8J83 | pdb_00008j83

Crystal structure of formate dehydrogenase from Methylorubrum extorquens AM1

PDB DOI: https://doi.org/10.2210/pdb8J83/pdb

Classification: OXIDOREDUCTASE
Organism(s): Methylorubrum extorquens AM1
Mutation(s): No

Deposited: 2023-04-29 Released: 2023-10-11
Deposition Author(s): Kobayashi, A., Taketa, M., Sowa, K., Kano, K., Higuchi, Y., Ogata, H.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.259 (Depositor), 0.262 (DCC)
R-Value Work:
0.219 (Depositor), 0.226 (DCC)
R-Value Observed:
0.221 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Structure and function relationship of formate dehydrogenases: an overview of recent progress.

Kobayashi, A., Taketa, M., Sowa, K., Kano, K., Higuchi, Y., Ogata, H.

(2023) IUCrJ 10: 544-554

PubMed: 37668215 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1107/S2052252523006437
Primary Citation Related Structures:
8J83

PubMed Abstract:
Formate dehydrogenases (FDHs) catalyze the two-electron oxidation of formate to carbon dioxide. FDHs can be divided into several groups depending on their subunit composition and active-site metal ions. Metal-dependent (Mo- or W-containing) FDHs from prokaryotic organisms belong to the superfamily of molybdenum enzymes and are members of the dimethylsulfoxide reductase family. In this short review, recent progress in the structural analysis of FDHs together with their potential biotechnological applications are summarized.

Organizational Affiliation

Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo, Kyoto 606-8502, Japan.

Macromolecule Content

Total Structure Weight: 174.31 kDa
Atom Count: 11,489
Modeled Residue Count: 1,468
Deposited Residue Count: 1,561
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tungsten-containing formate dehydrogenase alpha subunit	A	989	Methylorubrum extorquens AM1	Mutation(s): 0 EC: 1.17.1.9 (PDB Primary Data), 1.2.1.2 (UniProt)
UniProt
Find proteins for C5ATT7 (Methylorubrum extorquens (strain ATCC 14718 / DSM 1338 / JCM 2805 / NCIMB 9133 / AM1)) Explore C5ATT7 Go to UniProtKB: C5ATT7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	C5ATT7
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Tungsten-containing formate dehydrogenase beta subunit	B	572	Methylorubrum extorquens AM1	Mutation(s): 0 EC: 1.2.1.2
UniProt
Find proteins for C5ATT6 (Methylorubrum extorquens (strain ATCC 14718 / DSM 1338 / JCM 2805 / NCIMB 9133 / AM1)) Explore C5ATT6 Go to UniProtKB: C5ATT6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	C5ATT6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MGD Query on MGD Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [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]
FMN (Subject of Investigation/LOI) Query on FMN Download:Ideal Coordinates CCD File SDF format, chain N [auth B] MOL2 format, chain N [auth B] mmCIF format, chain N [auth B]	N [auth B]	FLAVIN MONONUCLEOTIDE C₁₇ H₂₁ N₄ O₉ P FVTCRASFADXXNN-SCRDCRAPSA-N		Interactions Focus chain N [auth B] Interactions & Density Focus chain N [auth B]
SF4 Query on SF4 Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain O [auth B] SDF format, chain I [auth A] SDF format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain O [auth B] MOL2 format, chain I [auth A] MOL2 format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain O [auth B] mmCIF format, chain I [auth A] mmCIF format, chain G [auth A]	G [auth A], H [auth A], I [auth A], O [auth B]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain O [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain O [auth B]
W Query on W Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	TUNGSTEN ION W FZFRVZDLZISPFJ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
FES Query on FES Download:Ideal Coordinates CCD File SDF format, chain P [auth B] SDF format, chain F [auth A] MOL2 format, chain P [auth B] MOL2 format, chain F [auth A] mmCIF format, chain P [auth B] mmCIF format, chain F [auth A]	F [auth A], P [auth B]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain P [auth B] Interactions & Density Focus chain F [auth A] Focus chain P [auth B]
PEG Query on PEG 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]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Interactions & Density Focus chain L [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain R [auth B] SDF format, chain Q [auth B] SDF format, chain M [auth A] SDF format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain R [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain M [auth A] MOL2 format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain R [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain M [auth A] mmCIF format, chain K [auth A]	J [auth A], K [auth A], M [auth A], Q [auth B], R [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth A] Focus chain Q [auth B] Focus chain R [auth B] Interactions & Density Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth A] Focus chain Q [auth B] Focus chain R [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.259 (Depositor), 0.262 (DCC)
R-Value Work: 0.219 (Depositor), 0.226 (DCC)
R-Value Observed: 0.221 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 232.86	α = 90
b = 73.95	β = 106.72
c = 95.74	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-10-11

Deposition Author(s):

Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	JP22K14831
Japan Society for the Promotion of Science (JSPS)	Japan	19H00984
Japan Society for the Promotion of Science (JSPS)	Japan	18H05516