2C3C

2.01 Angstrom X-ray crystal structure of a mixed disulfide between coenzyme M and NADPH-dependent oxidoreductase 2-ketopropyl coenzyme M carboxylase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.181 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Mechanistic Implications of the Structure of the Mixed-Disulfide Intermediate of the Disulfide Oxidoreductase, 2-Ketopropyl-Coenzyme M Oxidoreductase/Carboxylase.

Pandey, A.S.Nocek, B.Clark, D.D.Ensign, S.A.Peters, J.W.

(2006) Biochemistry 45: 113

  • DOI: 10.1021/bi051518o
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The structure of the mixed, enzyme-cofactor disulfide intermediate of ketopropyl-coenzyme M oxidoreductase/carboxylase has been determined by X-ray diffraction methods. Ketopropyl-coenzyme M oxidoreductase/carboxylase belongs to a family of pyridine ...

    The structure of the mixed, enzyme-cofactor disulfide intermediate of ketopropyl-coenzyme M oxidoreductase/carboxylase has been determined by X-ray diffraction methods. Ketopropyl-coenzyme M oxidoreductase/carboxylase belongs to a family of pyridine nucleotide-containing flavin-dependent disulfide oxidoreductases, which couple the transfer of hydride derived from the NADPH to the reduction of protein cysteine disulfide. Ketopropyl-coenzyme M oxidoreductase/carboxylase, a unique member of this enzyme class, catalyzes thioether bond cleavage of the substrate, 2-ketopropyl-coenzyme M, and carboxylation of what is thought to be an enzyme-stabilized enolacetone intermediate. The mixed disulfide of 2-ketopropyl-coenzyme M oxidoreductase/carboxylase was captured through crystallization of the enzyme with the physiological products of the reaction, acetoacetate, coenzyme M, and NADP, and reduction of the crystals with dithiothreitol just prior to data collection. Density in the active-site environment consistent with acetone, the product of reductive decarboxylation of acetoacetate, was revealed in this structure in addition to a well-defined hydrophobic pocket or channel that could be involved in the access for carbon dioxide. The analysis of this structure and that of a coenzyme-M-bound form provides insights into the stabilization of intermediates, substrate carboxylation, and product release.


    Organizational Affiliation

    Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
2-OXOPROPYL-COM REDUCTASE
A, B
523Xanthobacter autotrophicus (strain ATCC BAA-1158 / Py2)Mutation(s): 0 
Gene Names: xecC
EC: 1.8.1.5
Find proteins for Q56839 (Xanthobacter autotrophicus (strain ATCC BAA-1158 / Py2))
Go to UniProtKB:  Q56839
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
COM
Query on COM

Download SDF File 
Download CCD File 
A, B
1-THIOETHANESULFONIC ACID
C2 H6 O3 S2
ZNEWHQLOPFWXOF-UHFFFAOYSA-N
 Ligand Interaction
ACN
Query on ACN

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Download CCD File 
A, B
ACETONE
C3 H6 O
CSCPPACGZOOCGX-UHFFFAOYSA-N
 Ligand Interaction
FAD
Query on FAD

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Download CCD File 
A, B
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
NAP
Query on NAP

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Download CCD File 
A, B
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.181 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 88.060α = 90.00
b = 60.020β = 102.43
c = 105.960γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
CNSphasing
CNSrefinement
SCALAdata scaling
SOLVEphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-12-12
    Type: Initial release
  • Version 1.1: 2011-05-07
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance