1E2O

CATALYTIC DOMAIN FROM DIHYDROLIPOAMIDE SUCCINYLTRANSFERASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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: 655-668

  • DOI: 10.1006/jmbi.1998.1924

  • PubMed Abstract: 
  • The dihydrolipoamide succinyltransferase (E2o) component of the 2-oxoglutarate dehydrogenase multienzyme complex is composed of 24 subunits arranged with 432 point group symmetry. The catalytic domain (CD) of the E2o component catalyzes the transfer ...

    The dihydrolipoamide succinyltransferase (E2o) component of the 2-oxoglutarate dehydrogenase multienzyme complex is composed of 24 subunits arranged with 432 point group symmetry. The catalytic domain (CD) of the E2o component catalyzes the transfer of a succinyl group from the S-succinyldihydrolipoyl moiety to coenzyme A. The crystal structure of the Escherichia coli E2oCD has been solved to 3.0 A resolution using molecular replacement phases derived from the structure of the catalytic domain from the Azotobacter vinelandii dihydrolipoamide acetyltransferase (E2pCD). The refined model of the E. coli E2oCD consists of residues 172 to 404 and has an R-factor of 0.205 (Rfree=0.249) for 9696 reflections between 20.0 and 3.0 A resolution. Although both E2oCD and E2pCD form 24mers, subtle changes in the orientations of two helices in E2oCD increase the stability of the E2oCD 24mer in comparison to the less stable A. vinelandii E2pCD 24mer. Like E2pCD and chloramphenicol acetyltransferase (CAT), the active site of E2oCD is located in the middle of a channel formed at the interface between two 3-fold related subunits. Two of the active-site residues (His375 and Thr323) have a similar orientation to their counterparts in E2pCD and CAT. A third catalytic residue (Asp379) assumes a conformation similar to the corresponding residue in E2pCD (Asn614), but different from its counterpart in CAT (Asp199). Binding of the substrates to E2oCD is proposed to induce a change in the conformation of Asp379, allowing this residue to form a salt bridge with Arg184 that is analogous to that formed between Asp199 and Arg18 in CAT. Computer models of the active site of E2o complexed with dihydrolipoamide and with coenzyme A led to the identification of the probable succinyl-binding pocket. The residues which form this pocket (Ser330, Ser333, and His348) are probably responsible for E2o's substrate specificity.


    Related Citations: 
    • 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
    • Crystallization and Preliminary Structural Analysis of Dihydrolipoyl Transsuccinylase, the Core of the 2-Oxoglutarate Dehydrogenase Complex
      Derosier, D.J.,Oliver, R.M.,Reed, L.J.
      (1971) Proc.Natl.Acad.Sci.USA 68: 1135
    • Atomic Structure of the Cubic Core of the Pyruvate Dehydrogenase Multienzyme Complex
      Mattevi, A.,Obmolova, G.,Schulze, E.,Kalk, K.H.,Westphal, A.H.,De Kok, A.,Hol, W.G.
      (1992) Science 255: 1544


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DIHYDROLIPOAMIDE SUCCINYLTRANSFERASE
A
233Escherichia coli (strain K12)Gene Names: sucB
EC: 2.3.1.61
Find proteins for P0AFG6 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AFG6
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.205 
  • Space Group: F 4 3 2
Unit Cell:
Length (Å)Angle (°)
a = 222.800α = 90.00
b = 222.800β = 90.00
c = 222.800γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement
MOSFLMdata reduction
AGROVATA)data scaling
X-PLORphasing
X-PLORmodel building
CCP4data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-12-02
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance