1FFV

CARBON MONOXIDE DEHYDROGENASE FROM HYDROGENOPHAGA PSEUDOFLAVA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.209 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The effect of intracellular molybdenum in Hydrogenophaga pseudoflava on the crystallographic structure of the seleno-molybdo-iron-sulfur flavoenzyme carbon monoxide dehydrogenase.

Hanzelmann, P.Dobbek, H.Gremer, L.Huber, R.Meyer, O.

(2000) J.Mol.Biol. 301: 1221-1235

  • DOI: 10.1006/jmbi.2000.4023
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Crystal structures of carbon monoxide dehydrogenase (CODH), a seleno-molybdo-iron-sulfur flavoprotein from the aerobic carbon monoxide utilizing carboxidotrophic eubacterium Hydrogenophaga pseudoflava, have been determined from the enzyme synthesized ...

    Crystal structures of carbon monoxide dehydrogenase (CODH), a seleno-molybdo-iron-sulfur flavoprotein from the aerobic carbon monoxide utilizing carboxidotrophic eubacterium Hydrogenophaga pseudoflava, have been determined from the enzyme synthesized at high (Mo(plus) CODH) and low intracellular molybdenum content (Mo(minus) CODH) at 2.25 A and 2.35 A resolution, respectively. The structures were solved by Patterson search methods utilizing the enzyme from Oligotropha carboxidovorans as the initial model. The CODHs from both sources are structurally very much conserved and show the same overall fold, architecture and arrangements of the molybdopterin-cytosine dinucleotide-type of molybdenum cofactor, the type I and type II [2Fe-2S] clusters and the flavin-adenine dinucleotide. Unlike the CODH from O. carboxidovorans, the enzyme from H. pseudoflava reveals a unique post-translationally modified C(gamma)-hydroxy-Arg384 residue which precedes the catalytically essential S-selanyl-Cys385 in the active-site loop. In addition, the Trp193 which shields the isoalloxazine ring of the flavin-adenine dinucleotide in the M subunit of the H. pseudoflava CODH is a Tyr193 in the O. carboxidovorans CODH. The hydrogen bonding interaction pattern of the molybdenum cofactor involves 27 hydrogen bonds with the surrounding protein. Of these, eight are with the cytosine moiety, eight with the pyrophosphate, six with the pyranopterin, and five with the ligands of the Mo ion. The structure of the catalytically inactive Mo(minus) CODH indicates that an intracellular Mo-deficiency affects exclusively the active site of the enzyme as an incomplete non-functional molybdenum cofactor was synthesized. The 5'-CDP residue was present in Mo(minus) CODH, whereas the Mo-pyranopterin moiety was absent. In Mo(plus) CODH the selenium faces the Mo ion and flips away from the Mo site in Mo(minus) CODH. The different side-chain conformations of the active-site residues S-selanyl-Cys385 and Glu757 in Mo(plus) and Mo(minus) CODH indicate a side-chain flexibility and a function of the Mo ion in the proper orientation of both residues.


    Organizational Affiliation

    Lehrstuhl für Mikrobiologie, Universität Bayreuth, Universitätsstrasse 30, Bayreuth, D-95440, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CUTS, IRON-SULFUR PROTEIN OF CARBON MONOXIDE DEHYDROGENASE
A, D
163Hydrogenophaga pseudoflavaGene Names: cutS
EC: 1.2.5.3
Find proteins for P19915 (Hydrogenophaga pseudoflava)
Go to UniProtKB:  P19915
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
CUTL, MOLYBDOPROTEIN OF CARBON MONOXIDE DEHYDROGENASE
B, E
803Hydrogenophaga pseudoflavaGene Names: cutL
EC: 1.2.5.3
Find proteins for P19913 (Hydrogenophaga pseudoflava)
Go to UniProtKB:  P19913
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
CUTM, FLAVOPROTEIN OF CARBON MONOXIDE DEHYDROGENASE
C, F
287Hydrogenophaga pseudoflavaGene Names: cutM
EC: 1.2.5.3
Find proteins for P19914 (Hydrogenophaga pseudoflava)
Go to UniProtKB:  P19914
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download SDF File 
Download CCD File 
C, F
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
FES
Query on FES

Download SDF File 
Download CCD File 
A, D
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
PCD
Query on PCD

Download SDF File 
Download CCD File 
B, E
(MOLYBDOPTERIN-CYTOSINE DINUCLEOTIDE-S,S)-DIOXO-AQUA-MOLYBDENUM(V)
MOLYBDENUM COFACTOR; MOCO
C19 H26 Mo N8 O16 P2 S2
YEBYDVFRFUQMER-NBXMTLLYDD
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
ARO
Query on ARO
B, E
L-PEPTIDE LINKINGC6 H15 N4 O3ARG
CSZ
Query on CSZ
B, E
L-PEPTIDE LINKINGC3 H7 N O2 S SeCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.209 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 86.373α = 90.00
b = 193.793β = 90.00
c = 218.755γ = 90.00
Software Package:
Software NamePurpose
CCP4data scaling
AMoREphasing
MOSFLMdata reduction
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-09-15
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance