1EAB

ATOMIC STRUCTURE OF THE CUBIC CORE OF THE PYRUVATE DEHYDROGENASE MULTIENZYME COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Work: 0.198 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystallographic analysis of substrate binding and catalysis in dihydrolipoyl transacetylase (E2p).

Mattevi, A.Obmolova, G.Kalk, K.H.Teplyakov, A.Hol, W.G.

(1993) Biochemistry 32: 3887-3901

  • Primary Citation of Related Structures:  1EAA, 1EAC, 1EAD, 1EAE, 1EAF

  • PubMed Abstract: 
  • The catalytic domain of dihydrolipoyl transacetylase (E2pCD) forms the core of the pyruvate dehydrogenase multienzyme complex and catalyzes the acetyltransferase reaction using acetylCoA as acetyl donor and dihydrolipoamide (Lip(SH)2) as acceptor. Th ...

    The catalytic domain of dihydrolipoyl transacetylase (E2pCD) forms the core of the pyruvate dehydrogenase multienzyme complex and catalyzes the acetyltransferase reaction using acetylCoA as acetyl donor and dihydrolipoamide (Lip(SH)2) as acceptor. The crystal structures of six complexes and derivatives of Azotobacter vinelandii E2pCD were solved. The binary complexes of the enzyme with CoA and Lip(SH)2 were determined at 2.6- and 3.0-A resolutions, respectively. The two substrates are found in an extended conformation at the two opposite entrances of the 30 A long channel which runs at the interface between two 3-fold-related subunits and forms the catalytic center. The reactive thiol groups of both substrates are within hydrogen-bond distance from the side chain of His 610. This fact supports the indication, derived from the similarity with chloramphenicol acetyl transferase, that the histidine side chain acts as general-base catalyst in the deprotonation of the reactive thiol of CoA. The conformation of Asn 614 appears to be dependent on the protonation state of the active site histidine, whose function as base catalyst is modulated in this way. Studies on E2pCD soaked in a high concentration of dithionite lead to the structure of the binary complex between E2pCD and hydrogen sulfite solved at 2.3-A resolution. It appears that the anion is bound in the middle of the catalytic center and is therefore capable of hosting and stabilizing a negative charge, which is of special interest since the reaction catalyzed by E2pCD is thought to proceed via a negatively charged tetrahedral intermediate. The structure of the binary complex between E2pCD and hydrogen sulfite suggests that transition-state stabilization can be provided by a direct hydrogen bond between the side chain of Ser 558 and the oxy anion of the putative intermediate. In the binary complex with CoA, the hydroxyl group of Ser 558 is hydrogen bonded to the nitrogen atom of one of the two peptide-like units of the substrate. Thus, CoA itself is involved in keeping the Ser hydroxyl group in the proper position for transition-state stabilization. Quite unexpectedly, the structure at 2.6-A resolution of a ternary complex in which CoA and Lip(SH)2 are simultaneously bound to E2pCD reveals that CoA has an alternative, nonproductive binding mode. In this abortive ternary complex, CoA adopts a helical conformation with two intramolecular hydrogen bonds and the reactive sulfur of the pantetheine arm positioned 12 A away from the active site residues involved in the transferase reaction.(ABSTRACT TRUNCATED AT 400 WORDS)


    Related Citations: 
    • Crystallographic Analysis of Substrate Binding and Catalysis in Dihydrolipoyl Transacetylase (E2P)
      Mattevi, A.,Obmolova, G.,Kalk, K.H.,Teplyakov, A.,Hol, W.G.
      (1993) Biochemistry 32: 3887
    • Refined Crystal Structure of the Catalytic Domain of Dihydrolipoyl Transacetylase (E2P) from Azotobacter Vinelandii at 2.6 Angstroms Resolution
      Mattevi, A.,Obmolova, G.,Kalk, K.H.,Westphal, A.H.,De Kok, A.,Hol, W.G.
      (1993) J.Mol.Biol. 230: 1183
    • Three-Dimensional Structure of Lipoamide Dehydrogenase from Pseudomonas Fluorescens at 2.8 Angstroms Resolution. Analysis of Redox and Thermostability Properties
      Mattevi, A.,Obmolova, G.,Kalk, K.H.,Van Berkel, W.J.,Hol, W.G.
      (1993) J.Mol.Biol. 230: 1200


    Organizational Affiliation

    BIOSON Research Institute, University of Groningen, The Netherlands.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DIHYDROLIPOYL-TRANSACETYLASE
A
243Azotobacter vinelandiiEC: 2.3.1.12
Find proteins for P10802 (Azotobacter vinelandii)
Go to UniProtKB:  P10802
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
COA
Query on COA

Download SDF File 
Download CCD File 
A
COENZYME A
C21 H36 N7 O16 P3 S
RGJOEKWQDUBAIZ-IBOSZNHHSA-N
 Ligand Interaction
LPM
Query on LPM

Download SDF File 
Download CCD File 
A
6,8-DIMERCAPTO-OCTANOIC ACID AMIDE
C8 H17 N O S2
VLYUGYAKYZETRF-SSDOTTSWSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Work: 0.198 
  • Space Group: F 4 3 2
Unit Cell:
Length (Å)Angle (°)
a = 225.540α = 90.00
b = 225.540β = 90.00
c = 225.540γ = 90.00
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORphasing
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1993-10-31
    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