7VXQ

The Carbon Monoxide Complex of [NiFe]-hydrogenase (Hyb-type) from Citrobacter sp. S-77

PDB DOI: https://doi.org/10.2210/pdb7VXQ/pdb

Classification: OXIDOREDUCTASE
Organism(s): Citrobacter sp. S-77
Mutation(s): No

Deposited: 2021-11-13 Released: 2022-02-09
Deposition Author(s): Nishikawa, K., Higuchi, K., Imanishi, T., Higuchi, Y.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.77 Å
R-Value Free: 0.193
R-Value Work: 0.161
R-Value Observed: 0.163

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Structural and spectroscopic characterization of CO inhibition of [NiFe]-hydrogenase from Citrobacter sp. S-77.

Imanishi, T., Nishikawa, K., Taketa, M., Higuchi, K., Tai, H., Hirota, S., Hojo, H., Kawakami, T., Hataguchi, K., Matsumoto, K., Ogata, H., Higuchi, Y.

(2022) Acta Crystallogr F Struct Biol Commun 78: 66-74

PubMed: 35102895 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1107/S2053230X22000188
Primary Citation of Related Structures:
7VXQ

PubMed Abstract:
Hydrogenases catalyze the reversible oxidation of H ₂. Carbon monoxide (CO) is known to be a competitive inhibitor of O ₂-sensitive [NiFe]-hydrogenases. Although the activities of some O ₂-tolerant [NiFe]-hydrogenases are unaffected by CO, the partially O ₂-tolerant [NiFe]-hydrogenase from Citrobacter sp. S-77 (S77-HYB) is inhibited by CO. In this work, the CO-bound state of S77-HYB was characterized by activity assays, spectroscopic techniques and X-ray crystallography. Electron paramagnetic resonance spectroscopy showed a diamagnetic Ni ²⁺ state, and Fourier-transform infrared spectroscopy revealed the stretching vibration of the exogenous CO ligand. The crystal structure determined at 1.77 Å resolution revealed that CO binds weakly to the nickel ion in the Ni-Fe active site of S77-HYB. These results suggest a positive correlation between O ₂ and CO tolerance in [NiFe]-hydrogenases.

Organizational Affiliation

Graduate School of Science, University of Hyogo, 3-2-1 Koto, Kamigori, Ako, Hyogo 678-1297, Japan.

Macromolecule Content

Total Structure Weight: 196.43 kDa
Atom Count: 13,403
Modelled Residue Count: 1,638
Deposited Residue Count: 1,774
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
[NiFe]-hydrogenase 2 large subunit	A, C	552	Citrobacter sp. S-77	Mutation(s): 0
UniProt
Find proteins for A0A3B6UEQ1 (Citrobacter sp. S-77) Explore A0A3B6UEQ1 Go to UniProtKB: A0A3B6UEQ1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A3B6UEQ1
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
NiFe hydrogenase	B, D	335	Citrobacter sp. S-77	Mutation(s): 0 EC: 1.12.99.6
UniProt
Find proteins for A0A3B6UEQ0 (Citrobacter sp. S-77) Explore A0A3B6UEQ0 Go to UniProtKB: A0A3B6UEQ0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A3B6UEQ0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SF4 Query on SF4 Download Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain N [auth B] SDF format, chain R [auth D] SDF format, chain T [auth D] MOL2 format, chain L [auth B] MOL2 format, chain N [auth B] MOL2 format, chain R [auth D] MOL2 format, chain T [auth D]	L [auth B], N [auth B], R [auth D], T [auth D]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain L [auth B] Focus chain N [auth B] Focus chain R [auth D] Focus chain T [auth D] Interactions & Density Focus chain L [auth B] Focus chain N [auth B] Focus chain R [auth D] Focus chain T [auth D]
F3S Query on F3S Download Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain S [auth D] MOL2 format, chain M [auth B] MOL2 format, chain S [auth D]	M [auth B], S [auth D]	FE3-S4 CLUSTER Fe₃ S₄ FCXHZBQOKRZXKS-UHFFFAOYSA-N		Interactions Focus chain M [auth B] Focus chain S [auth D] Interactions & Density Focus chain M [auth B] Focus chain S [auth D]
NFU (Subject of Investigation/LOI) Query on NFU Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain P [auth C] MOL2 format, chain F [auth A] MOL2 format, chain P [auth C]	F [auth A], P [auth C]	formyl[bis(hydrocyanato-1kappaC)]ironnickel(Fe-Ni) C₃ H Fe N₂ Ni O QCZROEOIPZWDEO-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain P [auth C] Interactions & Density Focus chain F [auth A] Focus chain P [auth C]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth B] SDF format, chain K [auth B] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B]	H [auth A], I [auth A], J [auth B], K [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth B]
CMO (Subject of Investigation/LOI) Query on CMO Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain Q [auth C] MOL2 format, chain G [auth A] MOL2 format, chain Q [auth C]	G [auth A], Q [auth C]	CARBON MONOXIDE C O UGFAIRIUMAVXCW-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain Q [auth C] Interactions & Density Focus chain G [auth A] Focus chain Q [auth C]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain O [auth C] MOL2 format, chain E [auth A] MOL2 format, chain O [auth C]	E [auth A], O [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain O [auth C] Interactions & Density Focus chain E [auth A] Focus chain O [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.77 Å
R-Value Free: 0.193
R-Value Work: 0.161
R-Value Observed: 0.163
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.39	α = 90
b = 122.32	β = 103.115
c = 99.91	γ = 90

Software Package:

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

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2022-02-09

Deposition Author(s):

Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	JP20K06511
Japan Society for the Promotion of Science (JSPS)	Japan	JP21H02060
Japan Society for the Promotion of Science (JSPS)	Japan	JP20H03215
Japan Society for the Promotion of Science (JSPS)	Japan	JP19H00984

Revision History (Full details and data files)

Version 1.0: 2022-02-09
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Refinement description

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Help and Resources

7VXQ

The Carbon Monoxide Complex of [NiFe]-hydrogenase (Hyb-type) from Citrobacter sp. S-77

Structural and spectroscopic characterization of CO inhibition of [NiFe]-hydrogenase from Citrobacter sp. S-77.

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 2