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We are deeply saddened by the passing of Amos Bairoch (1957–2025), the creator of PROSITE. We wish to dedicate our latest paper, published shortly before his death, to him. He will always be a source of inspiration to us.
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Amos Bairoch

PROSITE documentation PDOC51905
Zinc finger UBZ1-, UBZ2-, UBZ3-, and UBZ4-type profiles


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PURL: https://purl.expasy.org/prosite/documentation/PDOC51905

Description

The ubiquitin-binding zinc finger (UBZ) is a type of zinc-coordinating β-β-α fold domain found mainly in proteins involved in DNA repair and transcriptional regulation. UBZ domains coordinate a zinc ion with cysteine or histidine residues; depending on their amino acid sequence, UBZ domains are classified into several families [1,2]. Type 1 UBZs are CCHH-type zinc fingers found in tandem UBZ domains of TAX1-binding protein 1 (TAX1BP1) [3,4,5], type 2 UBZs are CCHC-type zinc fingers found in FAAP20 which is a subunit of the Fanconi anemia (FA) core complex [6,7], type 3 UBZs are CCHH-type zinc fingers found only in the Y-family translesion polymerase eta [8,9,10], and type 4 UBZs are CCHC-type zinc fingers found in Y-family translesion polymerase kappa, Werner helicase-interacting protein 1 (WRNIP1), and Rad18 [11,12,13].

The UBZ domain consists of two short antiparallel β-strands followed by one α-helix. The α-helix packs against the β-strands with a zinc ion sandwiched between the α-helix and the β-strands. The zinc ion is coordinated by two cysteines located on the fingertip formed by the β-strands and two histidines (see <PDB:4BMJ>) [1,8] or one hisidine and one cysteine (see <PDB:2MUQ>) [6] on the α-helix [2].

The profiles we developed cover the entire UBZ1-, UBZ2-, UBZ3-, and UBZ4-type zinc fingers.

Last update:

April 2022 / Profile revised.

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Technical section

PROSITE methods (with tools and information) covered by this documentation:

ZF_UBZ1, PS51905; Zinc finger UBZ1-type profile  (MATRIX)

ZF_UBZ2, PS51906; Zinc finger UBZ2-type profile  (MATRIX)

ZF_UBZ3, PS51907; Zinc finger UBZ3-type profile  (MATRIX)

ZF_UBZ4, PS51908; Zinc finger UBZ4-type profile  (MATRIX)


References

1AuthorsHofmann K.
TitleUbiquitin-binding domains and their role in the DNA damage response.
SourceDNA Repair. (Amst). 8:544-556(2009).
PubMed ID19213613
DOI10.1016/j.dnarep.2009.01.003

2AuthorsSuzuki N. Rohaim A. Kato R. Dikic I. Wakatsuki S. Kawasaki M.
TitleA novel mode of ubiquitin recognition by the ubiquitin-binding zinc finger domain of WRNIP1.
SourceFEBS. J. 283:2004-2017(2016).
PubMed ID27062441
DOI10.1111/febs.13734

3AuthorsCeregido M.A. Spinola Amilibia M. Buts L. Rivera-Torres J. Garcia-Pino A. Bravo J. van Nuland N.A.J.
TitleThe structure of TAX1BP1 UBZ1+2 provides insight into target specificity and adaptability.
SourceJ. Mol. Biol. 426:674-690(2014).
PubMed ID24239949
DOI10.1016/j.jmb.2013.11.006

4AuthorsXie X. Li F. Wang Y. Wang Y. Lin Z. Cheng X. Liu J. Chen C. Pan L.
TitleMolecular basis of ubiquitin recognition by the autophagy receptor CALCOCO2.
SourceAutophagy 11:1775-1789(2015).
PubMed ID26506893
DOI10.1080/15548627.2015.1082025

5AuthorsThurston T.L.M. Boyle K.B. Allen M. Ravenhill B.J. Karpiyevich M. Bloor S. Kaul A. Noad J. Foeglein A. Matthews S.A. Komander D. Bycroft M. Randow F.
TitleRecruitment of TBK1 to cytosol-invading Salmonella induces WIPI2-dependent antibacterial autophagy.
SourceEMBO. J. 35:1779-1792(2016).
PubMed ID27370208
DOI10.15252/embj.201694491

6AuthorsWojtaszek J.L. Wang S. Kim H. Wu Q. D'Andrea A.D. Zhou P.
TitleUbiquitin recognition by FAAP20 expands the complex interface beyond the canonical UBZ domain.
SourceNucleic. Acids. Res. 42:13997-14005(2014).
PubMed ID25414354
DOI10.1093/nar/gku1153

7AuthorsToma A. Takahashi T.S. Sato Y. Yamagata A. Goto-Ito S. Nakada S. Fukuto A. Horikoshi Y. Tashiro S. Fukai S.
TitleStructural basis for ubiquitin recognition by ubiquitin-binding zinc finger of FAAP20.
SourcePLoS One. 10:E0120887-E0120887(2015).
PubMed ID25799058
DOI10.1371/journal.pone.0120887

8AuthorsBomar M.G. Pai M.-T. Tzeng S.-R. Li S.S.-C. Zhou P.
TitleStructure of the ubiquitin-binding zinc finger domain of human DNA Y-polymerase eta.
SourceEMBO. Rep. 8:247-251(2007).
PubMed ID17304240
DOI10.1038/sj.embor.7400901

9AuthorsGarcia-Ortiz M.V. Roldan-Arjona T. Ariza R.R.
TitleThe noncatalytic C-terminus of AtPOLK Y-family DNA polymerase affects synthesis fidelity, mismatch extension and translesion replication.
SourceFEBS. J. 274:3340-3350(2007).
PubMed ID17550419
DOI10.1111/j.1742-4658.2007.05868.x

10AuthorsWoodruff R.V. Bomar M.G. D'Souza S. Zhou P. Walker G.C.
TitleThe unusual UBZ domain of Saccharomyces cerevisiae polymerase eta.
SourceDNA Repair. (Amst). 9:1130-1141(2010).
PubMed ID20837403
DOI10.1016/j.dnarep.2010.08.001

11AuthorsYang K. Moldovan G.-L. D'Andrea A.D.
TitleRAD18-dependent recruitment of SNM1A to DNA repair complexes by a ubiquitin-binding zinc finger.
SourceJ. Biol. Chem. 285:19085-19091(2010).
PubMed ID20385554
DOI10.1074/jbc.M109.100032

12AuthorsRizzo A.A. Salerno P.E. Bezsonova I. Korzhnev D.M.
TitleNMR structure of the human Rad18 zinc finger in complex with ubiquitin defines a class of UBZ domains in proteins linked to the DNA damage response.
SourceBiochemistry 53:5895-5906(2014).
PubMed ID25162118
DOI10.1021/bi500823h

13AuthorsLachaud C. Castor D. Hain K. Munoz I. Wilson J. MacArtney T.J. Schindler D. Rouse J.
TitleDistinct functional roles for the two SLX4 ubiquitin-binding UBZ domains mutated in Fanconi anemia.
SourceJ. Cell. Sci. 127:2811-2817(2014).
PubMed ID24794496
DOI10.1242/jcs.146167



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