7B95

CooS-V with partially oxidized hybrid cluster by hydroxylamine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.166 
  • R-Value Work: 0.133 
  • R-Value Observed: 0.133 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

A Morphing [4Fe-3S-nO]-Cluster within a Carbon Monoxide Dehydrogenase Scaffold.

Jeoung, J.H.Fesseler, J.Domnik, L.Klemke, F.Sinnreich, M.Teutloff, C.Dobbek, H.

(2022) Angew Chem Int Ed Engl 61: e202117000-e202117000

  • DOI: https://doi.org/10.1002/anie.202117000
  • Primary Citation of Related Structures:  
    7B7Q, 7B7T, 7B95, 7B97, 7B9A

  • PubMed Abstract: 

    Ni,Fe-containing carbon monoxide dehydrogenases (CODHs) catalyze the reversible reduction of CO 2 to CO. Several anaerobic microorganisms encode multiple CODHs in their genome, of which some, despite being annotated as CODHs, lack a cysteine of the canonical binding motif for the active site Ni,Fe-cluster. Here, we report on the structure and reactivity of such a deviant enzyme, termed CooS-V Ch . Its structure reveals the typical CODH scaffold, but contains an iron-sulfur-oxo hybrid-cluster. Although closely related to true CODHs, CooS-V Ch catalyzes neither CO oxidation, nor CO 2 reduction. The active site of CooS-V Ch undergoes a redox-dependent restructuring between a reduced [4Fe-3S]-cluster and an oxidized [4Fe-2S-S*-2O-2(H 2 O)]-cluster. Hydroxylamine, a slow-turnover substrate of CooS-V Ch , oxidizes the hybrid-cluster in two structurally distinct steps. Overall, minor changes in CODHs are sufficient to accommodate a Fe/S/O-cluster in place of the Ni,Fe-heterocubane-cluster of CODHs.


  • Organizational Affiliation

    Humboldt-Universität zu Berlin, Institut für Biologie, Unter den Linden 6, 10099, Berlin, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Carbon monoxide dehydrogenase
A, B
629Carboxydothermus hydrogenoformans Z-2901Mutation(s): 0 
Gene Names: cooSVCHY_0034
EC: 1.2.7.4
UniProt
Find proteins for Q3AG28 (Carboxydothermus hydrogenoformans (strain ATCC BAA-161 / DSM 6008 / Z-2901))
Explore Q3AG28 
Go to UniProtKB:  Q3AG28
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ3AG28
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SF4 (Subject of Investigation/LOI)
Query on SF4

Download Ideal Coordinates CCD File 
D [auth A],
P [auth B]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
SF3 (Subject of Investigation/LOI)
Query on SF3

Download Ideal Coordinates CCD File 
E [auth A],
Q [auth B]
FE4-S3 CLUSTER
Fe4 S3
QQACTBFBZNWJMV-UHFFFAOYSA-N
FES (Subject of Investigation/LOI)
Query on FES

Download Ideal Coordinates CCD File 
C [auth A]FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
TAM
Query on TAM

Download Ideal Coordinates CCD File 
O [auth A],
T [auth B]
TRIS(HYDROXYETHYL)AMINOMETHANE
C7 H17 N O3
GKODZWOPPOTFGA-UHFFFAOYSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
H [auth A]
I [auth A]
J [auth A]
U [auth B]
V [auth B]
H [auth A],
I [auth A],
J [auth A],
U [auth B],
V [auth B],
W [auth B],
X [auth B]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
BU3
Query on BU3

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
K [auth A]
L [auth A]
M [auth A]
F [auth A],
G [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
R [auth B],
S [auth B],
Y [auth B]
(R,R)-2,3-BUTANEDIOL
C4 H10 O2
OWBTYPJTUOEWEK-QWWZWVQMSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.166 
  • R-Value Work: 0.133 
  • R-Value Observed: 0.133 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.148α = 90
b = 108.065β = 94.8
c = 82.237γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)Germany390540038

Revision History  (Full details and data files)

  • Version 1.0: 2022-01-12
    Type: Initial release
  • Version 1.1: 2022-07-27
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Refinement description