7T2R

Structure of electron bifurcating Ni-Fe hydrogenase complex HydABCSL in FMN-free apo state


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 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

Structure and electron transfer pathways of an electron-bifurcating NiFe-hydrogenase.

Feng, X.Schut, G.J.Haja, D.K.Adams, M.W.W.Li, H.

(2022) Sci Adv 8: eabm7546-eabm7546

  • DOI: https://doi.org/10.1126/sciadv.abm7546
  • Primary Citation of Related Structures:  
    7T2R, 7T30

  • PubMed Abstract: 

    Electron bifurcation enables thermodynamically unfavorable biochemical reactions. Four groups of bifurcating flavoenzyme are known and three use FAD to bifurcate. FeFe-HydABC hydrogenase represents the fourth group, but its bifurcation site is unknown. We report cryo-EM structures of the related NiFe-HydABCSL hydrogenase that reversibly oxidizes H 2 and couples endergonic reduction of ferredoxin with exergonic reduction of NAD. FMN surrounded by a unique arrangement of iron sulfur clusters forms the bifurcating center. NAD binds to FMN in HydB, and electrons from H 2 via HydA to a HydB [4Fe-4S] cluster enable the FMN to reduce NAD. Low-potential electron transfer from FMN to the HydC [2Fe-2S] cluster and subsequent reduction of a uniquely penta-coordinated HydB [2Fe-2S] cluster require conformational changes, leading to ferredoxin binding and reduction by a [4Fe-4S] cluster in HydB. This work clarifies the electron transfer pathways for a large group of hydrogenases underlying many essential functions in anaerobic microorganisms.


  • Organizational Affiliation

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


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NiFe hydrogenase subunit A
A, F
692Acetomicrobium mobileMutation(s): 0 
UniProt
Find proteins for I4BYB4 (Acetomicrobium mobile (strain ATCC BAA-54 / DSM 13181 / JCM 12221 / NGA))
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Go to UniProtKB:  I4BYB4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupI4BYB4
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
NiFe hydrogenase subunit B
B, G
597Acetomicrobium mobileMutation(s): 0 
UniProt
Find proteins for I4BYB5 (Acetomicrobium mobile (strain ATCC BAA-54 / DSM 13181 / JCM 12221 / NGA))
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Go to UniProtKB:  I4BYB5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupI4BYB5
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
NiFe hydrogenase subunit C
C, H
156Acetomicrobium mobileMutation(s): 0 
UniProt
Find proteins for I4BYB8 (Acetomicrobium mobile (strain ATCC BAA-54 / DSM 13181 / JCM 12221 / NGA))
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Go to UniProtKB:  I4BYB8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupI4BYB8
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
NiFe hydrogenase large subunit
D, I
475Acetomicrobium mobileMutation(s): 0 
UniProt
Find proteins for I4BYB2 (Acetomicrobium mobile (strain ATCC BAA-54 / DSM 13181 / JCM 12221 / NGA))
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UniProt GroupI4BYB2
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
NiFe hydrogenase small subunit
E, J
179Acetomicrobium mobileMutation(s): 0 
UniProt
Find proteins for I4BYB3 (Acetomicrobium mobile (strain ATCC BAA-54 / DSM 13181 / JCM 12221 / NGA))
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Go to UniProtKB:  I4BYB3
Entity Groups  
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UniProt GroupI4BYB3
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SF4 (Subject of Investigation/LOI)
Query on SF4

Download Ideal Coordinates CCD File 
AA [auth G]
FA [auth J]
L [auth A]
M [auth A]
N [auth A]
AA [auth G],
FA [auth J],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth B],
U [auth E],
W [auth F],
X [auth F],
Y [auth F],
Z [auth F]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
FES (Subject of Investigation/LOI)
Query on FES

Download Ideal Coordinates CCD File 
BA [auth G]
CA [auth H]
K [auth A]
Q [auth B]
R [auth C]
BA [auth G],
CA [auth H],
K [auth A],
Q [auth B],
R [auth C],
V [auth F]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
FCO (Subject of Investigation/LOI)
Query on FCO

Download Ideal Coordinates CCD File 
EA [auth I],
T [auth D]
CARBONMONOXIDE-(DICYANO) IRON
C3 Fe N2 O
VBQUCMTXYFMTTE-UHFFFAOYSA-N
3NI (Subject of Investigation/LOI)
Query on 3NI

Download Ideal Coordinates CCD File 
DA [auth I],
S [auth D]
NICKEL (III) ION
Ni
JDRCAGKFDGHRNQ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.1

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Department of Energy (DOE, United States)United StatesDE-SC0020085
Department of Energy (DOE, United States)United StatesDE-FG02-95ER20175

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-16
    Type: Initial release
  • Version 1.1: 2024-11-06
    Changes: Data collection, Structure summary