5JRD

E. coli Hydrogenase-1 variant P508A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.141 
  • R-Value Work: 0.121 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Importance of the Active Site "Canopy" Residues in an O2-Tolerant [NiFe]-Hydrogenase.

Brooke, E.J.Evans, R.M.Islam, S.T.Roberts, G.M.Wehlin, S.A.Carr, S.B.Phillips, S.E.Armstrong, F.A.

(2017) Biochemistry 56: 132-142

  • DOI: 10.1021/acs.biochem.6b00868

  • PubMed Abstract: 
  • The active site of Hyd-1, an oxygen-tolerant membrane-bound [NiFe]-hydrogenase from Escherichia coli, contains four highly conserved residues that form a "canopy" above the bimetallic center, closest to the site at which exogenous agents CO and O2 in ...

    The active site of Hyd-1, an oxygen-tolerant membrane-bound [NiFe]-hydrogenase from Escherichia coli, contains four highly conserved residues that form a "canopy" above the bimetallic center, closest to the site at which exogenous agents CO and O2 interact, substrate H2 binds, and a hydrido intermediate is stabilized. Genetic modification of the Hyd-1 canopy has allowed the first systematic and detailed kinetic and structural investigation of the influence of the immediate outer coordination shell on H2 activation. The central canopy residue, arginine 509, suspends a guanidine/guanidinium side chain at close range above the open coordination site lying between the Ni and Fe atoms (N-metal distance of 4.4 Å): its replacement with lysine lowers the H2 oxidation rate by nearly 2 orders of magnitude and markedly decreases the H2/D2 kinetic isotope effect. Importantly, this collapse in rate constant can now be ascribed to a very unfavorable activation entropy (easily overriding the more favorable activation enthalpy of the R509K variant). The second most important canopy residue for H2 oxidation is aspartate 118, which forms a salt bridge to the arginine 509 headgroup: its mutation to alanine greatly decreases the H2 oxidation efficiency, observed as a 10-fold increase in the potential-dependent Michaelis constant. Mutations of aspartate 574 (also salt-bridged to R509) to asparagine and proline 508 to alanine have much smaller effects on kinetic properties. None of the mutations significantly increase sensitivity to CO, but neutralizing the expected negative charges from D118 and D574 decreases O2 tolerance by stabilizing the oxidized resting NiIII-OH state ("Ni-B"). An extensive model of the catalytic importance of residues close to the active site now emerges, whereby a conserved gas channel culminates in the arginine headgroup suspended above the Ni and Fe.


    Organizational Affiliation

    Department of Chemistry, University of Oxford , Oxford, U.K.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Hydrogenase-1 small chain
S, T
335Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC)Mutation(s): 0 
Gene Names: hyaA
EC: 1.12.99.6
Find proteins for P69740 (Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC))
Go to UniProtKB:  P69740
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Hydrogenase-1 large chain
L, M
582Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: hyaB
EC: 1.12.99.6
Find proteins for P0ACD8 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ACD8
Small Molecules
Ligands 8 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

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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
SO4
Query on SO4

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L, M
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
SF3
Query on SF3

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S, T
FE4-S3 CLUSTER
Fe4 S3
QQACTBFBZNWJMV-DXQBTJNKAZ
 Ligand Interaction
NI
Query on NI

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L, M
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSO
Query on CSO
L, M
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.141 
  • R-Value Work: 0.121 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 94.691α = 90.00
b = 98.589β = 90.00
c = 185.373γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
PHASERphasing
DIALSdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research CouncilUnited Kingdom--

Revision History 

  • Version 1.0: 2017-03-08
    Type: Initial release
  • Version 1.1: 2017-08-30
    Type: Author supporting evidence
  • Version 1.2: 2018-01-24
    Type: Source and taxonomy