8RCG | pdb_00008rcg

W-formate dehydrogenase M405S from Desulfovibrio vulgaris

PDB DOI: https://doi.org/10.2210/pdb8RCG/pdb

Classification: OXIDOREDUCTASE
Organism(s): Nitratidesulfovibrio vulgaris str. Hildenborough
Expression System: Nitratidesulfovibrio vulgaris str. Hildenborough
Mutation(s): Yes

Deposited: 2023-12-06 Released: 2024-05-08
Deposition Author(s): Vilela-Alves, G., Manuel, R.R., Pereira, I.C., Romao, M.J., Mota, C.
Funding Organization(s): Fundacao para a Ciencia e a Tecnologia

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.253 (Depositor), 0.260 (DCC)
R-Value Work:
0.212 (Depositor), 0.221 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Structural and biochemical characterization of the M405S variant of Desulfovibrio vulgaris formate dehydrogenase.

Vilela-Alves, G., Rebelo Manuel, R., Pedrosa, N., Cardoso Pereira, I.A., Romao, M.J., Mota, C.

(2024) Acta Crystallogr F Struct Biol Commun 80: 98-106

PubMed: 38699971 Search on PubMed
DOI: https://doi.org/10.1107/S2053230X24003911
Primary Citation Related Structures:
8RCG

PubMed Abstract:
Molybdenum- or tungsten-dependent formate dehydrogenases have emerged as significant catalysts for the chemical reduction of CO ₂ to formate, with biotechnological applications envisaged in climate-change mitigation. The role of Met405 in the active site of Desulfovibrio vulgaris formate dehydrogenase AB (DvFdhAB) has remained elusive. However, its proximity to the metal site and the conformational change that it undergoes between the resting and active forms suggests a functional role. In this work, the M405S variant was engineered, which allowed the active-site geometry in the absence of methionine S ^δ interactions with the metal site to be revealed and the role of Met405 in catalysis to be probed. This variant displayed reduced activity in both formate oxidation and CO ₂ reduction, together with an increased sensitivity to oxygen inactivation.

Organizational Affiliation

UCIBIO, Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal.

Macromolecule Content

Total Structure Weight: 140.02 kDa
Atom Count: 9,609
Modeled Residue Count: 1,177
Deposited Residue Count: 1,228
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Formate dehydrogenase, alpha subunit, selenocysteine-containing	A	1,013	Nitratidesulfovibrio vulgaris str. Hildenborough	Mutation(s): 1 Gene Names: fdnG-1 EC: 1.2.1.2
UniProt
Find proteins for Q72EJ1 (Nitratidesulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / CCUG 34227 / NCIMB 8303 / VKM B-1760 / Hildenborough)) Explore Q72EJ1 Go to UniProtKB: Q72EJ1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q72EJ1
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Formate dehydrogenase, beta subunit, putative	B	215	Nitratidesulfovibrio vulgaris str. Hildenborough	Mutation(s): 0 Gene Names: DVU_0588
UniProt
Find proteins for Q72EJ0 (Nitratidesulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / CCUG 34227 / NCIMB 8303 / VKM B-1760 / Hildenborough)) Explore Q72EJ0 Go to UniProtKB: Q72EJ0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q72EJ0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MGD (Subject of Investigation/LOI) Query on MGD Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A]	C [auth A], D [auth A]	2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE C₂₀ H₂₆ N₁₀ O₁₃ P₂ S₂ VQAGYJCYOLHZDH-ILXWUORBSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]
SF4 (Subject of Investigation/LOI) Query on SF4 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] MOL2 format, chain E [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] mmCIF format, chain E [auth A] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B]	E [auth A], N [auth B], O [auth B], P [auth B]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Interactions & Density Focus chain E [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B]
W (Subject of Investigation/LOI) Query on W Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	TUNGSTEN ION W FZFRVZDLZISPFJ-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain M [auth A] MOL2 format, chain H [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain M [auth A] mmCIF format, chain H [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain M [auth A]	H [auth A], J [auth A], K [auth A], M [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth A] Interactions & Density Focus chain H [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain L [auth A] MOL2 format, chain L [auth A] mmCIF format, chain L [auth A]	L [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Interactions & Density Focus chain L [auth A]
H2S (Subject of Investigation/LOI) Query on H2S Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	HYDROSULFURIC ACID H₂ S RWSOTUBLDIXVET-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.253 (Depositor), 0.260 (DCC)
R-Value Work: 0.212 (Depositor), 0.221 (DCC)

Diffraction Data:

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.341	α = 90
b = 127.226	β = 90
c = 148.266	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
STARANISO	data scaling
PHASER	phasing
XDS	data reduction

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-05-08

Deposition Author(s):

Funding Organization	Location	Grant Number
Fundacao para a Ciencia e a Tecnologia	Portugal	PTDC/BII-BBF/2050/2020
Fundacao para a Ciencia e a Tecnologia	Portugal	2023.00286.BD
Fundacao para a Ciencia e a Tecnologia	Portugal	UIDP/04378/2020
Fundacao para a Ciencia e a Tecnologia	Portugal	UIDB/04378/2020
Fundacao para a Ciencia e a Tecnologia	Portugal	LA/P/0140/2020
Fundacao para a Ciencia e a Tecnologia	Portugal	LA/P/0087/2020
Fundacao para a Ciencia e a Tecnologia	Portugal	UIDB/04612/2020
Fundacao para a Ciencia e a Tecnologia	Portugal	UIDP/04612/2020