1ayz

From Proteopedia

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Current revision

CRYSTAL STRUCTURE OF THE SACCHAROMYCES CEREVISIAE UBIQUITIN-CONJUGATING ENZYME RAD6 (UBC2) AT 2.6A RESOLUTION

Structural highlights

1ayz is a 3 chain structure with sequence from Saccharomyces cerevisiae. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.6Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

UBC2_YEAST Catalyzes the covalent attachment of ubiquitin to other proteins. In association with the E3 enzyme BRE1 and LGE1, it plays a role in transcription regulation by catalyzing the monoubiquitination of histone H2B to form H2BK123ub1. H2BK123ub1 gives a specific tag for epigenetic transcriptional activation, elongation by RNA polymerase II, telomeric silencing, and is also a prerequisite for H3K4me and H3K79me formation. In association with the E3 enzyme RAD18, it catalyzes the monoubiquitination of POL30 'Lys-164', involved in postreplication repair of UV-damaged DNA. The RAD6/UBC2-RAD18 complex is also involved in prevention of spontaneous mutations caused by 7,8-dihydro-8-oxoguanine. In association with the E3 enzyme UBR1, is involved in N-end rule-dependent protein degradation. Also involved in sporulation.^[1] ^[2] ^[3] ^[4] ^[5] ^[6] ^[7] ^[8] ^[9] ^[10] ^[11] ^[12] ^[13] ^[14] ^[15] ^[16] ^[17]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

The Saccharomyces cerevisiae ubiquitin-conjugating enzyme (UBC) Rad6 is required for several functions, including the repair of UV damaged DNA, damage-induced mutagenesis, sporulation, and the degradation of cellular proteins that possess destabilizing N-terminal residues. Rad6 mediates its role in N-end rule-dependent protein degradation via interaction with the ubiquitin-protein ligase Ubr1 and in DNA repair via interactions with the DNA binding protein Rad18. We report here the crystal structure of Rad6 refined at 2.6 A resolution to an R factor of 21.3%. The protein adopts an alpha/beta fold that is very similar to other UBC structures. An apparent difference at the functionally important first helix, however, has prompted a reassessment of previously reported structures. The active site cysteine lies in a cleft formed by a coil region that includes the 310 helix and a loop that is in different conformations for the three molecules in the asymmetric unit. Residues important for Rad6 interaction with Ubr1 and Rad18 are on the opposite side of the structure from the active site, indicating that this part of the UBC surface participates in protein-protein interactions that define Rad6 substrate specificity.

Crystal structure of the Saccharomyces cerevisiae ubiquitin-conjugating enzyme Rad6 at 2.6 A resolution.,Worthylake DK, Prakash S, Prakash L, Hill CP J Biol Chem. 1998 Mar 13;273(11):6271-6. PMID:9497353^[18]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Jentsch S, McGrath JP, Varshavsky A. The yeast DNA repair gene RAD6 encodes a ubiquitin-conjugating enzyme. Nature. 1987 Sep 10-16;329(6135):131-4. PMID:3306404 doi:http://dx.doi.org/10.1038/329131a0
↑ Montelone BA, Prakash S, Prakash L. Recombination and mutagenesis in rad6 mutants of Saccharomyces cerevisiae: evidence for multiple functions of the RAD6 gene. Mol Gen Genet. 1981;184(3):410-5. PMID:7038392
↑ Sung P, Prakash S, Prakash L. Mutation of cysteine-88 in the Saccharomyces cerevisiae RAD6 protein abolishes its ubiquitin-conjugating activity and its various biological functions. Proc Natl Acad Sci U S A. 1990 Apr;87(7):2695-9. PMID:2157209
↑ Dohmen RJ, Madura K, Bartel B, Varshavsky A. The N-end rule is mediated by the UBC2(RAD6) ubiquitin-conjugating enzyme. Proc Natl Acad Sci U S A. 1991 Aug 15;88(16):7351-5. PMID:1651502
↑ Sung P, Berleth E, Pickart C, Prakash S, Prakash L. Yeast RAD6 encoded ubiquitin conjugating enzyme mediates protein degradation dependent on the N-end-recognizing E3 enzyme. EMBO J. 1991 Aug;10(8):2187-93. PMID:2065660
↑ Watkins JF, Sung P, Prakash S, Prakash L. The extremely conserved amino terminus of RAD6 ubiquitin-conjugating enzyme is essential for amino-end rule-dependent protein degradation. Genes Dev. 1993 Feb;7(2):250-61. PMID:8436296
↑ Bailly V, Lamb J, Sung P, Prakash S, Prakash L. Specific complex formation between yeast RAD6 and RAD18 proteins: a potential mechanism for targeting RAD6 ubiquitin-conjugating activity to DNA damage sites. Genes Dev. 1994 Apr 1;8(7):811-20. PMID:7926769
↑ Bailly V, Lauder S, Prakash S, Prakash L. Yeast DNA repair proteins Rad6 and Rad18 form a heterodimer that has ubiquitin conjugating, DNA binding, and ATP hydrolytic activities. J Biol Chem. 1997 Sep 12;272(37):23360-5. PMID:9287349
↑ Huang H, Kahana A, Gottschling DE, Prakash L, Liebman SW. The ubiquitin-conjugating enzyme Rad6 (Ubc2) is required for silencing in Saccharomyces cerevisiae. Mol Cell Biol. 1997 Nov;17(11):6693-9. PMID:9343433
↑ Ulrich HD, Jentsch S. Two RING finger proteins mediate cooperation between ubiquitin-conjugating enzymes in DNA repair. EMBO J. 2000 Jul 3;19(13):3388-97. PMID:10880451 doi:http://dx.doi.org/10.1093/emboj/19.13.3388
↑ Sun ZW, Allis CD. Ubiquitination of histone H2B regulates H3 methylation and gene silencing in yeast. Nature. 2002 Jul 4;418(6893):104-8. Epub 2002 Jun 23. PMID:12077605 doi:http://dx.doi.org/10.1038/nature00883
↑ Hoege C, Pfander B, Moldovan GL, Pyrowolakis G, Jentsch S. RAD6-dependent DNA repair is linked to modification of PCNA by ubiquitin and SUMO. Nature. 2002 Sep 12;419(6903):135-41. PMID:12226657 doi:10.1038/nature00991
↑ Kao CF, Hillyer C, Tsukuda T, Henry K, Berger S, Osley MA. Rad6 plays a role in transcriptional activation through ubiquitylation of histone H2B. Genes Dev. 2004 Jan 15;18(2):184-95. PMID:14752010 doi:10.1101/gad.1149604
↑ de Padula M, Slezak G, Auffret van Der Kemp P, Boiteux S. The post-replication repair RAD18 and RAD6 genes are involved in the prevention of spontaneous mutations caused by 7,8-dihydro-8-oxoguanine in Saccharomyces cerevisiae. Nucleic Acids Res. 2004 Sep 23;32(17):5003-10. Print 2004. PMID:15388802 doi:http://dx.doi.org/10.1093/nar/gkh831
↑ Wood A, Schneider J, Dover J, Johnston M, Shilatifard A. The Bur1/Bur2 complex is required for histone H2B monoubiquitination by Rad6/Bre1 and histone methylation by COMPASS. Mol Cell. 2005 Nov 23;20(4):589-99. PMID:16307922 doi:http://dx.doi.org/S1097-2765(05)01631-X
↑ Xiao T, Kao CF, Krogan NJ, Sun ZW, Greenblatt JF, Osley MA, Strahl BD. Histone H2B ubiquitylation is associated with elongating RNA polymerase II. Mol Cell Biol. 2005 Jan;25(2):637-51. PMID:15632065 doi:25/2/637
↑ Zhang H, Lawrence CW. The error-free component of the RAD6/RAD18 DNA damage tolerance pathway of budding yeast employs sister-strand recombination. Proc Natl Acad Sci U S A. 2005 Nov 1;102(44):15954-9. Epub 2005 Oct 24. PMID:16247017 doi:http://dx.doi.org/0504586102
↑ Worthylake DK, Prakash S, Prakash L, Hill CP. Crystal structure of the Saccharomyces cerevisiae ubiquitin-conjugating enzyme Rad6 at 2.6 A resolution. J Biol Chem. 1998 Mar 13;273(11):6271-6. PMID:9497353

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1ayz"

@@ Line 4: / Line 4: @@
 == Structural highlights ==
 <table><tr><td colspan='2'>[[1ayz]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AYZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1AYZ FirstGlance]. <br>
-</td></tr><tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Ubiquitin--protein_ligase Ubiquitin--protein ligase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.2.19 6.3.2.19] </span></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.6&#8491;</td></tr>
 <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1ayz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ayz OCA], [https://pdbe.org/1ayz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ayz RCSB], [https://www.ebi.ac.uk/pdbsum/1ayz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ayz ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/UBC2_YEAST UBC2_YEAST]] Catalyzes the covalent attachment of ubiquitin to other proteins. In association with the E3 enzyme BRE1 and LGE1, it plays a role in transcription regulation by catalyzing the monoubiquitination of histone H2B to form H2BK123ub1. H2BK123ub1 gives a specific tag for epigenetic transcriptional activation, elongation by RNA polymerase II, telomeric silencing, and is also a prerequisite for H3K4me and H3K79me formation. In association with the E3 enzyme RAD18, it catalyzes the monoubiquitination of POL30 'Lys-164', involved in postreplication repair of UV-damaged DNA. The RAD6/UBC2-RAD18 complex is also involved in prevention of spontaneous mutations caused by 7,8-dihydro-8-oxoguanine. In association with the E3 enzyme UBR1, is involved in N-end rule-dependent protein degradation. Also involved in sporulation.<ref>PMID:3306404</ref> <ref>PMID:7038392</ref> <ref>PMID:2157209</ref> <ref>PMID:1651502</ref> <ref>PMID:2065660</ref> <ref>PMID:8436296</ref> <ref>PMID:7926769</ref> <ref>PMID:9287349</ref> <ref>PMID:9343433</ref> <ref>PMID:10880451</ref> <ref>PMID:12077605</ref> <ref>PMID:12226657</ref> <ref>PMID:14752010</ref> <ref>PMID:15388802</ref> <ref>PMID:16307922</ref> <ref>PMID:15632065</ref> <ref>PMID:16247017</ref>
+[https://www.uniprot.org/uniprot/UBC2_YEAST UBC2_YEAST] Catalyzes the covalent attachment of ubiquitin to other proteins. In association with the E3 enzyme BRE1 and LGE1, it plays a role in transcription regulation by catalyzing the monoubiquitination of histone H2B to form H2BK123ub1. H2BK123ub1 gives a specific tag for epigenetic transcriptional activation, elongation by RNA polymerase II, telomeric silencing, and is also a prerequisite for H3K4me and H3K79me formation. In association with the E3 enzyme RAD18, it catalyzes the monoubiquitination of POL30 'Lys-164', involved in postreplication repair of UV-damaged DNA. The RAD6/UBC2-RAD18 complex is also involved in prevention of spontaneous mutations caused by 7,8-dihydro-8-oxoguanine. In association with the E3 enzyme UBR1, is involved in N-end rule-dependent protein degradation. Also involved in sporulation.<ref>PMID:3306404</ref> <ref>PMID:7038392</ref> <ref>PMID:2157209</ref> <ref>PMID:1651502</ref> <ref>PMID:2065660</ref> <ref>PMID:8436296</ref> <ref>PMID:7926769</ref> <ref>PMID:9287349</ref> <ref>PMID:9343433</ref> <ref>PMID:10880451</ref> <ref>PMID:12077605</ref> <ref>PMID:12226657</ref> <ref>PMID:14752010</ref> <ref>PMID:15388802</ref> <ref>PMID:16307922</ref> <ref>PMID:15632065</ref> <ref>PMID:16247017</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 37: / Line 37: @@
 [[Category: Large Structures]]
 [[Category: Saccharomyces cerevisiae]]
-[[Category: Ubiquitin--protein ligase]]
+[[Category: Hill CP]]
-[[Category: Hill, C P]]
+[[Category: Prakash L]]
-[[Category: Prakash, L]]
+[[Category: Prakash S]]
-[[Category: Prakash, S]]
+[[Category: Worthylake DK]]
-[[Category: Worthylake, D K]]
-[[Category: Ubiquitin conjugation]]
-[[Category: Ubiquitin-conjugating enzyme]]

1ayz

From Proteopedia

Current revision

CRYSTAL STRUCTURE OF THE SACCHAROMYCES CEREVISIAE UBIQUITIN-CONJUGATING ENZYME RAD6 (UBC2) AT 2.6A RESOLUTION

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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