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PDBsum entry 1qcq

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protein links
Ligase PDB id
1qcq
Jmol
Contents
Protein chain
148 a.a. *
* Residue conservation analysis
PDB id:
1qcq
Name: Ligase
Title: Ubiquitin conjugating enzyme
Structure: Protein (ubiquitin conjugating enzyme). Chain: a. Ec: 6.3.2.19
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932
Resolution:
2.70Å     R-factor:   0.240     R-free:   0.296
Authors: W.J.Cook,L.C.Jeffrey,Y.Xu,V.Chau
Key ref:
W.J.Cook et al. (1993). Tertiary structures of class I ubiquitin-conjugating enzymes are highly conserved: crystal structure of yeast Ubc4. Biochemistry, 32, 13809-13817. PubMed id: 8268156 DOI: 10.1021/bi00213a009
Date:
10-May-99     Release date:   17-May-99    
Supersedes: 2uce
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P15731  (UBC4_YEAST) -  Ubiquitin-conjugating enzyme E2 4
Seq:
Struc:
148 a.a.
148 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     proteasome complex   1 term 
  Biological process     response to stress   6 terms 
  Biochemical function     nucleotide binding     8 terms  

 

 
    reference    
 
 
DOI no: 10.1021/bi00213a009 Biochemistry 32:13809-13817 (1993)
PubMed id: 8268156  
 
 
Tertiary structures of class I ubiquitin-conjugating enzymes are highly conserved: crystal structure of yeast Ubc4.
W.J.Cook, L.C.Jeffrey, Y.Xu, V.Chau.
 
  ABSTRACT  
 
The three-dimensional structure of a yeast ubiquitin-conjugating enzyme, encoded by the Saccharomyces cerevisiae UBC4 gene, has been determined at 2.7 A. The structure was solved using molecular replacement techniques and refined by simulated annealing to an R-factor of 0.198. Bond lengths and angles in the molecule have root mean square deviations from ideal values of 0.018 A and 4.0 degrees, respectively. Ubc4 is an alpha/beta protein with four alpha-helices and a four-stranded antiparallel beta-sheet. The ubiquitin-accepting cysteine is located in a cleft between two loops. Comparison with the recently determined structure of a different plant enzyme suggests that class I ubiquitin-conjugating enzymes are highly conserved in their three-dimensional folding. Except for two extra residues at the N- and the C-terminus of the plant enzyme, the C alpha atoms of the two enzymes can be superimposed with a root mean square deviation of only 1.52 A. Greater variations are found between the surfaces of the two molecules, as most of the identical residues between the two enzymes are either buried or clustered on the surface that lies adjacent to the ubiquitin-accepting cysteine. We suggest that this conserved surface functions in protein-protein binding during ubiquitin thiol ester formation.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21229326 Y.Zhang, X.Zhou, L.Zhao, C.Li, H.Zhu, L.Xu, L.Shan, X.Liao, Z.Guo, and P.Huang (2011).
UBE2W interacts with FANCL and regulates the monoubiquitination of fanconi anemia protein FANCD2.
  Mol Cells, 31, 113-122.  
20797627 M.C.Rodrigo-Brenni, S.A.Foster, and D.O.Morgan (2010).
Catalysis of lysine 48-specific ubiquitin chain assembly by residues in E2 and ubiquitin.
  Mol Cell, 39, 548-559.  
18485199 Z.Xu, E.Kohli, K.I.Devlin, M.Bold, J.C.Nix, and S.Misra (2008).
Interactions between the quality control ubiquitin ligase CHIP and ubiquitin conjugating enzymes.
  BMC Struct Biol, 8, 26.
PDB code: 2oxq
  20103862 Y.Chen (2007).
The enzymes in ubiquitin-like post-translational modifications.
  Biosci Trends, 1, 16-25.  
15749714 L.Pastushok, T.F.Moraes, M.J.Ellison, and W.Xiao (2005).
A single Mms2 "key" residue insertion into a Ubc13 pocket determines the interface specificity of a human Lys63 ubiquitin conjugation complex.
  J Biol Chem, 280, 17891-17900.  
16014632 N.Merkley, K.R.Barber, and G.S.Shaw (2005).
Ubiquitin manipulation by an E2 conjugating enzyme using a novel covalent intermediate.
  J Biol Chem, 280, 31732-31738.  
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
15044434 H.Teo, D.B.Veprintsev, and R.L.Williams (2004).
Structural insights into endosomal sorting complex required for transport (ESCRT-I) recognition of ubiquitinated proteins.
  J Biol Chem, 279, 28689-28696.
PDB code: 1uzx
15328341 N.Merkley, and G.S.Shaw (2004).
Solution structure of the flexible class II ubiquitin-conjugating enzyme Ubc1 provides insights for polyubiquitin chain assembly.
  J Biol Chem, 279, 47139-47147.
PDB code: 1tte
12595721 J.A.Gavira J, D.P.Claxton, J.H.Wang, D.Toh, E.J.Meehan, and E.L.DiGiammarino (2003).
Purification, crystallization and preliminary X-ray analysis of Caenorhabditis elegans ubiquitin-conjugation enzyme M7.1.
  Acta Crystallogr D Biol Crystallogr, 59, 544-546.  
12569095 S.McKenna, T.Moraes, L.Pastushok, C.Ptak, W.Xiao, L.Spyracopoulos, and M.J.Ellison (2003).
An NMR-based model of the ubiquitin-bound human ubiquitin conjugation complex Mms2.Ubc13. The structural basis for lysine 63 chain catalysis.
  J Biol Chem, 278, 13151-13158.  
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.  
11877416 D.Lin, M.H.Tatham, B.Yu, S.Kim, R.T.Hay, and Y.Chen (2002).
Identification of a substrate recognition site on Ubc9.
  J Biol Chem, 277, 21740-21748.  
11861641 M.Furukawa, T.Ohta, and Y.Xiong (2002).
Activation of UBC5 ubiquitin-conjugating enzyme by the RING finger of ROC1 and assembly of active ubiquitin ligases by all cullins.
  J Biol Chem, 277, 15758-15765.  
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
11927573 Y.Lin, W.C.Hwang, and R.Basavappa (2002).
Structural and functional analysis of the human mitotic-specific ubiquitin-conjugating enzyme, UbcH10.
  J Biol Chem, 277, 21913-21921.
PDB code: 1i7k
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.  
11504715 S.McKenna, L.Spyracopoulos, T.Moraes, L.Pastushok, C.Ptak, W.Xiao, and M.J.Ellison (2001).
Noncovalent interaction between ubiquitin and the human DNA repair protein Mms2 is required for Ubc13-mediated polyubiquitination.
  J Biol Chem, 276, 40120-40126.  
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
10329663 H.Lin, and S.S.Wing (1999).
Identification of rabbit reticulocyte E217K as a UBC7 homologue and functional characterization of its core domain loop.
  J Biol Chem, 274, 14685-14691.  
10558980 L.Huang, E.Kinnucan, G.Wang, S.Beaudenon, P.M.Howley, J.M.Huibregtse, and N.P.Pavletich (1999).
Structure of an E6AP-UbcH7 complex: insights into ubiquitination by the E2-E3 enzyme cascade.
  Science, 286, 1321-1326.
PDB codes: 1c4z 1d5f
10358047 Q.Liu, C.Jin, X.Liao, Z.Shen, D.J.Chen, and Y.Chen (1999).
The binding interface between an E2 (UBC9) and a ubiquitin homologue (UBL1).
  J Biol Chem, 274, 16979-16987.  
9931006 Q.Liu, Y.C.Yuan, B.Shen, D.J.Chen, and Y.Chen (1999).
Conformational flexibility of a ubiquitin conjugation enzyme (E2).
  Biochemistry, 38, 1415-1425.  
10089880 R.M.Hofmann, and C.M.Pickart (1999).
Noncanonical MMS2-encoded ubiquitin-conjugating enzyme functions in assembly of novel polyubiquitin chains for DNA repair.
  Cell, 96, 645-653.  
10066826 U.Nuber, and M.Scheffner (1999).
Identification of determinants in E2 ubiquitin-conjugating enzymes required for hect E3 ubiquitin-protein ligase interaction.
  J Biol Chem, 274, 7576-7582.  
9497376 A.L.Talis, J.M.Huibregtse, and P.M.Howley (1998).
The role of E6AP in the regulation of p53 protein levels in human papillomavirus (HPV)-positive and HPV-negative cells.
  J Biol Chem, 273, 6439-6445.  
9497353 D.K.Worthylake, S.Prakash, L.Prakash, and C.P.Hill (1998).
Crystal structure of the Saccharomyces cerevisiae ubiquitin-conjugating enzyme Rad6 at 2.6 A resolution.
  J Biol Chem, 273, 6271-6276.
PDB code: 1ayz
  9418904 E.Sancho, M.R.Vilá, L.Sánchez-Pulido, J.J.Lozano, R.Paciucci, M.Nadal, M.Fox, C.Harvey, B.Bercovich, N.Loukili, A.Ciechanover, S.L.Lin, F.Sanz, X.Estivill, A.Valencia, and T.M.Thomson (1998).
Role of UEV-1, an inactive variant of the E2 ubiquitin-conjugating enzymes, in in vitro differentiation and cell cycle behavior of HT-29-M6 intestinal mucosecretory cells.
  Mol Cell Biol, 18, 576-589.  
9560342 J.F.Charles, S.L.Jaspersen, R.L.Tinker-Kulberg, L.Hwang, A.Szidon, and D.O.Morgan (1998).
The Polo-related kinase Cdc5 activates and is destroyed by the mitotic cyclin destruction machinery in S. cerevisiae.
  Curr Biol, 8, 497-507.  
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.  
9660812 R.Oughtred, N.Bédard, A.Vrielink, and S.S.Wing (1998).
Identification of amino acid residues in a class I ubiquitin-conjugating enzyme involved in determining specificity of conjugation of ubiquitin to proteins.
  J Biol Chem, 273, 18435-18442.  
9705497 W.Xiao, S.L.Lin, S.Broomfield, B.L.Chow, and Y.F.Wei (1998).
The products of the yeast MMS2 and two human homologs (hMMS2 and CROC-1) define a structurally and functionally conserved Ubc-like protein family.
  Nucleic Acids Res, 26, 3908-3914.  
9241264 E.V.Koonin, and R.A.Abagyan (1997).
TSG101 may be the prototype of a class of dominant negative ubiquitin regulators.
  Nat Genet, 16, 330-331.  
9261152 H.Tong, G.Hateboer, A.Perrakis, R.Bernards, and T.K.Sixma (1997).
Crystal structure of murine/human Ubc9 provides insight into the variability of the ubiquitin-conjugating system.
  J Biol Chem, 272, 21381-21387.
PDB codes: 1u9a 1u9b
9265633 M.T.Haldeman, G.Xia, E.M.Kasperek, and C.M.Pickart (1997).
Structure and function of ubiquitin conjugating enzyme E2-25K: the tail is a core-dependent activity element.
  Biochemistry, 36, 10526-10537.  
9048545 W.J.Cook, P.D.Martin, B.F.Edwards, R.K.Yamazaki, and V.Chau (1997).
Crystal structure of a class I ubiquitin conjugating enzyme (Ubc7) from Saccharomyces cerevisiae at 2.9 angstroms resolution.
  Biochemistry, 36, 1621-1627.
PDB codes: 1ucz 2ucz
8824207 J.Betting, and W.Seufert (1996).
A yeast Ubc9 mutant protein with temperature-sensitive in vivo function is subject to conditional proteolysis by a ubiquitin- and proteasome-dependent pathway.
  J Biol Chem, 271, 25790-25796.  
8910518 R.Hodgins, C.Gwozd, T.Arnason, M.Cummings, and M.J.Ellison (1996).
The tail of a ubiquitin-conjugating enzyme redirects multi-ubiquitin chain synthesis from the lysine 48-linked configuration to a novel nonlysine-linked form.
  J Biol Chem, 271, 28766-28771.  
  8754804 S.S.Wing, N.Bédard, C.Morales, P.Hingamp, and J.Trasler (1996).
A novel rat homolog of the Saccharomyces cerevisiae ubiquitin-conjugating enzymes UBC4 and UBC5 with distinct biochemical features is induced during spermatogenesis.
  Mol Cell Biol, 16, 4064-4072.  
8647807 S.van Nocker, J.M.Walker, and R.D.Vierstra (1996).
The Arabidopsis thaliana UBC7/13/14 genes encode a family of multiubiquitin chain-forming E2 enzymes.
  J Biol Chem, 271, 12150-12158.  
7592826 A.Banerjee, R.J.Deshaies, and V.Chau (1995).
Characterization of a dominant negative mutant of the cell cycle ubiquitin-conjugating enzyme Cdc34.
  J Biol Chem, 270, 26209-26215.  
7721857 J.A.Prendergast, C.Ptak, T.G.Arnason, and M.J.Ellison (1995).
Increased ubiquitin expression suppresses the cell cycle defect associated with the yeast ubiquitin conjugating enzyme, CDC34 (UBC3). Evidence for a noncovalent interaction between CDC34 and ubiquitin.
  J Biol Chem, 270, 9347-9352.  
  7565715 Y.Liu, N.Mathias, C.N.Steussy, and M.G.Goebl (1995).
Intragenic suppression among CDC34 (UBC3) mutations defines a class of ubiquitin-conjugating catalytic domains.
  Mol Cell Biol, 15, 5635-5644.  
  7862115 Z.W.Pitluk, M.McDonough, P.Sangan, and D.K.Gonda (1995).
Novel CDC34 (UBC3) ubiquitin-conjugating enzyme mutants obtained by charge-to-alanine scanning mutagenesis.
  Mol Cell Biol, 15, 1210-1219.  
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.