3CF4

Structure of the CODH component of the M. barkeri ACDS complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.209 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structure of the alpha2 epsilon2 Ni-dependent CO dehydrogenase component of the Methanosarcina barkeri acetyl-CoA decarboxylase/synthase complex

Gong, W.Hao, B.Wei, Z.Ferguson Jr., D.J.Tallant, T.Krzycki, J.A.Chan, M.K.

(2008) Proc Natl Acad Sci U S A 105: 9558-9563

  • DOI: 10.1073/pnas.0800415105
  • Primary Citation of Related Structures:  
    3CF4

  • PubMed Abstract: 
  • Ni-dependent carbon monoxide dehydrogenases (Ni-CODHs) are a diverse family of enzymes that catalyze reversible CO:CO(2) oxidoreductase activity in acetogens, methanogens, and some CO-using bacteria. Crystallography of Ni-CODHs from CO-using bacteria ...

    Ni-dependent carbon monoxide dehydrogenases (Ni-CODHs) are a diverse family of enzymes that catalyze reversible CO:CO(2) oxidoreductase activity in acetogens, methanogens, and some CO-using bacteria. Crystallography of Ni-CODHs from CO-using bacteria and acetogens has revealed the overall fold of the Ni-CODH core and has suggested structures for the C cluster that mediates CO:CO(2) interconversion. Despite these advances, the mechanism of CO oxidation has remained elusive. Herein, we report the structure of a distinct class of Ni-CODH from methanogenic archaea: the alpha(2)epsilon(2) component from the alpha(8)beta(8)gamma(8)delta(8)epsilon(8) CODH/acetyl-CoA decarbonylase/synthase complex, an enzyme responsible for the majority of biogenic methane production on Earth. The structure of this Ni-CODH component provides support for a hitherto unobserved state in which both CO and H(2)O/OH(-) bind to the Ni and the exogenous FCII iron of the C cluster, respectively, and offers insight into the structures and functional roles of the epsilon-subunit and FeS domain not present in nonmethanogenic Ni-CODHs.


    Organizational Affiliation

    Departments of Biochemistry, Chemistry and Microbiology, and Ohio State Biochemistry Program, Ohio State University, 484 West 12th Avenue, Columbus, OH 43210, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Acetyl-CoA decarboxylase/synthase alpha subunitA807Methanosarcina barkeriMutation(s): 0 
EC: 1.2.99.2 (PDB Primary Data), 1.2.7.4 (UniProt)
Find proteins for Q46G04 (Methanosarcina barkeri (strain Fusaro / DSM 804))
Explore Q46G04 
Go to UniProtKB:  Q46G04
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Acetyl-CoA decarboxylase/synthase epsilon subunitG170Methanosarcina barkeriMutation(s): 0 
EC: 1.2.99.2
Find proteins for Q46G05 (Methanosarcina barkeri (strain Fusaro / DSM 804))
Explore Q46G05 
Go to UniProtKB:  Q46G05
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
WCC
Query on WCC

Download CCD File 
A
FE(3)-NI(1)-S(4) CLUSTER
Fe3 Ni S4
SEEZYPKDPRYISB-KUBGLCDSAO
 Ligand Interaction
SF4
Query on SF4

Download CCD File 
A
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
PEG
Query on PEG

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G
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

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A, G
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
ACY
Query on ACY

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A, G
ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
 Ligand Interaction
FE
Query on FE

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A
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
CMO
Query on CMO

Download CCD File 
A
CARBON MONOXIDE
C O
UGFAIRIUMAVXCW-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.209 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 133.291α = 90
b = 81.681β = 90
c = 101.12γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
DMphasing
CNSrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SHELXDphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-07-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.2: 2012-03-07
    Changes: Atomic model
  • Version 1.3: 2017-10-25
    Changes: Advisory, Refinement description
  • Version 1.4: 2018-06-27
    Changes: Data collection, Derived calculations