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PDBsum entry 1ayz

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protein links
Ubiquitin conjugation PDB id
1ayz
Jmol
Contents
Protein chains
153 a.a. *
Waters ×103
* Residue conservation analysis
PDB id:
1ayz
Name: Ubiquitin conjugation
Title: Crystal structure of the saccharomyces cerevisiae ubiquitin- conjugating enzyme rad6 (ubc2) at 2.6a resolution
Structure: Ubiquitin-conjugating enzyme rad6. Chain: a, b, c. Synonym: ubc2. Ec: 6.3.2.19
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932
Resolution:
2.60Å     R-factor:   0.213     R-free:   0.246
Authors: D.K.Worthylake,S.Prakash,L.Prakash,C.P.Hill
Key ref:
D.K.Worthylake et al. (1998). Crystal structure of the Saccharomyces cerevisiae ubiquitin-conjugating enzyme Rad6 at 2.6 A resolution. J Biol Chem, 273, 6271-6276. PubMed id: 9497353 DOI: 10.1074/jbc.273.11.6271
Date:
12-Nov-97     Release date:   26-Aug-98    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P06104  (UBC2_YEAST) -  Ubiquitin-conjugating enzyme E2 2
Seq:
Struc:
172 a.a.
153 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.6.3.2.19  - Ubiquitin--protein ligase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + ubiquitin + protein lysine = AMP + diphosphate + protein N-ubiquityllysine
ATP
+ ubiquitin
+ protein lysine
= AMP
+ diphosphate
+ protein N-ubiquityllysine
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   5 terms 
  Biological process     error-free translesion synthesis   25 terms 
  Biochemical function     nucleotide binding     8 terms  

 

 
    reference    
 
 
DOI no: 10.1074/jbc.273.11.6271 J Biol Chem 273:6271-6276 (1998)
PubMed id: 9497353  
 
 
Crystal structure of the Saccharomyces cerevisiae ubiquitin-conjugating enzyme Rad6 at 2.6 A resolution.
D.K.Worthylake, S.Prakash, L.Prakash, C.P.Hill.
 
  ABSTRACT  
 
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.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. Electron density map calculated using density modified single isomorphous replacement phases displayed with the refined^ structure. 20.0-3.0 Å data were used in the map calculation, and the map is contoured at 1.3 . Dashed white lines indicate^ hydrogen bonding interactions of Asp-12, Arg-8, and Tyr-63. The^ figure was made using the program O (25).
Figure 2.
Fig. 2. Ribbon representation of Rad6. A, active site cysteine shown in green. Residues 24-29, 32-41, 52-58, and 69-72 constitute^ the sheet (strands 1-4 in yellow) and residues 4-19, 102-113, 124-132, and 134-152 are in an -helical conformation (helices 1-4 in blue, maroon, cyan, and orange). Residues 90-92 are in a 3[10] helical conformation (magenta). B, colored to indicate N- and C-terminal binding determinants for Ubr1 (blue and cyan) and^ Rad18 (orange and yellow). The loop that forms the roof of the^ active site and is in different conformations in the asymmetric^ unit (residues 115-121) is indicated in red. Secondary structure^ was determined using the program PROMOTIF (37). The figure was made using the programs MOLSCRIPT (38) and RASTER 3D (39).
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (1998, 273, 6271-6276) copyright 1998.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20382987 H.Walden (2010).
Selenium incorporation using recombinant techniques.
  Acta Crystallogr D Biol Crystallogr, 66, 352-357.  
20014027 T.Ju, W.Bocik, A.Majumdar, and J.R.Tolman (2010).
Solution structure and dynamics of human ubiquitin conjugating enzyme Ube2g2.
  Proteins, 78, 1291-1301.
PDB code: 2kly
19352404 B.A.Schulman, and J.W.Harper (2009).
Ubiquitin-like protein activation by E1 enzymes: the apex for downstream signalling pathways.
  Nat Rev Mol Cell Biol, 10, 319-331.  
18684991 S.Barik (2008).
An intronic microRNA silences genes that are functionally antagonistic to its host gene.
  Nucleic Acids Res, 36, 5232-5241.  
17426150 M.G.Malkowski, E.Quartley, A.E.Friedman, J.Babulski, Y.Kon, J.Wolfley, M.Said, J.R.Luft, E.M.Phizicky, G.T.DeTitta, and E.J.Grayhack (2007).
Blocking S-adenosylmethionine synthesis in yeast allows selenomethionine incorporation and multiwavelength anomalous dispersion phasing.
  Proc Natl Acad Sci U S A, 104, 6678-6683.
PDB code: 2ip1
17984971 S.Lall (2007).
Primers on chromatin.
  Nat Struct Mol Biol, 14, 1110-1115.  
16307922 A.Wood, J.Schneider, J.Dover, M.Johnston, and A.Shilatifard (2005).
The Bur1/Bur2 complex is required for histone H2B monoubiquitination by Rad6/Bre1 and histone methylation by COMPASS.
  Mol Cell, 20, 589-599.  
15062086 C.Dominguez, A.M.Bonvin, G.S.Winkler, F.M.van Schaik, H.T.Timmers, and R.Boelens (2004).
Structural model of the UbcH5B/CNOT4 complex revealed by combining NMR, mutagenesis, and docking approaches.
  Structure, 12, 633-644.
PDB code: 1ur6
15316916 H.Oku, T.Ohyama, A.Hiroki, K.Yamada, K.Fukuyama, H.Kawaguchi, and R.Katakai (2004).
Addition of a peptide fragment on an alpha-helical depsipeptide induces alpha/3(10)-conjugated helix: synthesis, crystal structure, and CD spectra of Boc-Leu-Leu-Ala-(Leu-Leu-Lac)3-Leu-Leu-OEt.
  Biopolymers, 75, 242-254.  
12944097 B.R.Wong, F.Parlati, K.Qu, S.Demo, T.Pray, J.Huang, D.G.Payan, and M.K.Bennett (2003).
Drug discovery in the ubiquitin regulatory pathway.
  Drug Discov Today, 8, 746-754.  
14517261 P.Y.Wu, M.Hanlon, M.Eddins, C.Tsui, R.S.Rogers, J.P.Jensen, M.J.Matunis, A.M.Weissman, A.M.Weisman, A.M.Weissman, C.Wolberger, C.P.Wolberger, and C.M.Pickart (2003).
A conserved catalytic residue in the ubiquitin-conjugating enzyme family.
  EMBO J, 22, 5241-5250.  
11953320 B.Sarcevic, A.Mawson, R.T.Baker, and R.L.Sutherland (2002).
Regulation of the ubiquitin-conjugating enzyme hHR6A by CDK-mediated phosphorylation.
  EMBO J, 21, 2009-2018.  
12006492 O.Pornillos, S.L.Alam, R.L.Rich, D.G.Myszka, D.R.Davis, and W.I.Sundquist (2002).
Structure and functional interactions of the Tsg101 UEV domain.
  EMBO J, 21, 2397-2406.
PDB codes: 1kpp 1kpq
12531181 T.R.Pray, F.Parlati, J.Huang, B.R.Wong, D.G.Payan, M.K.Bennett, S.D.Issakani, S.Molineaux, and S.D.Demo (2002).
Cell cycle regulatory E3 ubiquitin ligases as anticancer targets.
  Drug Resist Updat, 5, 249-258.  
11440714 A.P.VanDemark, R.M.Hofmann, C.Tsui, C.M.Pickart, and C.Wolberger (2001).
Molecular insights into polyubiquitin chain assembly: crystal structure of the Mms2/Ubc13 heterodimer.
  Cell, 105, 711-720.
PDB codes: 1jat 1jbb
11395416 C.M.Pickart (2001).
Mechanisms underlying ubiquitination.
  Annu Rev Biochem, 70, 503-533.  
11533242 C.Ptak, C.Gwozd, J.T.Huzil, T.J.Gwozd, G.Garen, and M.J.Ellison (2001).
Creation of a pluripotent ubiquitin-conjugating enzyme.
  Mol Cell Biol, 21, 6537-6548.  
11255249 D.Sleep, C.Finnis, A.Turner, and L.Evans (2001).
Yeast 2 microm plasmid copy number is elevated by a mutation in the nuclear gene UBC4.
  Yeast, 18, 403-421.  
10712706 P.Leng, P.E.Sudbery, and A.J.Brown (2000).
Rad6p represses yeast-hypha morphogenesis in the human fungal pathogen Candida albicans.
  Mol Microbiol, 35, 1264-1275.  
10350465 F.Jiang, and R.Basavappa (1999).
Crystal structure of the cyclin-specific ubiquitin-conjugating enzyme from clam, E2-C, at 2.0 A resolution.
  Biochemistry, 38, 6471-6478.
PDB code: 2e2c
10581257 Y.Xie, and A.Varshavsky (1999).
The E2-E3 interaction in the N-end rule pathway: the RING-H2 finger of E3 is required for the synthesis of multiubiquitin chain.
  EMBO J, 18, 6832-6844.  
9657692 L.D.Mastrandrea, E.M.Kasperek, E.G.Niles, and C.M.Pickart (1998).
Core domain mutation (S86Y) selectively inactivates polyubiquitin chain synthesis catalyzed by E2-25K.
  Biochemistry, 37, 9784-9792.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.