7P92 | pdb_00007p92

TmHydABC- T. maritima bifurcating hydrogenase with bridge domain up

PDB DOI: https://doi.org/10.2210/pdb7P92/pdb
EM Map EMD-13258: EMDB EMDataResource

Classification: OXIDOREDUCTASE
Organism(s): Thermotoga maritima MSB8
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2021-07-23 Released: 2022-09-14
Deposition Author(s): Furlan, C., Chongdar, N., Gupta, P., Lubitz, W., Ogata, H., Blaza, J.N., Birrell, J.A.
Funding Organization(s): UK Research and Innovation (UKRI), German Research Foundation (DFG), Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.70 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Structural insight on the mechanism of an electron-bifurcating [FeFe] hydrogenase.

Furlan, C., Chongdar, N., Gupta, P., Lubitz, W., Ogata, H., Blaza, J.N., Birrell, J.A.

(2022) Elife 11

PubMed: 36018003 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.7554/eLife.79361
Primary Citation Related Structures:
7P5H, 7P8N, 7P91, 7P92

PubMed Abstract:
Electron bifurcation is a fundamental energy conservation mechanism in nature in which two electrons from an intermediate-potential electron donor are split so that one is sent along a high-potential pathway to a high-potential acceptor and the other is sent along a low-potential pathway to a low-potential acceptor. This process allows endergonic reactions to be driven by exergonic ones and is an alternative, less recognized, mechanism of energy coupling to the well-known chemiosmotic principle. The electron-bifurcating [FeFe] hydrogenase from Thermotoga maritima (HydABC) requires both NADH and ferredoxin to reduce protons generating hydrogen. The mechanism of electron bifurcation in HydABC remains enigmatic in spite of intense research efforts over the last few years. Structural information may provide the basis for a better understanding of spectroscopic and functional information. Here, we present a 2.3 Å electron cryo-microscopy structure of HydABC. The structure shows a heterododecamer composed of two independent 'halves' each made of two strongly interacting HydABC heterotrimers connected via a [4Fe-4S] cluster. A central electron transfer pathway connects the active sites for NADH oxidation and for proton reduction. We identified two conformations of a flexible iron-sulfur cluster domain: a 'closed bridge' and an 'open bridge' conformation, where a Zn ²⁺ site may act as a 'hinge' allowing domain movement. Based on these structural revelations, we propose a possible mechanism of electron bifurcation in HydABC where the flavin mononucleotide serves a dual role as both the electron bifurcation center and as the NAD ⁺ reduction/NADH oxidation site.

Organizational Affiliation

Structural Biology Laboratory and York Biomedical Research Institute, Department of Chemistry, The University of York, York, United Kingdom.

Macromolecule Content

Total Structure Weight: 165.57 kDa
Atom Count: 10,436
Modeled Residue Count: 1,322
Deposited Residue Count: 1,460
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fe-hydrogenase, subunit alpha	A	645	Thermotoga maritima MSB8	Mutation(s): 0 Gene Names: TM_1426 EC: 1.12.1.4
UniProt
Find proteins for O52683 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore O52683 Go to UniProtKB: O52683
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O52683
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fe-hydrogenase, subunit beta	B	626	Thermotoga maritima MSB8	Mutation(s): 0 Gene Names: TM_1425 EC: 1.12.1.4
UniProt
Find proteins for O52682 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore O52682 Go to UniProtKB: O52682
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O52682
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Fe-hydrogenase, subunit gamma	C	189	Thermotoga maritima MSB8	Mutation(s): 0 Gene Names: TM_1424, HydC EC: 1.12.1.4
UniProt
Find proteins for O52681 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore O52681 Go to UniProtKB: O52681
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O52681
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FMN Query on FMN Download:Ideal Coordinates CCD File SDF format, chain L [auth B] MOL2 format, chain L [auth B] mmCIF format, chain L [auth B]	L [auth B]	FLAVIN MONONUCLEOTIDE C₁₇ H₂₁ N₄ O₉ P FVTCRASFADXXNN-SCRDCRAPSA-N		Interactions Focus chain L [auth B] Interactions & Density Focus chain L [auth B]
SF4 Query on SF4 Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B]	D [auth A] E [auth A] F [auth A] G [auth A] I [auth B] D [auth A], E [auth A], F [auth A], G [auth A], I [auth B], J [auth B], K [auth B]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B]
FES Query on FES Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain M [auth B] SDF format, chain O [auth C] MOL2 format, chain H [auth A] MOL2 format, chain M [auth B] MOL2 format, chain O [auth C] mmCIF format, chain H [auth A] mmCIF format, chain M [auth B] mmCIF format, chain O [auth C]	H [auth A], M [auth B], O [auth C]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain M [auth B] Focus chain O [auth C] Interactions & Density Focus chain H [auth A] Focus chain M [auth B] Focus chain O [auth C]
ZN Query on ZN 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]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain N [auth B] Interactions & Density Focus chain N [auth B]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.70 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	RELION	3.1

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-09-14

Deposition Author(s):

Funding Organization	Location	Grant Number
UK Research and Innovation (UKRI)	United Kingdom	MR/T040742/1
German Research Foundation (DFG)	Germany	BI 2198/1-1
Japan Society for the Promotion of Science (JSPS)	Japan	16K21748