4UE3

The Mechanism of Hydrogen Activation by NiFe-hydrogenases and the Importance of the active site Arginine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.160 
  • R-Value Work: 0.140 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Mechanism of Hydrogen Activation by [Nife] Hydrogenases.

Evans, R.M.Brooke, E.J.Wehlin, S.A.Nomerotskaia, E.Sargent, F.Carr, S.B.Phillips, S.E.Armstrong, F.A.

(2016) Nat Chem Biol 12: 46

  • DOI: 10.1038/nchembio.1976
  • Primary Citation of Related Structures:  
    5A4F, 5A4I, 5A4M, 5ADU, 4UE3

  • PubMed Abstract: 
  • The active site of [NiFe] hydrogenases contains a strictly conserved arginine that suspends a guanidine nitrogen atom <4.5 Å above the nickel and iron atoms. The guanidine headgroup interacts with the side chains of two conserved aspartic acid residues to complete an outer-shell canopy that has thus far proved intractable to investigation by site-directed mutagenesis ...

    The active site of [NiFe] hydrogenases contains a strictly conserved arginine that suspends a guanidine nitrogen atom <4.5 Å above the nickel and iron atoms. The guanidine headgroup interacts with the side chains of two conserved aspartic acid residues to complete an outer-shell canopy that has thus far proved intractable to investigation by site-directed mutagenesis. Using hydrogenase-1 from Escherichia coli, the strictly conserved residues R509 and D574 have been replaced by lysine (R509K) and asparagine (D574N) and the highly conserved D118 has been replaced by alanine (D118A) or asparagine (D118N/D574N). Each enzyme variant is stable, and their [(RS)2Niμ(SR)2Fe(CO)(CN)2] inner coordination shells are virtually unchanged. The R509K variant had >100-fold lower activity than native enzyme. Conversely, the variants D574N, D118A and D118N/D574N, in which the position of the guanidine headgroup is retained, showed 83%, 26% and 20% activity, respectively. The special kinetic requirement for R509 implicates the suspended guanidine group as the general base in H2 activation by [NiFe] hydrogenases.


    Organizational Affiliation

    Department of Chemistry, University of Oxford, Oxford, UK.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Hydrogenase-1 small chainA [auth SSS], C [auth TTT]264Escherichia coli K-12Mutation(s): 0 
Gene Names: hyaAb0972JW0954
EC: 1.12.99.6
UniProt
Find proteins for P69739 (Escherichia coli (strain K12))
Explore P69739 
Go to UniProtKB:  P69739
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 chainB [auth LLL], D [auth MMM]581Escherichia coli K-12Mutation(s): 1 
Gene Names: hyaBb0973JW0955
EC: 1.12.99.6
UniProt
Find proteins for P0ACD8 (Escherichia coli (strain K12))
Explore P0ACD8 
Go to UniProtKB:  P0ACD8
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 9 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

Download Ideal Coordinates CCD File 
E [auth SSS], N [auth TTT]IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
SF3 (Subject of Investigation/LOI)
Query on SF3

Download Ideal Coordinates CCD File 
G [auth SSS], P [auth TTT]FE4-S3 CLUSTER
Fe4 S3
QQACTBFBZNWJMV-DXQBTJNKAZ
 Ligand Interaction
F3S
Query on F3S

Download Ideal Coordinates CCD File 
F [auth SSS], O [auth TTT]FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-MZMDZPPWAW
 Ligand Interaction
FCO
Query on FCO

Download Ideal Coordinates CCD File 
K [auth LLL], U [auth MMM]CARBONMONOXIDE-(DICYANO) IRON
C3 Fe N2 O
VBQUCMTXYFMTTE-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
J [auth LLL], S [auth TTT], T [auth MMM], X [auth MMM]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
NI
Query on NI

Download Ideal Coordinates CCD File 
L [auth LLL], V [auth MMM]NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
H [auth SSS], I [auth SSS], Q [auth TTT], R [auth TTT]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
M [auth LLL], W [auth MMM]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
LI
Query on LI

Download Ideal Coordinates CCD File 
Y [auth MMM]LITHIUM ION
Li
HBBGRARXTFLTSG-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSO
Query on CSO
B [auth LLL], D [auth MMM]L-PEPTIDE LINKINGC3 H7 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.160 
  • R-Value Work: 0.140 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.521α = 90
b = 97.405β = 90
c = 183.229γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-12-24
    Type: Initial release
  • Version 1.1: 2015-12-09
    Changes: Database references
  • Version 1.2: 2016-01-13
    Changes: Database references
  • Version 2.0: 2019-12-04
    Type: Coordinate replacement
    Reason: Model completeness
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Experimental preparation, Non-polymer description, Other, Polymer sequence, Refinement description, Source and taxonomy, Structure summary, Version format compliance