4r62

From Proteopedia

(Difference between revisions)

Current revision

Structure of Rad6~Ub

Structural highlights

4r62 is a 2 chain structure with sequence from Homo sapiens and Saccharomyces cerevisiae S288C. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.28Å
Ligands:
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]

Publication Abstract from PubMed

Rad6 is a yeast E2 ubiquitin conjugating enzyme that monoubiquitinates histone H2B in conjunction with the E3, Bre1, but can non-specifically modify histones on its own. We determined the crystal structure of a Rad6 approximately Ub thioester mimic, which revealed a network of interactions in the crystal in which the ubiquitin in one conjugate contacts Rad6 in another. The region of Rad6 contacted is located on the distal face of Rad6 opposite the active site, but differs from the canonical E2 backside that mediates free ubiquitin binding and polyubiquitination activity in other E2 enzymes. We find that free ubiquitin interacts weakly with both non-canonical and canonical backside residues of Rad6 and that mutations of non-canonical residues have deleterious effects on Rad6 activity comparable to those observed to mutations in the canonical E2 backside. The effect of non-canonical backside mutations is similar in the presence and absence of Bre1, indicating that contacts with non-canonical backside residues govern the intrinsic activity of Rad6. Our findings shed light on the determinants of intrinsic Rad6 activity and reveal new ways in which contacts with an E2 backside can regulate ubiquitin conjugating activity.

Role of a non-canonical surface of Rad6 in ubiquitin conjugating activity.,Kumar P, Magala P, Geiger-Schuller KR, Majumdar A, Tolman JR, Wolberger C Nucleic Acids Res. 2015 Aug 18. pii: gkv845. PMID:26286193^[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
↑ Kumar P, Magala P, Geiger-Schuller KR, Majumdar A, Tolman JR, Wolberger C. Role of a non-canonical surface of Rad6 in ubiquitin conjugating activity. Nucleic Acids Res. 2015 Aug 18. pii: gkv845. PMID:26286193 doi:http://dx.doi.org/10.1093/nar/gkv845

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/4r62"

Categories: Homo sapiens | Large Structures | Saccharomyces cerevisiae S288C | Kumar P | Wolberger C

@@ Line 1: / Line 1: @@
 ==Structure of Rad6~Ub==
-<StructureSection load='4r62' size='340' side='right' caption='[[4r62]], [[Resolution|resolution]] 2.28&Aring;' scene=''>
+<StructureSection load='4r62' size='340' side='right'caption='[[4r62]], [[Resolution|resolution]] 2.28&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4r62]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4R62 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4R62 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4r62]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_S288C Saccharomyces cerevisiae S288C]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4R62 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4R62 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene></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]] 2.28&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4qwh|4qwh]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ubiquitin--protein_ligase Ubiquitin--protein ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.2.19 6.3.2.19] </span></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=4r62 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4r62 OCA], [https://pdbe.org/4r62 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4r62 RCSB], [https://www.ebi.ac.uk/pdbsum/4r62 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4r62 ProSAT]</span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4r62 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4r62 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4r62 RCSB], [http://www.ebi.ac.uk/pdbsum/4r62 PDBsum]</span></td></tr>
 </table>
 == Function ==
-[[http://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>  [[http://www.uniprot.org/uniprot/RS27A_HUMAN RS27A_HUMAN]] Ubiquitin exists either covalently attached to another protein, or free (unanchored). When covalently bound, it is conjugated to target proteins via an isopeptide bond either as a monomer (monoubiquitin), a polymer linked via different Lys residues of the ubiquitin (polyubiquitin chains) or a linear polymer linked via the initiator Met of the ubiquitin (linear polyubiquitin chains). Polyubiquitin chains, when attached to a target protein, have different functions depending on the Lys residue of the ubiquitin that is linked: Lys-6-linked may be involved in DNA repair; Lys-11-linked is involved in ERAD (endoplasmic reticulum-associated degradation) and in cell-cycle regulation; Lys-29-linked is involved in lysosomal degradation; Lys-33-linked is involved in kinase modification; Lys-48-linked is involved in protein degradation via the proteasome; Lys-63-linked is involved in endocytosis, DNA-damage responses as well as in signaling processes leading to activation of the transcription factor NF-kappa-B. Linear polymer chains formed via attachment by the initiator Met lead to cell signaling. Ubiquitin is usually conjugated to Lys residues of target proteins, however, in rare cases, conjugation to Cys or Ser residues has been observed. When polyubiquitin is free (unanchored-polyubiquitin), it also has distinct roles, such as in activation of protein kinases, and in signaling.<ref>PMID:16543144</ref> <ref>PMID:19754430</ref>   Ribosomal protein S27a is a component of the 40S subunit of the ribosome.<ref>PMID:16543144</ref> <ref>PMID:19754430</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>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 18: / Line 18: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 4r62" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[3D structures of ubiquitin conjugating enzyme|3D structures of ubiquitin conjugating enzyme]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Ubiquitin--protein ligase]]
+[[Category: Homo sapiens]]
-[[Category: Kumar, P]]
+[[Category: Large Structures]]
-[[Category: Wolberger, C]]
+[[Category: Saccharomyces cerevisiae S288C]]
-[[Category: Bre1]]
+[[Category: Kumar P]]
-[[Category: E2 conjugating enzyme]]
+[[Category: Wolberger C]]
-[[Category: Histone h2b]]
-[[Category: Monoubiquitination of histone h2b at k123 in saccharomyces cerevisiae]]
-[[Category: Nuclear protein]]
-[[Category: Nucleus]]
-[[Category: Pcna]]
-[[Category: Rad18]]
-[[Category: Ubc]]
-[[Category: Ubiquitin]]
-[[Category: Ubiquitination]]

4r62

From Proteopedia

Current revision

Structure of Rad6~Ub

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

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