6ONC | pdb_00006onc

Crystal structure of Desulfovibrio vulgaris carbon monoxide dehydrogenase produced without CooC, as-isolated

• PDB DOI: https://doi.org/10.2210/pdb6ONC/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Nitratidesulfovibrio vulgaris
• Expression System: Solidesulfovibrio fructosivorans
• Mutation(s): No 


• Deposited: 2019-04-21 Released: 2019-07-24 
• Deposition Author(s): Wittenborn, E.C., Cohen, S.E., Drennan, C.L.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.178 (Depositor), 0.179 (DCC) 
• R-Value Work: 
  0.154 (Depositor), 0.154 (DCC) 
• R-Value Observed: 
  0.155 (Depositor) 

Starting Model: experimental

Literature

Structural insight into metallocofactor maturation in carbon monoxide dehydrogenase.

Wittenborn, E.C., Cohen, S.E., Merrouch, M., Leger, C., Fourmond, V., Dementin, S., Drennan, C.L.

(2019) J Biological Chem 294: 13017-13026

• PubMed: 31296570 
• DOI: https://doi.org/10.1074/jbc.RA119.009610
• Primary Citation Related Structures: 
  6ONC, 6OND, 6ONS


• PubMed Abstract: 
  

  The nickel-dependent carbon monoxide dehydrogenase (CODH) employs a unique heterometallic nickel-iron-sulfur cluster, termed the C-cluster, to catalyze the interconversion of CO and CO ₂ Like other complex metalloenzymes, CODH requires dedicated assembly machinery to form the fully intact and functional C-cluster. In particular, nickel incorporation into the C-cluster depends on the maturation factor CooC; however, the mechanism of nickel insertion remains poorly understood. Here, we compare X-ray structures (1.50-2.48 Å resolution) of CODH from Desulfovibrio vulgaris ( Dv CODH) heterologously expressed in either the absence ( Dv CODH ^-CooC ) or presence ( Dv CODH ^+CooC ) of co-expressed CooC. We find that the C-cluster of Dv CODH ^-CooC is fully loaded with iron but does not contain any nickel. Interestingly, the so-called unique iron ion (Fe _u ) occupies both its canonical site (80% occupancy) and the nickel site (20% occupancy), with addition of reductant causing further mismetallation of the nickel site (60% iron occupancy). We also demonstrate that a Dv CODH variant that lacks a surface-accessible iron-sulfur cluster (the D-cluster) has a C-cluster that is also replete in iron but lacks nickel, despite co-expression with CooC. In this variant, all Fe _u is in its canonical location, and the nickel site is empty. This D-cluster-deficient CODH is inactive despite attempts to reconstitute it with nickel. Taken together, these results suggest that an empty nickel site is not sufficient for nickel incorporation. Based on our findings, we propose a model for C-cluster assembly that requires both CooC and a functioning D-cluster, involves precise redox-state control, and includes a two-step nickel-binding process.

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Organizational Affiliation: 
• Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139.
CNRS, Aix-Marseille Université, Laboratoire de Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditerranée, Marseille, France.
CNRS, Aix-Marseille Université, Laboratoire de Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditerranée, Marseille, France. Electronic address: [e-mail].
Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139; Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139; Bio-inspired Solar Energy Program, Canadian Institute for Advanced Research, Toronto, Ontario M5G 1M1, Canada. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: homology

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 275.03 kDa 
• Atom Count: 21,744 
• Modeled Residue Count: 2,503 
• Deposited Residue Count: 2,548 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbon monoxide dehydrogenase	A, B, C, D	637	Nitratidesulfovibrio vulgaris	Mutation(s): 0  Gene Names: cooS, DVU_2098 EC: 1.2.7.4
UniProt
Find proteins for Q72A99 (Nitratidesulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / CCUG 34227 / NCIMB 8303 / VKM B-1760 / Hildenborough)) Explore Q72A99  Go to UniProtKB:  Q72A99

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
XCC (Subject of Investigation/LOI)	F [auth A], L [auth B], R [auth C], Z [auth D]	FE(4)-NI(1)-S(4) CLUSTER Fe4 Ni S4 QGLWBXDZIHZONR-UHFFFAOYSA-N
SF4	E [auth A], K [auth B], Q [auth C], Y [auth D]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-UHFFFAOYSA-N
FES	J [auth B], X [auth D]	FE2/S2 (INORGANIC) CLUSTER Fe2 S2 NIXDOXVAJZFRNF-UHFFFAOYSA-N
GOL	BA [auth D], H [auth A], T [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
FE	AA [auth D], G [auth A], M [auth B], S [auth C]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N
CL	P [auth B], W [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	CA [auth D], DA [auth D], EA [auth D], I [auth A], N [auth B], O [auth B], U [auth C], V [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.178 (Depositor), 0.179 (DCC) 
• R-Value Work:  0.154 (Depositor), 0.154 (DCC) 
• R-Value Observed: 0.155 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.79	α = 90
b = 144.15	β = 98.5
c = 123.69	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-07-24 
Deposition Author(s): Wittenborn, E.C., Cohen, S.E., Drennan, C.L.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM069857
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM126982
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	T32 GM008334

Revision History  

• Version 1.0: 2019-07-24
  Type: Initial release
  
• Version 1.1: 2019-09-11
  Changes: Data collection, Database references
• Version 1.2: 2020-01-01
  Changes: Author supporting evidence
• Version 1.3: 2023-10-11
  Changes: Data collection, Database references, Derived calculations, Refinement description