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PDBsum entry 1tte

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protein links
Ligase PDB id
1tte
Jmol
Contents
Protein chain
215 a.a. *
* Residue conservation analysis
PDB id:
1tte
Name: Ligase
Title: The structure of a class ii ubiquitin-conjugating enzyme, ubc1.
Structure: Ubiquitin-conjugating enzyme e2-24 kda. Chain: a. Fragment: ubc1. Synonym: ubiquitin-protein ligase, ubiquitin carrier protein. Engineered: yes. Mutation: yes
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Gene: ubc1, ydr177w, yd9395.10. Expressed in: escherichia coli. Expression_system_taxid: 562.
NMR struc: 21 models
Authors: N.Merkley,G.S.Shaw
Key ref:
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. PubMed id: 15328341 DOI: 10.1074/jbc.M409576200
Date:
22-Jun-04     Release date:   31-Aug-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P21734  (UBC1_YEAST) -  Ubiquitin-conjugating enzyme E2 1
Seq:
Struc:
215 a.a.
215 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 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   5 terms 
  Biochemical function     nucleotide binding     5 terms  

 

 
    reference    
 
 
DOI no: 10.1074/jbc.M409576200 J Biol Chem 279:47139-47147 (2004)
PubMed id: 15328341  
 
 
Solution structure of the flexible class II ubiquitin-conjugating enzyme Ubc1 provides insights for polyubiquitin chain assembly.
N.Merkley, G.S.Shaw.
 
  ABSTRACT  
 
E2 conjugating enzymes form a thiol ester intermediate with ubiquitin, which is subsequently transferred to a substrate protein targeted for degradation. While all E2 proteins comprise a catalytic domain where the thiol ester is formed, several E2s (class II) have C-terminal extensions proposed to control substrate recognition, dimerization, or polyubiquitin chain formation. Here we present the novel solution structure of the class II E2 conjugating enzyme Ubc1 from Saccharomyces cerevisiae. The structure shows the N-terminal catalytic domain adopts an alpha/beta fold typical of other E2 proteins. This domain is physically separated from its C-terminal domain by a 22-residue flexible tether. The C-terminal domain adopts a three-helix bundle that we have identified as an ubiquitin-associated domain (UBA). NMR chemical shift perturbation experiments show this UBA domain interacts in a regioselective manner with ubiquitin. This two-domain structure of Ubc1 was used to identify other UBA-containing class II E2 proteins, including human E2-25K, that likely have a similar architecture and to determine the role of the UBA domain in facilitating polyubiquitin chain formation.
 
  Selected figure(s)  
 
Figure 1.
FIG. 1. Ubc1 contains two structurally distinct domains connected by a flexible tether. A, backbone superposition (N, Ca, C') of the secondary structure of the N-terminal 150 residues (catalytic domain) of the 21 lowest energy structures of Ubc1. Since the 22-residue tether region is flexible, the N- and C-terminal domains do not have a rigid orientation with respect to each other. In this figure the N-terminal domain is superimposed, and the C-terminal domain adopts many different relative orientations. B, residues that define the secondary structure of the N-terminal domain (catalytic domain) were superimposed (residues 5-13, 22-26, 34-40, 51-58, 68-70, 102-113, 124-131, and 134-147). r.m.s.d. for the backbone atoms relative to a mean structure was 0.78 ± 0.12 Å. C, ribbon diagram of Ubc1 catalytic domain (residues 1-150); helices 1, 2, 3, and 4 are colored blue, and strands 1, 2, 3, and 4, which form the central -sheet region, are colored magenta. D, residues from the regular secondary structure for the C terminus (residues 151-215) of Ubc1 were superimposed (residues 170-177, 183-191, and 204-213). r.m.s.d. for the backbone atoms relative to a mean structure of this region was 0.35 ± 0.06 Å. E, C-terminal domain (residues 170-215) of Ubc1 represented as a ribbon diagram showing the three helices 5, 6, and 7 in blue. For the entire structure no violations were observed >0.5 Å for the distance restraints or >5° for the dihedral restraints.
Figure 5.
FIG. 5. Surface representations showing the ubiquitin binding sites on the UBA domains from Ubc1 and HHR23A and the UBA binding sites on ubiquitin. A, surface representation of the UBA from Ubc1 where the blue regions indicate surface residues having chemical shift changes, > 0.05 ppm, upon ubiquitin binding. B and C, similar representations for HHR23A UBA(1) (Protein Data Bank code 1IFY [PDB] ) and UBA(2) (Protein Data Bank code 1DV0 [PDB] ) for ubiquitin binding. The surfaces for UBA domains from HHR23A are shown as described by Mueller et al. (61). D, surface diagram of ubiquitin where the blue regions represent surface residues that underwent chemical shift changes, > 0.03 ppm, upon Ubc1 binding. E, surface diagram of ubiquitin in which the magenta regions represent the residues that underwent a change in chemical shift upon binding UBA(2) as described by Mueller et al. (61). F, surface diagram of ubiquitin in which the green regions represent the amide cross-peaks that underwent a decrease in intensity upon thiol ester formation with truncated Ubc1 as described by Hamilton et al. (63).
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2004, 279, 47139-47147) copyright 2004.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20480050 A.Patil, K.Kinoshita, and H.Nakamura (2010).
Hub promiscuity in protein-protein interaction networks.
  Int J Mol Sci, 11, 1930-1943.  
21158740 D.M.Wenzel, K.E.Stoll, and R.E.Klevit (2010).
E2s: structurally economical and functionally replete.
  Biochem J, 433, 31-42.  
20152160 E.Sakata, T.Satoh, S.Yamamoto, Y.Yamaguchi, M.Yagi-Utsumi, E.Kurimoto, K.Tanaka, S.Wakatsuki, and K.Kato (2010).
Crystal structure of UbcH5b~ubiquitin intermediate: insight into the formation of the self-assembled E2~Ub conjugates.
  Structure, 18, 138-147.
PDB code: 3a33
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.  
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
19252184 M.E.French, B.R.Kretzmann, and L.Hicke (2009).
Regulation of the RSP5 ubiquitin ligase by an intrinsic ubiquitin-binding site.
  J Biol Chem, 284, 12071-12079.  
19851334 Y.Ye, and M.Rape (2009).
Building ubiquitin chains: E2 enzymes at work.
  Nat Rev Mol Cell Biol, 10, 755-764.  
18762867 S.C.Shih, I.Stoica, and N.K.Goto (2008).
Investigation of the utility of selective methyl protonation for determination of membrane protein structures.
  J Biomol NMR, 42, 49-58.  
17873885 D.E.Christensen, P.S.Brzovic, and R.E.Klevit (2007).
E2-BRCA1 RING interactions dictate synthesis of mono- or specific polyubiquitin chain linkages.
  Nat Struct Mol Biol, 14, 941-948.  
17632060 M.C.Rodrigo-Brenni, and D.O.Morgan (2007).
Sequential E2s drive polyubiquitin chain assembly on APC targets.
  Cell, 130, 127-139.  
17663792 R.A.Howard, P.Sharma, C.Hajjar, K.A.Caldwell, G.A.Caldwell, R.du Breuil, R.Moore, and L.Boyd (2007).
Ubiquitin conjugating enzymes participate in polyglutamine protein aggregation.
  BMC Cell Biol, 8, 32.  
16868077 D.Flierman, C.S.Coleman, C.M.Pickart, T.A.Rapoport, and V.Chau (2006).
E2-25K mediates US11-triggered retro-translocation of MHC class I heavy chains in a permeabilized cell system.
  Proc Natl Acad Sci U S A, 103, 11589-11594.  
16691492 J.R.Cavey, S.H.Ralston, P.W.Sheppard, B.Ciani, T.R.Gallagher, J.E.Long, M.S.Searle, and R.Layfield (2006).
Loss of ubiquitin binding is a unifying mechanism by which mutations of SQSTM1 cause Paget's disease of bone.
  Calcif Tissue Int, 78, 271-277.  
16064137 L.Hicke, H.L.Schubert, and C.P.Hill (2005).
Ubiquitin-binding domains.
  Nat Rev Mol Cell Biol, 6, 610-621.  
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.