1C4T

CATALYTIC DOMAIN FROM TRIMERIC DIHYDROLIPOAMIDE SUCCINYLTRANSFERASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.257 
  • R-Value Observed: 0.257 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Expression, purification, and structural analysis of the trimeric form of the catalytic domain of the Escherichia coli dihydrolipoamide succinyltransferase.

Knapp, J.E.Carroll, D.Lawson, J.E.Ernst, S.R.Reed, L.J.Hackert, M.L.

(2000) Protein Sci 9: 37-48

  • DOI: 10.1110/ps.9.1.37
  • Primary Citation of Related Structures:  
    1C4T

  • PubMed 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 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.


    Related Citations: 
    • Crystal Structure of the Truncated Cubic Core Component of the Escherichia Coli 2-Oxoglutarate Dehydrogenase Multienzyme Complex
      Knapp, J.E., Mitchell, D.T., Yazdi, M.A., Ernst, S.R., Reed, L.J., Hackert, M.L.
      (1998) J Mol Biol 280: 655
    • Nucleotide Sequence of the Sucb Gene Encoding the Dihydrolipoamide Succinyltransferase of Escherichia Coli K12 and Homology with the Corresponding Acetyltransferase
      Spencer, M.E., Darlison, M.G., Stephens, P.E., Duckenfield, I.K., Guest, J.R.
      (1984) Eur J Biochem 141: 361

    Organizational Affiliation

    Department of Chemistry and Biochemistry, The University of Texas at Austin, 78712, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (DIHYDROLIPOAMIDE SUCCINYLTRANSFERASE)A, B, C233Escherichia coli BL21(DE3)Mutation(s): 0 
Gene Names: sucB
EC: 2.3.1.61
UniProt
Find proteins for P0AFG6 (Escherichia coli (strain K12))
Explore P0AFG6 
Go to UniProtKB:  P0AFG6
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.257 
  • R-Value Observed: 0.257 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 112.175α = 90
b = 112.175β = 90
c = 134.417γ = 120
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-02-18
    Type: Initial release
  • Version 1.1: 2008-04-26
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Source and taxonomy, Version format compliance