7B9A

CooS-V with Xe-soaked


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.238 

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, C, D
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 
CB [auth C],
DA [auth B],
E [auth A],
FC [auth D]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
T2N (Subject of Investigation/LOI)
Query on T2N

Download Ideal Coordinates CCD File 
AB [auth B],
RB [auth C],
VC [auth D],
X [auth A]
3,5-dioxa-7-thia-1-thionia-2$l^{2},4$l^{2},6$l^{3},8$l^{2}-tetraferrabicyclo[4.2.0]octane
Fe4 O2 S2
ZZXANUDJVNRRAL-UHFFFAOYSA-N
FES
Query on FES

Download Ideal Coordinates CCD File 
CA [auth B],
ZB [auth D]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
XE (Subject of Investigation/LOI)
Query on XE

Download Ideal Coordinates CCD File 
AA [auth A]
BB [auth B]
DB [auth C]
EA [auth B]
EB [auth C]
AA [auth A],
BB [auth B],
DB [auth C],
EA [auth B],
EB [auth C],
F [auth A],
FA [auth B],
FB [auth C],
G [auth A],
GA [auth B],
GB [auth C],
GC [auth D],
H [auth A],
HA [auth B],
HB [auth C],
HC [auth D],
I [auth A],
IA [auth B],
IB [auth C],
IC [auth D],
J [auth A],
JA [auth B],
JB [auth C],
JC [auth D],
K [auth A],
KA [auth B],
KB [auth C],
KC [auth D],
L [auth A],
LA [auth B],
LB [auth C],
LC [auth D],
M [auth A],
MA [auth B],
MB [auth C],
MC [auth D],
N [auth A],
NA [auth B],
NB [auth C],
NC [auth D],
O [auth A],
OA [auth B],
OB [auth C],
OC [auth D],
P [auth A],
PA [auth B],
PB [auth C],
PC [auth D],
Q [auth A],
QA [auth B],
QB [auth C],
QC [auth D],
R [auth A],
RC [auth D],
S [auth A],
SC [auth D],
T [auth A],
TC [auth D],
UC [auth D],
Y [auth A],
Z [auth A]
XENON
Xe
FHNFHKCVQCLJFQ-UHFFFAOYSA-N
BR
Query on BR

Download Ideal Coordinates CCD File 
AC [auth D]
BC [auth D]
CC [auth D]
DC [auth D]
EC [auth D]
AC [auth D],
BC [auth D],
CC [auth D],
DC [auth D],
EC [auth D],
RA [auth B],
SA [auth B],
SB [auth C],
TA [auth B],
TB [auth C],
U [auth A],
UA [auth B],
UB [auth C],
V [auth A],
VA [auth B],
VB [auth C],
W [auth A],
WA [auth B],
WB [auth C],
XA [auth B],
XB [auth C],
YA [auth B],
ZA [auth B]
BROMIDE ION
Br
CPELXLSAUQHCOX-UHFFFAOYSA-M
H2S (Subject of Investigation/LOI)
Query on H2S

Download Ideal Coordinates CCD File 
BA [auth A],
WC [auth D],
YB [auth C]
HYDROSULFURIC ACID
H2 S
RWSOTUBLDIXVET-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.238 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.41α = 90
b = 230.05β = 101.52
c = 82.74γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
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