8W6X | pdb_00008w6x

Neutron structure of [NiFe]-hydrogenase from D. vulgaris Miyazaki F in its oxidized state

PDB DOI: https://doi.org/10.2210/pdb8W6X/pdb
Entry: 8W6X supersedes: 7YW6

Classification: OXIDOREDUCTASE
Organism(s): Nitratidesulfovibrio vulgaris str. 'Miyazaki F
Mutation(s): No

Deposited: 2023-08-30 Released: 2023-09-13
Deposition Author(s): Hiromoto, T., Tamada, T.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.04 Å
R-Value Free:
0.147 (Depositor), 0.147 (DCC)
R-Value Work:
0.143 (Depositor), 0.143 (DCC)
R-Value Observed:
0.143 (Depositor)

Method: NEUTRON DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.220 (Depositor)
R-Value Work:
0.189 (Depositor)
R-Value Observed:
0.191 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

New insights into the oxidation process from neutron and X-ray crystal structures of an O 2 -sensitive [NiFe]-hydrogenase.

Hiromoto, T., Nishikawa, K., Inoue, S., Ogata, H., Hori, Y., Kusaka, K., Hirano, Y., Kurihara, K., Shigeta, Y., Tamada, T., Higuchi, Y.

(2023) Chem Sci 14: 9306-9315

PubMed: 37712026 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1039/d3sc02156d
Primary Citation Related Structures:
8W6X

PubMed Abstract:
[NiFe]-hydrogenase from Desulfovibrio vulgaris Miyazaki F is an O ₂-sensitive enzyme that is inactivated in the presence of O ₂ but the oxidized enzyme can recover its catalytic activity by reacting with H ₂ under anaerobic conditions. Here, we report the first neutron structure of [NiFe]-hydrogenase in its oxidized state, determined at a resolution of 2.20 Å. This resolution allowed us to reinvestigate the structure of the oxidized active site and to observe the positions of protons in several short hydrogen bonds. X-ray anomalous scattering data revealed that a part of the Ni ion is dissociated from the active site Ni-Fe complex and forms a new square-planar Ni complex, accompanied by rearrangement of the coordinated thiolate ligands. One of the thiolate Sγ atoms is oxidized to a sulfenate anion but remains attached to the Ni ion, which was evaluated by quantum chemical calculations. These results suggest that the square-planar complex can be generated by the attack of reactive oxygen species derived from O ₂, as distinct from one-electron oxidation leading to a conventional oxidized form of the Ni-Fe complex. Another major finding of this neutron structure analysis is that the Cys17 ^S thiolate Sγ atom coordinating to the proximal Fe-S cluster forms an unusual hydrogen bond with the main-chain amide N atom of Gly19 ^S with a distance of 3.25 Å, where the amide proton appears to be delocalized between the donor and acceptor atoms. This observation provides insight into the contribution of the coordinated thiolate ligands to the redox reaction of the Fe-S cluster.

Organizational Affiliation

Institute for Quantum Life Science, National Institutes for Quantum Science and Technology 4-9-1 Anagawa, Inage Chiba 263-8555 Japan tamada.taro@qst.go.jp.

Macromolecule Content

Total Structure Weight: 90.13 kDa
Atom Count: 7,883
Modeled Residue Count: 800
Deposited Residue Count: 800
Unique protein chains: 2

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Periplasmic [NiFe] hydrogenase large subunit	A [auth L]	533	Nitratidesulfovibrio vulgaris str. 'Miyazaki F	Mutation(s): 0 EC: 1.12.2.1
UniProt
Find proteins for P21852 (Nitratidesulfovibrio vulgaris (strain DSM 19637 / Miyazaki F)) Explore P21852 Go to UniProtKB: P21852
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P21852
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Periplasmic [NiFe] hydrogenase small subunit	B [auth S]	266	Nitratidesulfovibrio vulgaris str. 'Miyazaki F	Mutation(s): 0 EC: 1.12.2.1
UniProt
Find proteins for P21853 (Nitratidesulfovibrio vulgaris (strain DSM 19637 / Miyazaki F)) Explore P21853 Go to UniProtKB: P21853
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P21853
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SF4 Query on SF4 Download:Ideal Coordinates CCD File SDF format, chain M [auth S] SDF format, chain N [auth S] MOL2 format, chain M [auth S] MOL2 format, chain N [auth S] mmCIF format, chain M [auth S] mmCIF format, chain N [auth S]	M [auth S], N [auth S]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain M [auth S] Focus chain N [auth S]
F3S Query on F3S Download:Ideal Coordinates CCD File SDF format, chain O [auth S] MOL2 format, chain O [auth S] mmCIF format, chain O [auth S]	O [auth S]	FE3-S4 CLUSTER Fe₃ S₄ FCXHZBQOKRZXKS-UHFFFAOYSA-N		Interactions Focus chain O [auth S]
NFU (Subject of Investigation/LOI) Query on NFU Download:Ideal Coordinates CCD File SDF format, chain C [auth L] MOL2 format, chain C [auth L] mmCIF format, chain C [auth L]	C [auth L]	formyl[bis(hydrocyanato-1kappaC)]ironnickel(Fe-Ni) C₃ H Fe N₂ Ni O QCZROEOIPZWDEO-UHFFFAOYSA-N		Interactions Focus chain C [auth L]
MPD Query on MPD Download:Ideal Coordinates CCD File SDF format, chain D [auth L] SDF format, chain E [auth L] SDF format, chain F [auth L] SDF format, chain G [auth L] SDF format, chain H [auth L] SDF format, chain I [auth L] SDF format, chain P [auth S] SDF format, chain Q [auth S] SDF format, chain R [auth S] MOL2 format, chain D [auth L] MOL2 format, chain E [auth L] MOL2 format, chain F [auth L] MOL2 format, chain G [auth L] MOL2 format, chain H [auth L] MOL2 format, chain I [auth L] MOL2 format, chain P [auth S] MOL2 format, chain Q [auth S] MOL2 format, chain R [auth S] mmCIF format, chain D [auth L] mmCIF format, chain E [auth L] mmCIF format, chain F [auth L] mmCIF format, chain G [auth L] mmCIF format, chain H [auth L] mmCIF format, chain I [auth L] mmCIF format, chain P [auth S] mmCIF format, chain Q [auth S] mmCIF format, chain R [auth S]	D [auth L] E [auth L] F [auth L] G [auth L] H [auth L] D [auth L], E [auth L], F [auth L], G [auth L], H [auth L], I [auth L], P [auth S], Q [auth S], R [auth S]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain D [auth L] Focus chain E [auth L] Focus chain F [auth L] Focus chain G [auth L] Focus chain H [auth L] Focus chain I [auth L] Focus chain P [auth S] Focus chain Q [auth S] Focus chain R [auth S]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain L MOL2 format, chain L mmCIF format, chain L	L	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain L
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain K [auth L] MOL2 format, chain K [auth L] mmCIF format, chain K [auth L]	K [auth L]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain K [auth L]
OH (Subject of Investigation/LOI) Query on OH Download:Ideal Coordinates CCD File SDF format, chain J [auth L] MOL2 format, chain J [auth L] mmCIF format, chain J [auth L]	J [auth L]	HYDROXIDE ION H O XLYOFNOQVPJJNP-UHFFFAOYSA-M		Interactions Focus chain J [auth L]