3USC

Crystal Structure of E. coli hydrogenase-1 in a ferricyanide-oxidized form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.141 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

X-ray crystallographic and computational studies of the O2-tolerant [NiFe]-hydrogenase 1 from Escherichia coli.

Volbeda, A.Amara, P.Darnault, C.Mouesca, J.M.Parkin, A.Roessler, M.M.Armstrong, F.A.Fontecilla-Camps, J.C.

(2012) Proc.Natl.Acad.Sci.USA 109: 5305-5310

  • DOI: 10.1073/pnas.1119806109
  • Primary Citation of Related Structures:  3UQY, 3USE
  • Also Cited By: 4GD3

  • PubMed Abstract: 
  • The crystal structure of the membrane-bound O(2)-tolerant [NiFe]-hydrogenase 1 from Escherichia coli (EcHyd-1) has been solved in three different states: as-isolated, H(2)-reduced, and chemically oxidized. As very recently reported for similar enzyme ...

    The crystal structure of the membrane-bound O(2)-tolerant [NiFe]-hydrogenase 1 from Escherichia coli (EcHyd-1) has been solved in three different states: as-isolated, H(2)-reduced, and chemically oxidized. As very recently reported for similar enzymes from Ralstonia eutropha and Hydrogenovibrio marinus, two supernumerary Cys residues coordinate the proximal [FeS] cluster in EcHyd-1, which lacks one of the inorganic sulfide ligands. We find that the as-isolated, aerobically purified species contains a mixture of at least two conformations for one of the cluster iron ions and Glu76. In one of them, Glu76 and the iron occupy positions that are similar to those found in O(2)-sensitive [NiFe]-hydrogenases. In the other conformation, this iron binds, besides three sulfur ligands, the amide N from Cys20 and one Oε of Glu76. Our calculations show that oxidation of this unique iron generates the high-potential form of the proximal cluster. The structural rearrangement caused by oxidation is confirmed by our H(2)-reduced and oxidized EcHyd-1 structures. Thus, thanks to the peculiar coordination of the unique iron, the proximal cluster can contribute two successive electrons to secure complete reduction of O(2) to H(2)O at the active site. The two observed conformations of Glu76 are consistent with this residue playing the role of a base to deprotonate the amide moiety of Cys20 upon iron binding and transfer the resulting proton away, thus allowing the second oxidation to be electroneutral. The comparison of our structures also shows the existence of a dynamic chain of water molecules, resulting from O(2) reduction, located near the active site.


    Organizational Affiliation

    Metalloproteins Unit, Institut de Biologie Structurale J.-P. Ebel, Commissariat à l'Energie Atomique-Centre National de la Recherche Scientifique-l'Université Joseph Fourier, 41 Rue Jules Horowitz, 38027 Grenoble, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Hydrogenase-1 small chain
S, T
335Escherichia coli (strain K12)Gene Names: hyaA
EC: 1.12.99.6
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Oxidoreductases
Protein: 
O2-tolerant Hydrogenase-1 in complex with cytochrome b
Find proteins for P69739 (Escherichia coli (strain K12))
Go to UniProtKB:  P69739
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Hydrogenase-1 large chain
L, M
582Escherichia coli (strain K12)Gene Names: hyaB
EC: 1.12.99.6
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Oxidoreductases
Protein: 
O2-tolerant Hydrogenase-1 in complex with cytochrome b
Find proteins for P0ACD8 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ACD8
Small Molecules
Ligands 10 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

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Download CCD File 
S, T
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
F3S
Query on F3S

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S, T
FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-MZMDZPPWAW
 Ligand Interaction
FCO
Query on FCO

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L, M
CARBONMONOXIDE-(DICYANO) IRON
C3 Fe N2 O
VBQUCMTXYFMTTE-UHFFFAOYSA-N
 Ligand Interaction
3NI
Query on 3NI

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L, M
NICKEL (III) ION
Ni
JDRCAGKFDGHRNQ-UHFFFAOYSA-N
 Ligand Interaction
LI
Query on LI

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L
LITHIUM ION
Li
HBBGRARXTFLTSG-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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M, S, T
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CL
Query on CL

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S, T
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

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L, M
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
LMT
Query on LMT

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S, T
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
 Ligand Interaction
SF3
Query on SF3

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S, T
FE4-S3 CLUSTER
Fe4 S3
QQACTBFBZNWJMV-DXQBTJNKAZ
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.141 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 94.170α = 90.00
b = 98.160β = 90.00
c = 183.960γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
MxCuBEdata collection
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
REFMACphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-03-28
    Type: Initial release
  • Version 1.1: 2012-04-18
    Type: Database references