1MO9

NADPH DEPENDENT 2-KETOPROPYL COENZYME M OXIDOREDUCTASE/CARBOXYLASE COMPLEXED WITH 2-KETOPROPYL COENZYME M


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural Basis for CO2 Fixation by a Novel Member of the Disulfide Oxidoreductase Family of Enzymes, 2-Ketopropyl Coenzyme M Oxidoreductase/Carboxylase

Nocek, B.Jang, S.B.Jeong, M.S.Clark, D.D.Ensign, S.A.Peters, J.W.

(2002) Biochemistry 41: 12907-12913

  • Primary Citation of Related Structures:  1MOK

  • PubMed Abstract: 
  • The NADPH:2-ketopropyl-coenzyme M oxidoreductase/carboxylase (2-KPCC) is the terminal enzyme in a metabolic pathway that results in the conversion of propylene to the central metabolite acetoacetate in Xanthobacter autotrophicus Py2. This enzyme is a ...

    The NADPH:2-ketopropyl-coenzyme M oxidoreductase/carboxylase (2-KPCC) is the terminal enzyme in a metabolic pathway that results in the conversion of propylene to the central metabolite acetoacetate in Xanthobacter autotrophicus Py2. This enzyme is an FAD-containing enzyme that is a member of the NADPH:disulfide oxidoreductase (DSOR) family of enzymes that include glutathione reductase, dihydrolipoamide dehydrogenase, trypanothione reductase, thioredoxin reductase, and mercuric reductase. In contrast to the prototypical reactions catalyzed by members of the DSOR family, the NADPH:2-ketopropyl-coenzyme M oxidoreductase/carboxylase catalyzes the reductive cleavage of the thioether linkage of 2-ketopropyl-coenzyme M, and the subsequent carboxylation of the ketopropyl cleavage product, yielding the products acetoacetate and free coenzyme M. The structure of 2-KPCC reveals a unique active site in comparison to those of other members of the DSOR family of enzymes and demonstrates how the enzyme architecture has been adapted for the more sophisticated biochemical reaction. In addition, comparison of the structures in the native state and in the presence of bound substrate indicates the binding of the substrate 2-ketopropyl-coenzyme M induces a conformational change resulting in the collapse of the substrate access channel. The encapsulation of the substrate in this manner is reminiscent of the conformational changes observed in the well-characterized CO2-fixing enzyme ribulose 1,5-bisphosphate carboxylase/oxidase (Rubisco).


    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
orf3
A, B
523Xanthobacter autotrophicus (strain ATCC BAA-1158 / Py2)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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
KPC
Query on KPC

Download SDF File 
Download CCD File 
A, B
(2-[2-KETOPROPYLTHIO]ETHANESULFONATE
C5 H10 O4 S2
CRNXHFXAXBWIRH-UHFFFAOYSA-N
 Ligand Interaction
FAD
Query on FAD

Download SDF File 
Download CCD File 
A, B
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.188 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 87.980α = 90.00
b = 60.120β = 102.50
c = 105.600γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
ARP/wARPmodel building
WARPmodel building
DENZOdata reduction
SCALEPACKdata scaling
Blu-Icedata collection
SCALAdata scaling
SOLVEphasing
CNSrefinement
CCP4data scaling
DMmodel building
DMphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-11-27
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Source and taxonomy, Version format compliance
  • Version 1.3: 2012-05-09
    Type: Structure summary