7Z0T

Structure of the Escherichia coli formate hydrogenlyase complex (aerobic preparation, composite structure)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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Literature

Structure of the membrane-bound formate hydrogenlyase complex from Escherichia coli.

Steinhilper, R.Hoff, G.Heider, J.Murphy, B.J.

(2022) Nat Commun 13: 5395-5395

  • DOI: https://doi.org/10.1038/s41467-022-32831-x
  • Primary Citation of Related Structures:  
    7Z0S, 7Z0T

  • PubMed Abstract: 

    The prototypical hydrogen-producing enzyme, the membrane-bound formate hydrogenlyase (FHL) complex from Escherichia coli, links formate oxidation at a molybdopterin-containing formate dehydrogenase to proton reduction at a [NiFe] hydrogenase. It is of intense interest due to its ability to efficiently produce H 2 during fermentation, its reversibility, allowing H 2 -dependent CO 2 reduction, and its evolutionary link to respiratory complex I. FHL has been studied for over a century, but its atomic structure remains unknown. Here we report cryo-EM structures of FHL in its aerobically and anaerobically isolated forms at resolutions reaching 2.6 Å. This includes well-resolved density for conserved loops linking the soluble and membrane arms believed to be essential in coupling enzymatic turnover to ion translocation across the membrane in the complex I superfamily. We evaluate possible structural determinants of the bias toward hydrogen production over its oxidation and describe an unpredicted metal-binding site near the interface of FdhF and HycF subunits that may play a role in redox-dependent regulation of FdhF interaction with the complex.


  • Organizational Affiliation

    Redox and Metalloprotein Research Group, Max Planck Institute of Biophysics, 60438, Frankfurt am Main, Germany.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Formate hydrogenlyase subunit 3A [auth C]608Escherichia coli K-12Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P16429 (Escherichia coli (strain K12))
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UniProt GroupP16429
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Formate hydrogenlyase subunit 5B [auth E]581Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P16431 (Escherichia coli (strain K12))
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UniProt GroupP16431
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Formate hydrogenlyase subunit 2C [auth B]203Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P0AAK1 (Escherichia coli (strain K12))
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Formate hydrogenlyase subunit 7D [auth G]255Escherichia coli K-12Mutation(s): 0 
UniProt
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UniProt GroupP16433
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Formate hydrogenlyase subunit 6E [auth F]180Escherichia coli K-12Mutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Formate hydrogenlyase subunit 4F [auth D]307Escherichia coli K-12Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Formate dehydrogenase HG [auth A]715Escherichia coli K-12Mutation(s): 0 
EC: 1.17.98.4
UniProt
Find proteins for P07658 (Escherichia coli (strain K12))
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Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MGD (Subject of Investigation/LOI)
Query on MGD

Download Ideal Coordinates CCD File 
S [auth A],
T [auth A]
2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE
C20 H26 N10 O13 P2 S2
VQAGYJCYOLHZDH-ILXWUORBSA-N
SF4 (Subject of Investigation/LOI)
Query on SF4

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J [auth B]
K [auth B]
L [auth B]
M [auth B]
N [auth G]
J [auth B],
K [auth B],
L [auth B],
M [auth B],
N [auth G],
O [auth F],
P [auth F],
R [auth A]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
FCO (Subject of Investigation/LOI)
Query on FCO

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I [auth E]CARBONMONOXIDE-(DICYANO) IRON
C3 Fe N2 O
VBQUCMTXYFMTTE-UHFFFAOYSA-N
6MO (Subject of Investigation/LOI)
Query on 6MO

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U [auth A]MOLYBDENUM(VI) ION
Mo
HCNGUXXTNNIKCQ-UHFFFAOYSA-N
NI (Subject of Investigation/LOI)
Query on NI

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H [auth E]NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
FE (Subject of Investigation/LOI)
Query on FE

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Q [auth F]FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Max Planck SocietyGermany--

Revision History  (Full details and data files)

  • Version 1.0: 2022-09-28
    Type: Initial release