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PDBsum entry 2e2c

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protein links
Ubiquitin conjugation PDB id
2e2c
Jmol
Contents
Protein chain
156 a.a. *
Waters ×172
* Residue conservation analysis
PDB id:
2e2c
Name: Ubiquitin conjugation
Title: E2-c, an ubiquitin conjugating enzyme required for the destr mitotic cyclins
Structure: Ubiquitin conjugating enzyme. Chain: a. Ec: 6.3.2.19
Source: Spisula solidissima. Atlantic surf clam. Organism_taxid: 6584
Biol. unit: Dimer (from PQS)
Resolution:
2.00Å     R-factor:   0.216     R-free:   0.271
Authors: F.Jiang,R.Basavappa
Key ref:
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. PubMed id: 10350465 DOI: 10.1021/bi9901329
Date:
19-Jan-99     Release date:   27-Jan-99    
Supersedes: 1br7
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q95044  (UBE2C_SPISO) -  Ubiquitin-conjugating enzyme E2 C
Seq:
Struc:
177 a.a.
156 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!
  Biochemical function     acid-amino acid ligase activity     1 term  

 

 
    reference    
 
 
DOI no: 10.1021/bi9901329 Biochemistry 38:6471-6478 (1999)
PubMed id: 10350465  
 
 
Crystal structure of the cyclin-specific ubiquitin-conjugating enzyme from clam, E2-C, at 2.0 A resolution.
F.Jiang, R.Basavappa.
 
  ABSTRACT  
 
The destruction of the cyclin B protein is necessary for the cell to exit from mitosis. The destruction of cyclin B occurs via the ubiquitin/proteasome system and involves a specific ubiquitin-conjugating enzyme (Ubc) that donates ubiquitin to cyclin B. Here we present the crystal structure of the cyclin-specific Ubc from clam, E2-C, determined at 2.0 A resolution. The E2-C enzyme contains an N-terminal extension in addition to the Ubc core domain. The N-terminal extension is disordered, perhaps reflecting a need for flexibility as it interacts with various partners in the ubiquitination system. The overall structure of the E2-C core domain is quite similar to those in previously determined Ubc proteins. The interaction between particular pairs of E2-C proteins in the crystal has some of the hallmarks of a functional dimer, though solution studies suggest that the E2-C protein exists as a monomer. Comparison of the E2-C structure with that of the other available Ubc structures indicates conserved surface residues that may interact with common components of the ubiquitination system. Such comparison also reveals a remarkable spine of conserved hydrophobic residues in the center of the protein that may drive the protein to fold and stabilize the protein once folded. Comparison of residues conserved only among E2-C and its homologues indicates surface areas that may be involved in mitotic-specific ubiquitination.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
18722180 M.K.Summers, B.Pan, K.Mukhyala, and P.K.Jackson (2008).
The unique N terminus of the UbcH10 E2 enzyme controls the threshold for APC activation and enhances checkpoint regulation of the APC.
  Mol Cell, 31, 544-556.  
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
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.  
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.  
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
11336713 C.Gieffers, P.Dube, J.R.Harris, H.Stark, and J.M.Peters (2001).
Three-dimensional structure of the anaphase-promoting complex.
  Mol Cell, 7, 907-913.  
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.  
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.  
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.