7T2R | pdb_00007t2r

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

Validation slider image for 7T2R

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 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.

Macromolecule Content 

  • Total Structure Weight: 471.86 kDa 
  • Atom Count: 29,216 
  • Modeled Residue Count: 3,736 
  • Deposited Residue Count: 4,198 
  • Unique protein chains: 5

Macromolecules

Find similar proteins by:|  3D Structure
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))
Explore I4BYB4 
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))
Explore I4BYB5 
Go to UniProtKB:  I4BYB5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupI4BYB5
Sequence Annotations
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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))
Explore I4BYB8 
Go to UniProtKB:  I4BYB8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupI4BYB8
Sequence Annotations
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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))
Explore I4BYB2 
Go to UniProtKB:  I4BYB2
Entity Groups
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UniProt GroupI4BYB2
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Reference Sequence
Find similar proteins by:|  3D Structure
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))
Explore I4BYB3 
Go to UniProtKB:  I4BYB3
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupI4BYB3
Sequence Annotations
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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