9E1J | pdb_00009e1j

Alpha-Delta heterodimeric form of soluble hydrogenase I from Pyrococcus furiosus. Data processed and model refined in P21221

PDB DOI: https://doi.org/10.2210/pdb9E1J/pdb

Classification: LYASE
Organism(s): Pyrococcus furiosus
Expression System: Pyrococcus furiosus
Mutation(s): No

Deposited: 2024-10-21 Released: 2025-07-16
Deposition Author(s): Lanzilotta, W.N., Adams, M.W.W.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.313 (Depositor), 0.314 (DCC)
R-Value Work:
0.256 (Depositor), 0.258 (DCC)
R-Value Observed:
0.258 (Depositor)

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

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

Literature

Structural insights into the biotechnologically relevant reversible NADPH-oxidizing NiFe-hydrogenase from P.furiosus.

Xiao, X., Schut, G.J., Feng, X., McTernan, P.M., Haja, D.K., Lanzilotta, W.N., Adams, M.W.W., Li, H.

(2025) Structure 33: 1470-1483.e3

PubMed: 40570843 Search on PubMed
DOI: https://doi.org/10.1016/j.str.2025.05.017
Primary Citation Related Structures:
9E15, 9E1J, 9NEZ, 9NF0

PubMed Abstract:
The cytoplasmic hydrogenase I (SHI) from the hyperthermophilic archaeon Pyrococcus furiosus belongs to the group III hydrogenase family. SHI oxidizes NADPH rather than NADH to reduce protons and evolve hydrogen gas, and because of this property, coupled with its high thermal stability, the enzyme holds great potential for economical hydrogen production. Despite decades of efforts, the SHI structure has remained unknown. Here, we report the cryoelectron microscopic (cryo-EM) structures of the heterotetrameric SHI holoenzyme (αδβγ). SHI is a symmetric dimer of two individually functional heterotetramers. SHI-αδ resembles the standard [NiFe] hydrogenase, and SHI-βγ function as the NADPH oxidoreductase. SHI-β contains three [4Fe-4S] clusters that relay electrons from NADPH in SHI-γ to the catalytic [NiFe] cluster in SHI-αδ for H ₂ production. These structures will guide the adaptation of this unique enzyme for biotechnological applications.

Organizational Affiliation

Department of Structural Biology, Van Andel Institute, Grand Rapids, MI 49503, USA.

Macromolecule Content

Total Structure Weight: 154.93 kDa
Atom Count: 10,787
Modeled Residue Count: 1,348
Deposited Residue Count: 1,350
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sulfhydrogenase 1 subunit delta	A, C	256	Pyrococcus furiosus	Mutation(s): 0 Gene Names: hydD, PF0893 EC: 1.12.1.3
UniProt
Find proteins for E7FHU4 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)) Explore E7FHU4 Go to UniProtKB: E7FHU4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	E7FHU4
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Sulfhydrogenase 1 subunit alpha	B, D	419	Pyrococcus furiosus	Mutation(s): 0 Gene Names: hydA, PF0894 EC: 1.12.1.3
UniProt
Find proteins for E7FI44 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)) Explore E7FI44 Go to UniProtKB: E7FI44
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	E7FI44
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SF4 Query on SF4 Download:Ideal Coordinates CCD File SDF format, chain O [auth C] SDF format, chain N [auth C] SDF format, chain M [auth C] SDF format, chain L [auth C] SDF format, chain K [auth C] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain O [auth C] MOL2 format, chain N [auth C] MOL2 format, chain M [auth C] MOL2 format, chain L [auth C] MOL2 format, chain K [auth C] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain O [auth C] mmCIF format, chain N [auth C] mmCIF format, chain M [auth C] mmCIF format, chain L [auth C] mmCIF format, chain K [auth C] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A] F [auth A] G [auth A] K [auth C] L [auth C] E [auth A], F [auth A], G [auth A], K [auth C], L [auth C], M [auth C], N [auth C], O [auth C]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth C] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth C]
FCO Query on FCO Download:Ideal Coordinates CCD File SDF format, chain H [auth B] MOL2 format, chain H [auth B] mmCIF format, chain H [auth B]	H [auth B]	CARBONMONOXIDE-(DICYANO) IRON C₃ Fe N₂ O VBQUCMTXYFMTTE-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Interactions & Density Focus chain H [auth B]
NI Query on NI Download:Ideal Coordinates CCD File SDF format, chain P [auth D] SDF format, chain I [auth B] MOL2 format, chain P [auth D] MOL2 format, chain I [auth B] mmCIF format, chain P [auth D] mmCIF format, chain I [auth B]	I [auth B], P [auth D]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Focus chain P [auth D] Interactions & Density Focus chain I [auth B] Focus chain P [auth D]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain J [auth B] MOL2 format, chain J [auth B] mmCIF format, chain J [auth B]	J [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain J [auth B] Interactions & Density Focus chain J [auth B]