6RP2

Threonine to Cysteine (T225C) variant of E coli hydrogenase-1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 
    0.159 (Depositor), 0.160 (DCC) 
  • R-Value Work: 
    0.141 (Depositor), 0.150 (DCC) 
  • R-Value Observed: 
    0.142 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

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This is version 1.3 of the entry. See complete history


Literature

Aerobic Photocatalytic H2Production by a [NiFe] Hydrogenase Engineered to Place a Silver Nanocluster in the Electron Relay.

Zhang, L.Morello, G.Carr, S.B.Armstrong, F.A.

(2020) J Am Chem Soc 142: 12699-12707

  • DOI: https://doi.org/10.1021/jacs.0c04302
  • Primary Citation of Related Structures:  
    6RP2

  • PubMed Abstract: 

    Hydrogenase-1 (Hyd-1) from E. coli poses a conundrum regarding the properties of electrocatalytic reversibility and associated bidirectionality now established for many redox enzymes. Its excellent H 2 -oxidizing activity begins only once a substantial overpotential is applied, and it cannot produce H 2 . A major reason for its unidirectional behavior is that the reduction potentials of its electron-relaying FeS clusters are too positive relative to the 2H + /H 2 couple at neutral pH; consequently, electrons held within the enzyme lack the energy to drive H 2 production. However, Hyd-1 is O 2 -tolerant and even functions in air. Changing a tyrosine (Y) or threonine (T), located on the protein surface within 10 Å of the distal [4Fe-4S] and medial [3Fe-4S] clusters, to cysteine (C), allows site-selective attachment of a silver nanocluster (AgNC), the reduced or photoexcited state of which is a powerful reductant. The AgNC provides a new additional redox site, capturing externally supplied electrons with sufficiently high energy to drive H 2 production. Assemblies of Y'227C (or T'225C) with AgNCs/PMAA (PMAA = polymethyl acrylate templating several AgNC) are also electroactive for H 2 production at a TiO 2 electrode. A colloidal system for visible-light photo-H 2 generation is made by building the hybrid enzyme into a heterostructure with TiO 2 and graphitic carbon nitride (g-C 3 N 4 ), the resulting scaffold promoting uptake of electrons excited at the AgNC. Each hydrogenase produces 40 molecules of H 2 per second and sustains 20% activity in air.


  • Organizational Affiliation

    Inorganic Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QR, Oxfordshire United Kingdom.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hydrogenase-1 small chainA [auth S],
C [auth T]
324Escherichia coli K-12Mutation(s): 0 
Gene Names: D8B36_14215
EC: 1.12.99.6
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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Hydrogenase-1 large chainB [auth L],
D [auth M]
582Escherichia coli K-12Mutation(s): 0 
Gene Names: hyaBb0973JW0955
EC: 1.12.99.6
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
Expand
  • Reference Sequence
Small Molecules
Ligands 10 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
LMT
Query on LMT

Download Ideal Coordinates CCD File 
H [auth S],
R [auth T]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
SF4
Query on SF4

Download Ideal Coordinates CCD File 
E [auth S],
O [auth T]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
SF3
Query on SF3

Download Ideal Coordinates CCD File 
G [auth S],
Q [auth T]
FE4-S3 CLUSTER
Fe4 S3
QQACTBFBZNWJMV-UHFFFAOYSA-N
F3S
Query on F3S

Download Ideal Coordinates CCD File 
F [auth S],
P [auth T]
FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-UHFFFAOYSA-N
FCO
Query on FCO

Download Ideal Coordinates CCD File 
K [auth L],
T [auth M]
CARBONMONOXIDE-(DICYANO) IRON
C3 Fe N2 O
VBQUCMTXYFMTTE-UHFFFAOYSA-N
SO4
Query on SO4

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J [auth L],
W [auth M]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
NI
Query on NI

Download Ideal Coordinates CCD File 
L,
U [auth M]
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
I [auth S],
S [auth T]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG

Download Ideal Coordinates CCD File 
M [auth L],
V [auth M]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
LI
Query on LI

Download Ideal Coordinates CCD File 
N [auth L],
X [auth M]
LITHIUM ION
Li
HBBGRARXTFLTSG-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CSO
Query on CSO
B [auth L],
D [auth M]
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free:  0.159 (Depositor), 0.160 (DCC) 
  • R-Value Work:  0.141 (Depositor), 0.150 (DCC) 
  • R-Value Observed: 0.142 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.72α = 90
b = 97.52β = 90
c = 183.06γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted LMTClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/N006321/1

Revision History  (Full details and data files)

  • Version 1.0: 2020-03-25
    Type: Initial release
  • Version 1.1: 2020-07-08
    Changes: Database references
  • Version 1.2: 2020-07-29
    Changes: Database references, Derived calculations
  • Version 1.3: 2024-11-06
    Changes: Data collection, Database references, Structure summary