6G94

Structure of E. coli hydrogenase-1 C19G variant in complex with cytochrome b


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.223 

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

X-ray structural, functional and computational studies of the O2-sensitive E. coli hydrogenase-1 C19G variant reveal an unusual [4Fe-4S] cluster.

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

(2018) Chem Commun (Camb) 54: 7175-7178

  • DOI: 10.1039/c8cc02896f
  • Primary Citation of Related Structures:  
    6G94

  • PubMed Abstract: 
  • The crystal structure of the Escherichia coli O2-sensitive C19G [NiFe]-hydrogenase-1 variant shows that the mutation results in a novel FeS cluster, proximal to the Ni-Fe active site. While the proximal cluster of the native O2-tolerant enzyme can transfer two electrons to that site, EPR spectroscopy shows that the modified cluster can transfer only one electron, this shortfall coinciding with O2 sensitivity ...

    The crystal structure of the Escherichia coli O2-sensitive C19G [NiFe]-hydrogenase-1 variant shows that the mutation results in a novel FeS cluster, proximal to the Ni-Fe active site. While the proximal cluster of the native O2-tolerant enzyme can transfer two electrons to that site, EPR spectroscopy shows that the modified cluster can transfer only one electron, this shortfall coinciding with O2 sensitivity. Computational studies on electron transfer help to explain how the structural and redox properties of the novel FeS cluster modulate the observed phenotype.


    Related Citations: 
    • 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
    • Principles of sustained enzymatic hydrogen oxidation in the presence of oxygen--the crucial influence of high potential Fe-S clusters in the electron relay of [NiFe]-hydrogenases.
      Evans, R.M., Parkin, A., Roessler, M.M., Murphy, B.J., Adamson, H., Lukey, M.J., Sargent, F., Volbeda, A., Fontecilla-Camps, J.C., Armstrong, F.A.
      (2013) J Am Chem Soc 135: 2694
    • 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 U S A 109: 5305

    Organizational Affiliation

    Univ. Grenoble Alpes, CEA, CNRS, IBS, F-38000 Grenoble, France. anne.volbeda@ibs.fr.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Hydrogenase-1 small chainE [auth Q], G [auth R], A [auth S], C [auth T]335Escherichia coli K-12Mutation(s): 0 
Gene Names: hyaAb0972JW0954
EC: 1.12.99.6
Membrane Entity: Yes 
UniProt
Find proteins for P69740 (Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC))
Explore P69740 
Go to UniProtKB:  P69740
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Hydrogenase-1 large chainF [auth J], H [auth K], B [auth L], D [auth M]582Escherichia coli K-12Mutation(s): 0 
Gene Names: hyaBb0973JW0955
EC: 1.12.99.6
Membrane Entity: Yes 
UniProt
Find proteins for P0ACD8 (Escherichia coli (strain K12))
Explore P0ACD8 
Go to UniProtKB:  P0ACD8
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Probable Ni/Fe-hydrogenase 1 B-type cytochrome subunitI [auth A], J [auth B]235Escherichia coli K-12Mutation(s): 0 
Gene Names: hyaCb0974JW0956
Membrane Entity: Yes 
UniProt
Find proteins for P0AAM2 (Escherichia coli O157:H7)
Explore P0AAM2 
Go to UniProtKB:  P0AAM2
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 8 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM (Subject of Investigation/LOI)
Query on HEM

Download Ideal Coordinates CCD File 
MA [auth A], NA [auth B]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
ER2 (Subject of Investigation/LOI)
Query on ER2

Download Ideal Coordinates CCD File 
AA [auth Q], HA [auth R], M [auth S], TFe4S4
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
 Ligand Interaction
SF4
Query on SF4

Download Ideal Coordinates CCD File 
FA [auth R], K [auth S], R [auth T], Y [auth Q]IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
F3S
Query on F3S

Download Ideal Coordinates CCD File 
GA [auth R], L [auth S], S [auth T], Z [auth Q]FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-MZMDZPPWAW
 Ligand Interaction
FCO
Query on FCO

Download Ideal Coordinates CCD File 
BA [auth J], IA [auth K], N [auth L], U [auth M]CARBONMONOXIDE-(DICYANO) IRON
C3 Fe N2 O
VBQUCMTXYFMTTE-UHFFFAOYSA-N
 Ligand Interaction
NI
Query on NI

Download Ideal Coordinates CCD File 
CA [auth J], JA [auth K], O [auth L], V [auth M]NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
EA [auth J], LA [auth K], Q [auth L], X [auth M]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
DA [auth J], KA [auth K], P [auth L], W [auth M]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.223 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 124.41α = 90
b = 165.03β = 90
c = 206.22γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-06-13
    Type: Initial release
  • Version 1.1: 2018-06-20
    Changes: Data collection, Database references
  • Version 1.2: 2018-07-04
    Changes: Data collection, Database references
  • Version 1.3: 2019-08-21
    Changes: Data collection, Database references
  • Version 1.4: 2020-02-05
    Changes: Database references, Source and taxonomy