6VW8 | pdb_00006vw8

Formate Dehydrogenase FdsABG subcomplex FdsBG from C. necator

PDB DOI: https://doi.org/10.2210/pdb6VW8/pdb

Classification: OXIDOREDUCTASE
Organism(s): Cupriavidus necator
Expression System: Escherichia coli DH5[alpha]
Mutation(s): No

Deposited: 2020-02-18 Released: 2020-04-08
Deposition Author(s): Young, T.
Funding Organization(s): Department of Energy (DOE, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.223 (Depositor), 0.224 (DCC)
R-Value Work:
0.182 (Depositor), 0.183 (DCC)
R-Value Observed:
0.183 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystallographic and kinetic analyses of the FdsBG subcomplex of the cytosolic formate dehydrogenase FdsABG fromCupriavidus necator.

Young, T., Niks, D., Hakopian, S., Tam, T.K., Yu, X., Hille, R., Blaha, G.M.

(2020) J Biological Chem 295: 6570-6585

PubMed: 32249211 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1074/jbc.RA120.013264
Primary Citation Related Structures:
6VW7, 6VW8

PubMed Abstract:
Formate oxidation to carbon dioxide is a key reaction in one-carbon compound metabolism, and its reverse reaction represents the first step in carbon assimilation in the acetogenic and methanogenic branches of many anaerobic organisms. The molybdenum-containing dehydrogenase FdsABG is a soluble NAD ⁺-dependent formate dehydrogenase and a member of the NADH dehydrogenase superfamily. Here, we present the first structure of the FdsBG subcomplex of the cytosolic FdsABG formate dehydrogenase from the hydrogen-oxidizing bacterium Cupriavidus necator H16 both with and without bound NADH. The structures revealed that the two iron-sulfur clusters, Fe ₄S ₄ in FdsB and Fe ₂S ₂ in FdsG, are closer to the FMN than they are in other NADH dehydrogenases. Rapid kinetic studies and EPR measurements of rapid freeze-quenched samples of the NADH reduction of FdsBG identified a neutral flavin semiquinone, FMNH ^•, not previously observed to participate in NADH-mediated reduction of the FdsABG holoenzyme. We found that this semiquinone forms through the transfer of one electron from the fully reduced FMNH ^-, initially formed via NADH-mediated reduction, to the Fe ₂S ₂ cluster. This Fe ₂S ₂ cluster is not part of the on-path chain of iron-sulfur clusters connecting the FMN of FdsB with the active-site molybdenum center of FdsA. According to the NADH-bound structure, the nicotinamide ring stacks onto the re -face of the FMN. However, NADH binding significantly reduced the electron density for the isoalloxazine ring of FMN and induced a conformational change in residues of the FMN-binding pocket that display peptide-bond flipping upon NAD ⁺ binding in proper NADH dehydrogenases.

Organizational Affiliation

Department of Biochemistry, University of California, Riverside, California 92521.

Macromolecule Content

Total Structure Weight: 159.56 kDa
Atom Count: 10,508
Modeled Residue Count: 1,330
Deposited Residue Count: 1,470
Unique protein chains: 2

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD-dependent formate dehydrogenase gamma subunit	A, C	215	Cupriavidus necator	Mutation(s): 0 Gene Names: fdsG, H16_A0640 EC: 1.2.1.2
UniProt
Find proteins for Q0KDY3 (Cupriavidus necator (strain ATCC 17699 / DSM 428 / KCTC 22496 / NCIMB 10442 / H16 / Stanier 337)) Explore Q0KDY3 Go to UniProtKB: Q0KDY3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q0KDY3
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD-dependent formate dehydrogenase beta subunit	B, D	520	Cupriavidus necator	Mutation(s): 0 Gene Names: fdsB, H16_A0641 EC: 1.2.1.2
UniProt
Find proteins for Q0KDY2 (Cupriavidus necator (strain ATCC 17699 / DSM 428 / KCTC 22496 / NCIMB 10442 / H16 / Stanier 337)) Explore Q0KDY2 Go to UniProtKB: Q0KDY2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q0KDY2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FMN Query on FMN Download:Ideal Coordinates CCD File SDF format, chain M [auth D] SDF format, chain G [auth B] MOL2 format, chain M [auth D] MOL2 format, chain G [auth B] mmCIF format, chain M [auth D] mmCIF format, chain G [auth B]	G [auth B], M [auth D]	FLAVIN MONONUCLEOTIDE C₁₇ H₂₁ N₄ O₉ P FVTCRASFADXXNN-SCRDCRAPSA-N		Interactions Focus chain G [auth B] Focus chain M [auth D] Interactions & Density Focus chain G [auth B] Focus chain M [auth D]
SF4 Query on SF4 Download:Ideal Coordinates CCD File SDF format, chain N [auth D] SDF format, chain H [auth B] MOL2 format, chain N [auth D] MOL2 format, chain H [auth B] mmCIF format, chain N [auth D] mmCIF format, chain H [auth B]	H [auth B], N [auth D]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Focus chain N [auth D] Interactions & Density Focus chain H [auth B] Focus chain N [auth D]
FES Query on FES Download:Ideal Coordinates CCD File SDF format, chain K [auth C] SDF format, chain E [auth A] MOL2 format, chain K [auth C] MOL2 format, chain E [auth A] mmCIF format, chain K [auth C] mmCIF format, chain E [auth A]	E [auth A], K [auth C]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain K [auth C] Interactions & Density Focus chain E [auth A] Focus chain K [auth C]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B]	I [auth B], J [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain I [auth B] Focus chain J [auth B] Interactions & Density Focus chain I [auth B] Focus chain J [auth B]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain L [auth C] SDF format, chain F [auth A] MOL2 format, chain L [auth C] MOL2 format, chain F [auth A] mmCIF format, chain L [auth C] mmCIF format, chain F [auth A]	F [auth A], L [auth C]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain L [auth C] Interactions & Density Focus chain F [auth A] Focus chain L [auth C]