9E15 | pdb_00009e15

Alpha-Delta heterodimeric form of soluble hydrogenase I from Pyrococcus furiosus. Data processed and model refined in P1

PDB DOI: https://doi.org/10.2210/pdb9E15/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., McTernan, P.M., Adams, M.W.W.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.305 (Depositor), 0.305 (DCC)
R-Value Work:
0.267 (Depositor), 0.267 (DCC)
R-Value Observed:
0.267 (Depositor)

Starting Model: in silico
View more details

wwPDB Validation 3D Report Full Report

This is version 1.0 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

PubMed: 40570843 Search on PubMed
DOI: https://doi.org/10.1016/j.str.2025.05.017
Primary Citation of 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: 635.52 kDa
Atom Count: 43,445
Modeled Residue Count: 5,406
Deposited Residue Count: 5,520
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sulfhydrogenase 1 subunit delta	A, C, E, G, I A, C, E, G, I, K, M, O	266	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	E7FHU4
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Sulfhydrogenase 1 subunit alpha	B, D, F, H, J B, D, F, H, J, L, N, P	424	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	E7FI44
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SF4 Query on SF4 Download Ideal Coordinates CCD File SDF format, chain CA [auth E] SDF format, chain DA [auth E] SDF format, chain DB [auth M] SDF format, chain EA [auth E] SDF format, chain EB [auth M] SDF format, chain FB [auth M] SDF format, chain IB [auth O] SDF format, chain JA [auth G] SDF format, chain JB [auth O] SDF format, chain KA [auth G] SDF format, chain KB [auth O] SDF format, chain LA [auth G] SDF format, chain Q [auth A] SDF format, chain QA [auth I] SDF format, chain R [auth A] SDF format, chain RA [auth I] SDF format, chain S [auth A] SDF format, chain SA [auth I] SDF format, chain X [auth C] SDF format, chain XA [auth K] SDF format, chain Y [auth C] SDF format, chain YA [auth K] SDF format, chain Z [auth C] SDF format, chain ZA [auth K] MOL2 format, chain CA [auth E] MOL2 format, chain DA [auth E] MOL2 format, chain DB [auth M] MOL2 format, chain EA [auth E] MOL2 format, chain EB [auth M] MOL2 format, chain FB [auth M] MOL2 format, chain IB [auth O] MOL2 format, chain JA [auth G] MOL2 format, chain JB [auth O] MOL2 format, chain KA [auth G] MOL2 format, chain KB [auth O] MOL2 format, chain LA [auth G] MOL2 format, chain Q [auth A] MOL2 format, chain QA [auth I] MOL2 format, chain R [auth A] MOL2 format, chain RA [auth I] MOL2 format, chain S [auth A] MOL2 format, chain SA [auth I] MOL2 format, chain X [auth C] MOL2 format, chain XA [auth K] MOL2 format, chain Y [auth C] MOL2 format, chain YA [auth K] MOL2 format, chain Z [auth C] MOL2 format, chain ZA [auth K] mmCIF format, chain CA [auth E] mmCIF format, chain DA [auth E] mmCIF format, chain DB [auth M] mmCIF format, chain EA [auth E] mmCIF format, chain EB [auth M] mmCIF format, chain FB [auth M] mmCIF format, chain IB [auth O] mmCIF format, chain JA [auth G] mmCIF format, chain JB [auth O] mmCIF format, chain KA [auth G] mmCIF format, chain KB [auth O] mmCIF format, chain LA [auth G] mmCIF format, chain Q [auth A] mmCIF format, chain QA [auth I] mmCIF format, chain R [auth A] mmCIF format, chain RA [auth I] mmCIF format, chain S [auth A] mmCIF format, chain SA [auth I] mmCIF format, chain X [auth C] mmCIF format, chain XA [auth K] mmCIF format, chain Y [auth C] mmCIF format, chain YA [auth K] mmCIF format, chain Z [auth C] mmCIF format, chain ZA [auth K]	CA [auth E] DA [auth E] DB [auth M] EA [auth E] EB [auth M] CA [auth E], DA [auth E], DB [auth M], EA [auth E], EB [auth M], FB [auth M], IB [auth O], JA [auth G], JB [auth O], KA [auth G], KB [auth O], LA [auth G], Q [auth A], QA [auth I], R [auth A], RA [auth I], S [auth A], SA [auth I], X [auth C], XA [auth K], Y [auth C], YA [auth K], Z [auth C], ZA [auth K]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain CA [auth E] Focus chain DA [auth E] Focus chain DB [auth M] Focus chain EA [auth E] Focus chain EB [auth M] Focus chain FB [auth M] Focus chain IB [auth O] Focus chain JA [auth G] Focus chain JB [auth O] Focus chain KA [auth G] Focus chain KB [auth O] Focus chain LA [auth G] Focus chain Q [auth A] Focus chain QA [auth I] Focus chain R [auth A] Focus chain RA [auth I] Focus chain S [auth A] Focus chain SA [auth I] Focus chain X [auth C] Focus chain XA [auth K] Focus chain Y [auth C] Focus chain YA [auth K] Focus chain Z [auth C] Focus chain ZA [auth K] Interactions & Density Focus chain CA [auth E] Focus chain DA [auth E] Focus chain DB [auth M] Focus chain EA [auth E] Focus chain EB [auth M] Focus chain FB [auth M] Focus chain IB [auth O] Focus chain JA [auth G] Focus chain JB [auth O] Focus chain KA [auth G] Focus chain KB [auth O] Focus chain LA [auth G] Focus chain Q [auth A] Focus chain QA [auth I] Focus chain R [auth A] Focus chain RA [auth I] Focus chain S [auth A] Focus chain SA [auth I] Focus chain X [auth C] Focus chain XA [auth K] Focus chain Y [auth C] Focus chain YA [auth K] Focus chain Z [auth C] Focus chain ZA [auth K]
FCO Query on FCO Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain AB [auth L] SDF format, chain FA [auth F] SDF format, chain GB [auth N] SDF format, chain LB [auth P] SDF format, chain MA [auth H] SDF format, chain T [auth B] SDF format, chain UA [auth J] MOL2 format, chain AA [auth D] MOL2 format, chain AB [auth L] MOL2 format, chain FA [auth F] MOL2 format, chain GB [auth N] MOL2 format, chain LB [auth P] MOL2 format, chain MA [auth H] MOL2 format, chain T [auth B] MOL2 format, chain UA [auth J] mmCIF format, chain AA [auth D] mmCIF format, chain AB [auth L] mmCIF format, chain FA [auth F] mmCIF format, chain GB [auth N] mmCIF format, chain LB [auth P] mmCIF format, chain MA [auth H] mmCIF format, chain T [auth B] mmCIF format, chain UA [auth J]	AA [auth D] AB [auth L] FA [auth F] GB [auth N] LB [auth P] AA [auth D], AB [auth L], FA [auth F], GB [auth N], LB [auth P], MA [auth H], T [auth B], UA [auth J]	CARBONMONOXIDE-(DICYANO) IRON C₃ Fe N₂ O VBQUCMTXYFMTTE-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain AB [auth L] Focus chain FA [auth F] Focus chain GB [auth N] Focus chain LB [auth P] Focus chain MA [auth H] Focus chain T [auth B] Focus chain UA [auth J] Interactions & Density Focus chain AA [auth D] Focus chain AB [auth L] Focus chain FA [auth F] Focus chain GB [auth N] Focus chain LB [auth P] Focus chain MA [auth H] Focus chain T [auth B] Focus chain UA [auth J]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain CB [auth L] SDF format, chain HA [auth F] SDF format, chain IA [auth F] SDF format, chain NB [auth P] SDF format, chain OA [auth H] SDF format, chain OB [auth P] SDF format, chain PB [auth P] SDF format, chain TA [auth I] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain WA [auth J] MOL2 format, chain CB [auth L] MOL2 format, chain HA [auth F] MOL2 format, chain IA [auth F] MOL2 format, chain NB [auth P] MOL2 format, chain OA [auth H] MOL2 format, chain OB [auth P] MOL2 format, chain PB [auth P] MOL2 format, chain TA [auth I] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain WA [auth J] mmCIF format, chain CB [auth L] mmCIF format, chain HA [auth F] mmCIF format, chain IA [auth F] mmCIF format, chain NB [auth P] mmCIF format, chain OA [auth H] mmCIF format, chain OB [auth P] mmCIF format, chain PB [auth P] mmCIF format, chain TA [auth I] mmCIF format, chain V [auth B] mmCIF format, chain W [auth B] mmCIF format, chain WA [auth J]	CB [auth L] HA [auth F] IA [auth F] NB [auth P] OA [auth H] CB [auth L], HA [auth F], IA [auth F], NB [auth P], OA [auth H], OB [auth P], PB [auth P], TA [auth I], V [auth B], W [auth B], WA [auth J]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain CB [auth L] Focus chain HA [auth F] Focus chain IA [auth F] Focus chain NB [auth P] Focus chain OA [auth H] Focus chain OB [auth P] Focus chain PB [auth P] Focus chain TA [auth I] Focus chain V [auth B] Focus chain W [auth B] Focus chain WA [auth J] Interactions & Density Focus chain CB [auth L] Focus chain HA [auth F] Focus chain IA [auth F] Focus chain NB [auth P] Focus chain OA [auth H] Focus chain OB [auth P] Focus chain PB [auth P] Focus chain TA [auth I] Focus chain V [auth B] Focus chain W [auth B] Focus chain WA [auth J]
NI Query on NI Download Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain BB [auth L] SDF format, chain GA [auth F] SDF format, chain HB [auth N] SDF format, chain MB [auth P] SDF format, chain NA [auth H] SDF format, chain U [auth B] SDF format, chain VA [auth J] MOL2 format, chain BA [auth D] MOL2 format, chain BB [auth L] MOL2 format, chain GA [auth F] MOL2 format, chain HB [auth N] MOL2 format, chain MB [auth P] MOL2 format, chain NA [auth H] MOL2 format, chain U [auth B] MOL2 format, chain VA [auth J] mmCIF format, chain BA [auth D] mmCIF format, chain BB [auth L] mmCIF format, chain GA [auth F] mmCIF format, chain HB [auth N] mmCIF format, chain MB [auth P] mmCIF format, chain NA [auth H] mmCIF format, chain U [auth B] mmCIF format, chain VA [auth J]	BA [auth D] BB [auth L] GA [auth F] HB [auth N] MB [auth P] BA [auth D], BB [auth L], GA [auth F], HB [auth N], MB [auth P], NA [auth H], U [auth B], VA [auth J]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain BA [auth D] Focus chain BB [auth L] Focus chain GA [auth F] Focus chain HB [auth N] Focus chain MB [auth P] Focus chain NA [auth H] Focus chain U [auth B] Focus chain VA [auth J] Interactions & Density Focus chain BA [auth D] Focus chain BB [auth L] Focus chain GA [auth F] Focus chain HB [auth N] Focus chain MB [auth P] Focus chain NA [auth H] Focus chain U [auth B] Focus chain VA [auth J]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain PA [auth H] SDF format, chain QB [auth P] MOL2 format, chain PA [auth H] MOL2 format, chain QB [auth P] mmCIF format, chain PA [auth H] mmCIF format, chain QB [auth P]	PA [auth H], QB [auth P]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain PA [auth H] Focus chain QB [auth P] Interactions & Density Focus chain PA [auth H] Focus chain QB [auth P]