”
From PU.1 and partners: regulation of haematopoietic stem cell fate in normal and malignant haematopoiesis (2009) · cites this paper as [47]
In the crystal structure of PU.1, its β3/β4 region does not interact with DNA but is exposed to the solvent.
“It has been shown in the crystal structure of PU.1 that its β3/β4 region does not interact with DNA, but is exposed to the solvent [47].”
From PU.1 and partners: regulation of haematopoietic stem cell fate in normal and malignant haematopoiesis (2009) · cites this paper as [47]
The C terminus of the PU.1 Ets-homology domain is a winged helix-turn-helix motif that serves as a DNA binding domain.
“The C terminus of the PU.1 Ets-homology domain is a winged helix–turn–helix motif (8) that serves as a DNA binding domain.”
From Negative cross-talk between hematopoietic regulators: GATA proteins repress PU.1 (1999) · cites this paper as [8]
The overall structure and DNA-binding mechanism of the ETS domain is based on high-resolution molecular models of ten family members from X-ray crystallography and NMR.
“The overall structure and DNA-binding mechanism of the ETS domain is based on high-resolution molecular models of ten family members derived from both X-ray crystallography and nuclear magnetic resonance (NMR) spectroscopy (Figure 1b, Supplemental Table 2) (37–51).”
From Genomic and biochemical insights into the specificity of ETS transcription factors (2011) · cites this paper as [38]
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BackgroundInfluentialJayaraman, G., Srinivas, R., Duggan, C. R., Ferreira, E., Swaminathan, S., Somasundaram, K., Williams, J. T., Hauser, C. A., Kurkinen, M. T., Dhar, R., et al. (1999) · Journal of Biological Chemistry · doi:10.1074/jbc.274.24.17342 · Cited by 137 · see citing works
When Ets transcription factors meet their partners
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Helix bending as a factor in protein/DNA recognition
Dickerson, R. E., & Chiu, T. K. (1997) · Biopolymers · doi:10.1002/(sici)1097-0282(1997)44:4 · Cited by 127 · see citing works
Ternary complex factors: prime nuclear targets for mitogen-activated protein kinases
Shaw, P. E., & Saxton, J. (2003) · The International Journal of Biochemistry & Cell Biology · doi:10.1016/s1357-2725(03)00031-1 · Cited by 123 · see citing works
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Pharmacological inhibition of the transcription factor PU.1 in leukemia
Antony-Debré, I., Paul, A., Leite, J., Mitchell, K., Kim, H. M., Carvajal, L. A., Todorova, T. I., Huang, K., Kumar, A., Farahat, A. A., et al. (2017) · Journal of Clinical Investigation · doi:10.1172/jci92504 · Cited by 120 · see citing works
MULTIPROTEIN-DNA COMPLEXES IN TRANSCRIPTIONAL REGULATION
Wolberger, C. (1999) · Annual Review of Biophysics and Biomolecular Structure · doi:10.1146/annurev.biophys.28.1.29 · Cited by 119 · see citing works
Packing of aromatic rings against tryptophan residues in proteins
Samanta, U., Pal, D., & Chakrabarti, P. (1999) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s090744499900726x · Cited by 118 · see citing works
“D55, 1421±1427 et al., 1995), transcription factor (Kodandapani et al., 1996) and streptavidin (Chilkoti et al., 1995), the latter binding its substrate, biotin, with an af®nity which is among the highest displayed for non-covalent interactions between a ligand and a protein (Ka ' 1013 Mÿ1).”
BackgroundSunnerhagen, M., Nilges, M., Otting, G., & Carey, J. (1997) · Nature Structural Biology · doi:10.1038/nsb1097-819 · Cited by 118 · see citing works
The Role of Ets Transcription Factors in the Development and Function of the Mammalian Immune System
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Structures of SAP-1 Bound to DNA Targets from the E74 and c-fos Promoters
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“This is in contrast to the DNA in complex with PU.1 (Kodandapani et al., 1996),nine or cytosine base at position 5 of the DNA target.”
BackgroundInfluentialEukaryotic transcription factors
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Expression of a novel factor in human breast cancer cells with metastatic potential.
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Binding to four‐way junction DNA: a common property of architectural proteins?
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The Structural and Dynamic Basis of Ets-1 DNA Binding Autoinhibition
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The RUNX1–PU.1 axis in the control of hematopoiesis
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The Transcription Factor PU.1 is a Critical Regulator of Cellular Communication in the Immune System
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PU.1: A crucial and versatile player in hematopoiesis and leukemia
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The emergence of protein complexes: quaternary structure, dynamics and allostery
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Determinants of DNA-Binding Specificity of ETS-Domain Transcription Factors
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PU.1/Interferon Regulatory Factor Interactions; Mechanisms of Transcriptional Regulation
Marecki, S., & Fenton, M. J. (2000) · Cell Biochemistry and Biophysics · doi:10.1385/cbb:33:2:127 · Cited by 74 · see citing works
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“1 may contribute to the formation of a transcriptional competent complex by DNA bending, a feature also known for NFkB factors (43, 44).”
BackgroundEts regulation of the erbB2 promoter
Scott, G. K., Chang, C.-H., Erny-Albrecht, K. M., Xu, F., Fredericks, W. J., Rauscher, F. J., Thor, A. D., & Benz, C. C. (2000) · Oncogene · doi:10.1038/sj.onc.1204041 · Cited by 76 · see citing works
“…degrees of DNA bending induced by the truncated Ets domains from PU.1 and ESX/Elf-3 are in reasonable accord with the crystallographic results (Kodandapani et al., 1996), the enhanced bending observed by both of the full-length PU.1 and ESX/Elf-3 proteins is surprising given their lack of…”
BackgroundResultConstrained chromatin accessibility in PU.1-mutated agammaglobulinemia patients
Le Coz, C., Nguyen, D. N., Su, C., Nolan, B. E., Albrecht, A. V., Xhani, S., Sun, D., Demaree, B., Pillarisetti, P., Khanna, C., et al. (2021) · Journal of Experimental Medicine · doi:10.1084/jem.20201750 · Cited by 69 · see citing works
“1 ETS crystal structure is a winged helix-turn-helix motif containing three α-helices and a four-stranded β-sheet (Fig. 1 B; Kodandapani et al., 1996).”
BackgroundStructural mechanisms of human RecQ helicases WRN and BLM
Kitano, K. (2014) · Frontiers in Genetics · doi:10.3389/fgene.2014.00366 · Cited by 75 · see citing works
“RQC IS AN UNCONVENTIONAL WINGED-HELIX DOMAIN Figure 4 shows a comparison of the DNA-binding modes of the WRN (A) and BLM (B) RQC domains with those of the conventional winged-helix domains of the transcription factors ETS (Kodandapani et al., 1996; C) and RFX1 (Gajiwala et al., 2000; D).”
MethodMyeloid-specific gene expression
Clarke, S., & Gordon, S. (1998) · Journal of Leukocyte Biology · doi:10.1002/jlb.63.2.153 · Cited by 72 · see citing works
Transcriptional regulation during myelopoiesis
Lenny, N. T., Westendorf, J. J., & Hiebert, S. W. (1997) · Molecular Biology Reports · doi:10.1023/a:1006859700409 · Cited by 73 · see citing works
- Authors
- Kodandapani, R., Pio, F., Ni, C.-Z., Piccialli, G., Klemsz, M., McKercher, S., Maki, R. A., & Ely, K. R.
- Affiliations
- Sanford Burnham Prebys Medical Discovery Institute (US)
- University of Naples Federico II (IT)
- Indiana University School of Medicine (US)
- Venue
- Nature
- Published
- 1996-04
- Volume
- 380
- Issue
- 6573
- Pages
- 456-460
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- OpenAlex
- W1985177466
- Cited by
- 315
- References
- 23
- Citations by year
- 2026: 5 · 2025: 9 · 2024: 2 · 2023: 4 · 2022: 10 · 2021: 6 · 2020: 2 · 2019: 3 · 2018: 6 · 2017: 8 · 2016: 10 · 2015: 7 · 2014: 6 · 2013: 7 · 2012: 7
- FWCI
- 12.37
- Type
- journal article
- Language
- en
- Open access
- closed
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA and Nucleic Acid Chemistry
- Keywords
- ETS transcription factors, ETS domain, DNA-binding domain, helix-turn-helix motif, winged helix-turn-helix, DNA recognition sequence, protein-DNA complex, crystal structure, major groove, transcriptional regulation
- MeSH terms
- Amino Acid Sequence, Animals, DNA, DNA-Binding Proteins, Humans, Models, Molecular, Molecular Sequence Data, Nucleic Acid Conformation, Protein Binding, Protein Conformation, Retroviridae Proteins, Oncogenic, Sequence Homology, Amino Acid, Crystallography, X-Ray, Helix-Turn-Helix Motifs
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