9GNK | pdb_00009gnk

Nitratidesulfovibrio vulgaris [FeFe]-hydrogenase variant with both subunits linked by a 13 amino acid linker peptide derived from CpI of Clostridium pasteurianum


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.05 Å
  • R-Value Free: 
    0.185 (Depositor), 0.186 (DCC) 
  • R-Value Work: 
    0.168 (Depositor), 0.169 (DCC) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9GNK

Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history

Literature

Subunit fusion unlocks rapid in vitro maturation for slowly activating heterodimeric [FeFe]-hydrogenases.

Jaenecke, J.Bikbaev, K.Malagnini, M.Bronold, J.Yadav, S.Apfel, U.P.Leger, C.Birrell, J.A.Span, I.Plumere, N.Winkler, M.

(2026) Chem Sci 17: 7678-7689

  • DOI: https://doi.org/10.1039/d5sc07299a
  • Primary Citation Related Structures: 
    9GBU, 9GNK, 9QD6

  • PubMed Abstract: 

    Hydrogenases offer a sustainable alternative to noble metals for catalyzing H 2 -oxidation and H 2 -production. The heterodimeric [FeFe]-hydrogenase of Desulfovibrio desulfuricans ATCC 7757 ( Dd HydAB) is most promising due to its exceptional catalytic activity and high-yield heterologous expression of its apo-form. Scalable production of the holo-form relies on in vitro maturation of the apo-enzyme using a chemically synthesized 2Fe H cofactor mimic. However, the unusually slow in vitro maturation of Dd HydAB raises mechanistic questions and limits its scalability. Through structural and sequence analysis, we identified the cause of this slow maturation and redesigned the enzyme via subunit fusion, inserting short peptide linkers near the active site. This modification facilitates the rearrangement of a critical locking element after cofactor uptake, increasing the maturation rate by up to 41-fold without compromising catalytic performance. Our findings elucidate a key step in the plug-lock-lid mechanism underlying maturation and promote the industrial applicability of Dd HydAB.


  • Organizational Affiliation
    • Professorship for Electrobiotechnology, Technical University of Munich, Campus Straubing for Biotechnology and Sustainability Uferstrasse 53 94315 Straubing Germany martin-h.winkler@tum.de nicolas.plumere@tum.de.

Macromolecule Content 

  • Total Structure Weight: 56.89 kDa 
  • Atom Count: 4,471 
  • Modeled Residue Count: 485 
  • Deposited Residue Count: 492 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Periplasmic [Fe] hydrogenase large subunit,Periplasmic [Fe] hydrogenase small subunit492Nitratidesulfovibrio vulgarisMutation(s): 0 
Gene Names: hydADVU_1769hydBDVU_1770
EC: 1.12.7.2
UniProt
Find proteins for P07598 (Nitratidesulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / CCUG 34227 / NCIMB 8303 / VKM B-1760 / Hildenborough))
Explore P07598 
Go to UniProtKB:  P07598
Find proteins for P07603 (Nitratidesulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / CCUG 34227 / NCIMB 8303 / VKM B-1760 / Hildenborough))
Explore P07603 
Go to UniProtKB:  P07603
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP07603P07598
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
402
(Subject of Investigation/LOI)

Query on 402



Download:Ideal Coordinates CCD File
C [auth A]dicarbonyl[bis(cyanide-kappaC)]-mu-(iminodimethanethiolatato-1kappaS:2kappaS)-mu-(oxomethylidene)diiron(2+)
C7 H5 Fe2 N3 O3 S2
LJPDYWPSPOWMIB-UHFFFAOYSA-N
SF4
(Subject of Investigation/LOI)

Query on SF4



Download:Ideal Coordinates CCD File
D [auth A],
E [auth A],
F [auth A]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
EPE

Query on EPE



Download:Ideal Coordinates CCD File
G [auth A]4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
PG4

Query on PG4



Download:Ideal Coordinates CCD File
H [auth A],
L [auth A],
M [auth A]
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
PEG

Query on PEG



Download:Ideal Coordinates CCD File
I [auth A],
J [auth A],
K [auth A]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
CMO
(Subject of Investigation/LOI)

Query on CMO



Download:Ideal Coordinates CCD File
B [auth A]CARBON MONOXIDE
C O
UGFAIRIUMAVXCW-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.05 Å
  • R-Value Free:  0.185 (Depositor), 0.186 (DCC) 
  • R-Value Work:  0.168 (Depositor), 0.169 (DCC) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.137α = 90
b = 89.213β = 90
c = 106.449γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Cootmodel building
MOLREPphasing
XDSdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanySP 1476/4-1

Revision History  (Full details and data files)

  • Version 1.0: 2025-09-24
    Type: Initial release
  • Version 1.1: 2026-02-25
    Changes: Database references, Source and taxonomy, Structure summary
  • Version 1.2: 2026-03-11
    Changes: Database references
  • Version 2.0: 2026-05-06
    Changes: Atomic model, Data collection, Database references