7VW6 | pdb_00007vw6

Cryo-EM Structure of Formate Dehydrogenase 1 from Methylorubrum extorquens AM1

PDB DOI: https://doi.org/10.2210/pdb7VW6/pdb
EM Map EMD-32151: EMDB EMDataResource

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

Deposited: 2021-11-09 Released: 2022-06-01
Deposition Author(s): Yoshikawa, T., Makino, F., Miyata, T., Suzuki, Y., Tanaka, H., Namba, K., Sowa, K., Kitazumi, Y., Shirai, O.
Funding Organization(s): Japan Agency for Medical Research and Development (AMED), Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.19 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Multiple electron transfer pathways of tungsten-containing formate dehydrogenase in direct electron transfer-type bioelectrocatalysis.

Yoshikawa, T., Makino, F., Miyata, T., Suzuki, Y., Tanaka, H., Namba, K., Kano, K., Sowa, K., Kitazumi, Y., Shirai, O.

(2022) Chem Commun (Camb) 58: 6478-6481

PubMed: 35535582 Search on PubMed
DOI: https://doi.org/10.1039/d2cc01541b
Primary Citation Related Structures:
7VW6

PubMed Abstract:
Tungsten-containing formate dehydrogenase from Methylorubrum extroquens AM1 (FoDH1)-a promising biocatalyst for the interconversion of carbon dioxide/formate and nicotine adenine dinucleotide (NAD ⁺)/NADH redox couples-was investigated using structural biology and bioelectrochemistry. FoDH1 is reported to be an enzyme that can realize "direct electron transfer (DET)-type bioelectrocatalysis." However, its 3-D structure, electrode-active sites, and electron transfer (ET) pathways remain unclear. The ET pathways were investigated using structural information, electrostatic interactions between the electrode and the enzyme, and the differences in the substrates. Two electrode-active sites and multiple ET pathways in FoDH1 were discovered.

Organizational Affiliation

Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo Kyoto, 606-8502, Japan. sowa.keisei.2u@kyoto-u.ac.jp.

Macromolecule Content

Total Structure Weight: 173.74 kDa
Atom Count: 11,485
Modeled Residue Count: 1,473
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
Formate dehydrogenase	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

Find similar proteins by:

| 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 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MGD Query on MGD Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A], H [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 G [auth A] Focus chain H [auth A] Interactions & Density Focus chain G [auth A] Focus chain H [auth A]
FMN (Subject of Investigation/LOI) Query on FMN Download:Ideal Coordinates CCD File SDF format, chain M [auth B] MOL2 format, chain M [auth B] mmCIF format, chain M [auth B]	M [auth B]	FLAVIN MONONUCLEOTIDE C₁₇ H₂₁ N₄ O₉ P FVTCRASFADXXNN-SCRDCRAPSA-N		Interactions Focus chain M [auth B] Interactions & Density Focus chain M [auth B]
SF4 Query on SF4 Download:Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain F [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain L [auth B] MOL2 format, chain F [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain L [auth B] mmCIF format, chain F [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A], F [auth A], L [auth B]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain F [auth A] Focus chain L [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain F [auth A] Focus chain L [auth B]
W Query on W 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]	TUNGSTEN ION W FZFRVZDLZISPFJ-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
FES Query on FES Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain E [auth A] MOL2 format, chain K [auth B] MOL2 format, chain E [auth A] mmCIF format, chain K [auth B] mmCIF format, chain E [auth A]	E [auth A], K [auth B]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain K [auth B] Interactions & Density Focus chain E [auth A] Focus chain K [auth B]
UNX Query on UNX Download:Ideal Coordinates CCD File SDF format, chain J [auth A] MOL2 format, chain J [auth A] mmCIF format, chain J [auth A]	J [auth A]	UNKNOWN ATOM OR ION X		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]