4XDD | pdb_00004xdd

Apo [FeFe]-Hydrogenase CpI


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 
    0.166 (Depositor), 0.170 (DCC) 
  • R-Value Work: 
    0.144 (Depositor), 0.148 (DCC) 
  • R-Value Observed: 
    0.145 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

A structural view of synthetic cofactor integration into [FeFe]-hydrogenases.

Esselborn, J.Muraki, N.Klein, K.Engelbrecht, V.Metzler-Nolte, N.Apfel, U.P.Hofmann, E.Kurisu, G.Happe, T.

(2016) Chem Sci 7: 959-968

  • DOI: https://doi.org/10.1039/c5sc03397g
  • Primary Citation Related Structures: 
    4XDC, 4XDD, 5BYQ, 5BYR, 5BYS

  • PubMed Abstract: 

    [FeFe]-hydrogenases are nature's fastest catalysts for the evolution or oxidation of hydrogen. Numerous synthetic model complexes for the [2Fe] subcluster (2Fe H ) of their active site are known, but so far none of these could compete with the enzymes. The complex Fe 2 [μ-(SCH 2 ) 2 X](CN) 2 (CO) 4 2- with X = NH was shown to integrate into the apo-form of [FeFe]-hydrogenases to yield a fully active enzyme. Here we report the first crystal structures of the apo-form of the bacterial [FeFe]-hydrogenase CpI from Clostridium pasteurianum at 1.60 Å and the active semisynthetic enzyme, CpI ADT , at 1.63 Å. The structures illustrate the significant changes in ligand coordination upon integration and activation of the [2Fe] complex. These changes are induced by a rigid 2Fe H cavity as revealed by the structure of apoCpI, which is remarkably similar to CpI ADT . Additionally we present the high resolution crystal structures of the semisynthetic bacterial [FeFe]-hydrogenases CpI PDT (X = CH 2 ), CpI ODT (X = O) and CpI SDT (X = S) with changes in the headgroup of the dithiolate bridge in the 2Fe H cofactor. The structures of these inactive enzymes demonstrate that the 2Fe H -subcluster and its protein environment remain largely unchanged when compared to the active enzyme CpI ADT . As the active site shows an open coordination site in all structures, the absence of catalytic activity is probably not caused by steric obstruction. This demonstrates that the chemical properties of the dithiolate bridge are essential for enzyme activity.


  • Organizational Affiliation
    • AG Photobiotechnologie , Fakultät für Biologie und Biotechnologie , Ruhr-Universität Bochum , Universitätsstraße 150 , 44801 Bochum , Germany . Email: thomas.happe@rub.de.

Macromolecule Content 

  • Total Structure Weight: 133.64 kDa 
  • Atom Count: 10,548 
  • Modeled Residue Count: 1,163 
  • Deposited Residue Count: 1,166 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Iron hydrogenase 1
A, B
583Clostridium pasteurianumMutation(s): 0 
EC: 1.12.7.2
UniProt
Find proteins for P29166 (Clostridium pasteurianum)
Explore P29166 
Go to UniProtKB:  P29166
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP29166
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SF4

Query on SF4



Download:Ideal Coordinates CCD File
C [auth A]
D [auth A]
E [auth A]
F [auth A]
M [auth B]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
M [auth B],
N [auth B],
O [auth B],
P [auth B]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
FES

Query on FES



Download:Ideal Coordinates CCD File
H [auth A],
Q [auth B]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
K [auth A],
V [auth B],
W [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
J [auth A],
L [auth A],
R [auth B],
S [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG

Query on MG



Download:Ideal Coordinates CCD File
G [auth A],
I [auth A],
T [auth B],
U [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free:  0.166 (Depositor), 0.170 (DCC) 
  • R-Value Work:  0.144 (Depositor), 0.148 (DCC) 
  • R-Value Observed: 0.145 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.057α = 90
b = 71.807β = 97.93
c = 103.308γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-11-11
    Type: Initial release
  • Version 1.1: 2018-07-11
    Changes: Data collection, Database references
  • Version 1.2: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Refinement description