1EF9

THE CRYSTAL STRUCTURE OF METHYLMALONYL COA DECARBOXYLASE COMPLEXED WITH 2S-CARBOXYPROPYL COA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Observed: 0.190 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

New reactions in the crotonase superfamily: structure of methylmalonyl CoA decarboxylase from Escherichia coli.

Benning, M.M.Haller, T.Gerlt, J.A.Holden, H.M.

(2000) Biochemistry 39: 4630-4639

  • DOI: 10.1021/bi9928896
  • Primary Citation of Related Structures:  
    1EF8, 1EF9

  • PubMed Abstract: 
  • The molecular structure of methylmalonyl CoA decarboxylase (MMCD), a newly defined member of the crotonase superfamily encoded by the Escherichia coli genome, has been solved by X-ray crystallographic analyses to a resolution of 1.85 A for the unliganded form and to a resolution of 2 ...

    The molecular structure of methylmalonyl CoA decarboxylase (MMCD), a newly defined member of the crotonase superfamily encoded by the Escherichia coli genome, has been solved by X-ray crystallographic analyses to a resolution of 1.85 A for the unliganded form and to a resolution of 2.7 A for a complex with an inert thioether analogue of methylmalonyl CoA. Like two other structurally characterized members of the crotonase superfamily (crotonase and dienoyl CoA isomerase), MMCD is a hexamer (dimer of trimers) with each polypeptide chain composed of two structural motifs. The larger N-terminal domain contains the active site while the smaller C-terminal motif is alpha-helical and involved primarily in trimerization. Unlike the other members of the crotonase superfamily, however, the C-terminal motif is folded back onto the N-terminal domain such that each active site is wholly contained within a single subunit. The carboxylate group of the thioether analogue of methylmalonyl CoA is hydrogen bonded to the peptidic NH group of Gly 110 and the imidazole ring of His 66. From modeling studies, it appears that Tyr 140 is positioned within the active site to participate in the decarboxylation reaction by orienting the carboxylate group of methylmalonyl CoA so that it is orthogonal to the plane of the thioester carbonyl group. Surprisingly, while the active site of MMCD contains Glu 113, which is homologous to the general acid/base Glu 144 in the active site of crotonase, its carboxylate side chain is hydrogen bonded to Arg 86, suggesting that it is not directly involved in catalysis. The new constellation of putative functional groups observed in the active site of MMCD underscores the diversity of function in this superfamily.


    Organizational Affiliation

    Department of Biochemistry, University of Illinois, Urbana, Illinois 61801, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
METHYLMALONYL COA DECARBOXYLASEA261Escherichia coliMutation(s): 0 
EC: 4.1.1.41 (PDB Primary Data), 4.1.1 (UniProt)
UniProt
Find proteins for P52045 (Escherichia coli (strain K12))
Explore P52045 
Go to UniProtKB:  P52045
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2CP (Subject of Investigation/LOI)
Query on 2CP

Download Ideal Coordinates CCD File 
B [auth A]2-CARBOXYPROPYL-COENZYME A
C25 H42 N7 O18 P3 S
YLEVKEKTOJAHCY-UQCJFRAESA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Observed: 0.190 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.7α = 90
b = 142.4β = 109.2
c = 89.7γ = 90
Software Package:
Software NamePurpose
AMoREphasing
TNTrefinement
FRAMBOdata collection
XDSdata scaling

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-05-24
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Refinement description