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PDBsum entry 1c4t

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protein ligands Protein-protein interface(s) links
Transferase PDB id
1c4t
Jmol
Contents
Protein chains
226 a.a. *
Ligands
SO4 ×6
Waters ×28
* Residue conservation analysis
PDB id:
1c4t
Name: Transferase
Title: Catalytic domain from trimeric dihydrolipoamide succinyltran
Structure: Protein (dihydrolipoamide succinyltransferase). Chain: a, b, c. Fragment: catalytic domain, residues 172 - 404. Synonym: e2o. Engineered: yes
Source: Escherichia coli. Organism_taxid: 469008. Strain: bl21(de3). Cellular_location: mitochondria. Gene: sucb. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Biol. unit: Hexamer (from PQS)
Resolution:
3.00Å     R-factor:   0.257     R-free:   0.286
Authors: J.E.Knapp,D.Carroll,J.E.Lawson,S.R.Ernst,L.J.Reed,M.L.Hacker
Key ref: J.E.Knapp et al. (2000). Expression, purification, and structural analysis of the trimeric form of the catalytic domain of the Escherichia coli dihydrolipoamide succinyltransferase. Protein Sci, 9, 37-48. PubMed id: 10739245 DOI: 10.1110/ps.9.1.37
Date:
22-Sep-99     Release date:   18-Feb-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P0AFG6  (ODO2_ECOLI) -  Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex
Seq:
Struc:
405 a.a.
226 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.2.3.1.61  - Dihydrolipoyllysine-residue succinyltransferase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
Citric acid cycle
      Reaction: Succinyl-CoA + enzyme N6-(dihydrolipoyl)lysine = CoA + enzyme N6- (S-succinyldihydrolipoyl)lysine
Succinyl-CoA
+ enzyme N(6)-(dihydrolipoyl)lysine
= CoA
+ enzyme N(6)- (S-succinyldihydrolipoyl)lysine
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     oxoglutarate dehydrogenase complex   1 term 
  Biological process     metabolic process   2 terms 
  Biochemical function     transferase activity, transferring acyl groups     2 terms  

 

 
    reference    
 
 
DOI no: 10.1110/ps.9.1.37 Protein Sci 9:37-48 (2000)
PubMed id: 10739245  
 
 
Expression, purification, and structural analysis of the trimeric form of the catalytic domain of the Escherichia coli dihydrolipoamide succinyltransferase.
J.E.Knapp, D.Carroll, J.E.Lawson, S.R.Ernst, L.J.Reed, M.L.Hackert.
 
  ABSTRACT  
 
The dihydrolipoamide succinyltransferase (E2o) component of the alpha-ketoglutarate dehydrogenase complex catalyzes the transfer of a succinyl group from the S-succinyldihydrolipoyl moiety to coenzyme A. E2o is normally a 24-mer, but is found as a trimer when E2o is expressed with a C-terminal [His]6 tag. The crystal structure of the trimeric form of the catalytic domain (CD) of the Escherichia coli E2o has been solved to 3.0 A resolution using the Molecular Replacement method. The refined model contains an intact trimer in the asymmetric unit and has an R-factor of 0.257 (Rfree = 0.286) for 18,699 reflections between 10.0 and 3.0 A resolution. The core of tE2oCD (residues 187-396) superimposes onto that of the cubic E2oCD with an RMS difference of 0.4 A for all main-chain atoms. The C-terminal end of tE2oCD (residues 397-404) rotates by an average of 37 degrees compared to cubic E2oCD, disrupting the normal twofold interface. Despite the alteration of quaternary structure, the active site of tE2oCD shows no significant differences from that of the cubic E2oCD, although several side chains in the active site are more ordered in the trimeric form of E2oCD. Analysis of the available sequence data suggests that the majority of E2 components have active sites that resemble that of E. coli E2oCD. The remaining E2 components can be divided into three groups based on active-site sequence similarity. Analysis of the surface properties of both crystal forms of E. coli E2oCD suggests key residues that may be involved in the protein-protein contacts that occur between the catalytic and lipoyl domains of E2o.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
16579849 G.E.Homanics, K.Skvorak, C.Ferguson, S.Watkins, and H.S.Paul (2006).
Production and characterization of murine models of classic and intermediate maple syrup urine disease.
  BMC Med Genet, 7, 33.  
17124494 M.Kato, R.M.Wynn, J.L.Chuang, C.A.Brautigam, M.Custorio, and D.T.Chuang (2006).
A synchronized substrate-gating mechanism revealed by cubic-core structure of the bovine branched-chain alpha-ketoacid dehydrogenase complex.
  EMBO J, 25, 5983-5994.
PDB codes: 2ihw 2ii3 2ii4 2ii5
16288665 S.Rey, J.L.Gardy, and F.S.Brinkman (2005).
Assessing the precision of high-throughput computational and laboratory approaches for the genome-wide identification of protein subcellular localization in bacteria.
  BMC Genomics, 6, 162.  
12044183 A.F.Hengeveld, C.P.van Mierlo, H.W.van den Hooven, A.J.Visser, and A.de Kok (2002).
Functional and structural characterization of a synthetic peptide representing the N-terminal domain of prokaryotic pyruvate dehydrogenase.
  Biochemistry, 41, 7490-7500.  
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 codes are shown on the right.