4GD3

Structure of E. coli hydrogenase-1 in complex with cytochrome b


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.202 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

Crystal Structure of the O(2)-Tolerant Membrane-Bound Hydrogenase 1 from Escherichia coli in Complex with Its Cognate Cytochrome b.

Volbeda, A.Darnault, C.Parkin, A.Sargent, F.Armstrong, F.A.Fontecilla-Camps, J.C.

(2013) Structure 21: 184-190

  • DOI: https://doi.org/10.1016/j.str.2012.11.010
  • Primary Citation of Related Structures:  
    4GD3

  • PubMed Abstract: 

    We report the 3.3 Å resolution structure of dimeric membrane-bound O(2)-tolerant hydrogenase 1 from Escherichia coli in a 2:1 complex with its physiological partner, cytochrome b. From the short distance between distal [Fe(4)S(4)] clusters, we predict rapid transfer of H(2)-derived electrons between hydrogenase heterodimers. Thus, under low O(2) levels, a functional active site in one heterodimer can reductively reactivate its O(2)-exposed counterpart in the other. Hydrogenase 1 is maximally expressed during fermentation, when electron acceptors are scarce. These conditions are achieved in the lower part of the host's intestinal tract when E. coli is soon to be excreted and undergo an anaerobic-to-aerobic metabolic transition. The apparent paradox of having an O(2)-tolerant hydrogenase expressed under anoxia makes sense if the enzyme functions to keep intracellular O(2) levels low by reducing it to water, protecting O(2)-sensitive enzymes during the transition. Cytochrome b's main role may be anchoring the hydrogenase to the membrane.


  • Organizational Affiliation

    Metalloproteins Unit, Institut de Biologie Structurale J.-P. Ebel CEA-CNRS-Université Joseph Fourier, UMR 5075, 41 rue Jules Horowitz, 38027 Grenoble, France.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hydrogenase-1 small chainA [auth S],
C [auth T],
E [auth Q],
G [auth R]
335Escherichia coli K-12Mutation(s): 1 
Gene Names: b0972hyaAJW0954
EC: 1.12.99.6
Membrane Entity: Yes 
UniProt
Find proteins for P69739 (Escherichia coli (strain K12))
Explore P69739 
Go to UniProtKB:  P69739
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP69739
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Hydrogenase-1 large chainB [auth L],
D [auth M],
F [auth J],
H [auth K]
582Escherichia coli K-12Mutation(s): 0 
Gene Names: b0973hyaBJW0955
EC: 1.12.99.6
Membrane Entity: Yes 
UniProt
Find proteins for P0ACD8 (Escherichia coli (strain K12))
Explore P0ACD8 
Go to UniProtKB:  P0ACD8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0ACD8
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Ni/Fe-hydrogenase 1 B-type cytochrome subunitI [auth A],
J [auth B]
235Escherichia coli K-12Mutation(s): 0 
Gene Names: b0974hyaCJW0956
Membrane Entity: Yes 
UniProt
Find proteins for P0AAM1 (Escherichia coli (strain K12))
Explore P0AAM1 
Go to UniProtKB:  P0AAM1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AAM1
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 8 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
UA [auth A],
WA [auth B]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
LMT
Query on LMT

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OA [auth R],
VA [auth A],
W [auth T],
XA [auth B]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
SF4
Query on SF4

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CA [auth Q]
DA [auth Q]
K [auth S]
L [auth S]
LA [auth R]
CA [auth Q],
DA [auth Q],
K [auth S],
L [auth S],
LA [auth R],
MA [auth R],
T,
U [auth T]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
F4S
Query on F4S

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EA [auth Q],
M [auth S],
NA [auth R],
V [auth T]
FE4-S3 CLUSTER
Fe4 S3
QQACTBFBZNWJMV-UHFFFAOYSA-N
FCO
Query on FCO

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HA [auth J],
P [auth L],
QA [auth K],
Y [auth M]
CARBONMONOXIDE-(DICYANO) IRON
C3 Fe N2 O
VBQUCMTXYFMTTE-UHFFFAOYSA-N
NI
Query on NI

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IA [auth J],
Q [auth L],
RA [auth K],
Z [auth M]
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
CL
Query on CL

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BA [auth M]
FA [auth Q]
GA [auth Q]
KA [auth J]
N [auth S]
BA [auth M],
FA [auth Q],
GA [auth Q],
KA [auth J],
N [auth S],
O [auth S],
PA [auth K],
S [auth L],
TA [auth K],
X [auth M]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG

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AA [auth M],
JA [auth J],
R [auth L],
SA [auth K]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.202 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 126α = 90
b = 165.3β = 90
c = 212.8γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
MxCuBEdata collection
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-01-02
    Type: Initial release
  • Version 1.1: 2013-01-09
    Changes: Database references
  • Version 1.2: 2013-01-30
    Changes: Database references
  • Version 1.3: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description