1C4A

BINDING OF EXOGENOUSLY ADDED CARBON MONOXIDE AT THE ACTIVE SITE OF THE FE-ONLY HYDROGENASE (CPI) FROM CLOSTRIDIUM PASTEURIANUM


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.199 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Binding of exogenously added carbon monoxide at the active site of the iron-only hydrogenase (CpI) from Clostridium pasteurianum.

Lemon, B.J.Peters, J.W.

(1999) Biochemistry 38: 12969-12973

  • DOI: 10.1021/bi9913193
  • Primary Citation of Related Structures:  
    1C4A, 1C4C

  • PubMed Abstract: 
  • A site for the binding of exogenously added carbon monoxide has been identified at the active site of the Fe-only hydrogenase (CpI) from Clostridium pasteurianum. The binding and inhibition of carbon monoxide have been exploited in biochemical and spectroscopic studies to gain mechanistic insights ...

    A site for the binding of exogenously added carbon monoxide has been identified at the active site of the Fe-only hydrogenase (CpI) from Clostridium pasteurianum. The binding and inhibition of carbon monoxide have been exploited in biochemical and spectroscopic studies to gain mechanistic insights. In the present study, we have taken advantage of the ability to generate an irreversibly carbon monoxide bound state of CpI. The crystallization and structural characterization of CpI inhibited in the presence of carbon monoxide indicates the addition of a single molecule of carbon monoxide. The ability to generate crystals of the carbon monoxide bound state of the hydrogenase that are isomorphous to those of the native enzyme has allowed for a direct comparison of the crystallographic data and an unambiguous identification of the site of carbon monoxide binding at the active site of CpI. Carbon monoxide binds to an Fe atom of the 2Fe subcluster at the site of a terminally bound water molecule in the as crystallized native state of CpI that has been previously suggested to be a potential site of reversible hydrogen oxidation. Binding of carbon monoxide at this site results in an active site that is coordinately saturated with strong ligands (S, CO, and CN), providing a rational potential mechanism for inhibition of reversible hydrogen oxidation at the active site of CpI.


    Organizational Affiliation

    Department of Chemistry and Biochemistry, Utah State University, Logan 84322, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (FE-ONLY HYDROGENASE)A574Clostridium pasteurianumMutation(s): 0 
EC: 1.18.99.1 (PDB Primary Data), 1.12.7.2 (UniProt)
UniProt
Find proteins for P29166 (Clostridium pasteurianum)
Explore P29166 
Go to UniProtKB:  P29166
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HC1 (Subject of Investigation/LOI)
Query on HC1

Download Ideal Coordinates CCD File 
B [auth A]2 IRON/2 SULFUR/5 CARBONYL/2 WATER INORGANIC CLUSTER
C5 H8 Fe2 O7 S2
DXKOXSKJHMBSFW-WPRITKAGAV
 Ligand Interaction
SF4
Query on SF4

Download Ideal Coordinates CCD File 
C [auth A], D [auth A], E [auth A], F [auth A]IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
FES
Query on FES

Download Ideal Coordinates CCD File 
G [auth A]FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.199 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 133.7α = 90
b = 84β = 90
c = 55.7γ = 90
Software Package:
Software NamePurpose
AMoREphasing
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-12-22
    Type: Initial release
  • Version 1.1: 2008-04-26
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance