4RTB

X-ray structure of the FeFe-hydrogenase maturase HydG from Carboxydothermus hydrogenoformans


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.79 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.223 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal Structure of HydG from Carboxydothermus hydrogenoformans: A Trifunctional [FeFe]-Hydrogenase Maturase.

Nicolet, Y.Pagnier, A.Zeppieri, L.Martin, L.Amara, P.Fontecilla-Camps, J.C.

(2015) Chembiochem 16: 397-402

  • DOI: 10.1002/cbic.201402661

  • PubMed Abstract: 
  • The structure of the radical S-adenosyl-L-methionine (SAM) [FeFe]-hydrogenase maturase HydG involved in CN(-) /CO synthesis is characterized by two internal tunnels connecting its tyrosine-binding pocket with the external medium and the C-terminal Fe ...

    The structure of the radical S-adenosyl-L-methionine (SAM) [FeFe]-hydrogenase maturase HydG involved in CN(-) /CO synthesis is characterized by two internal tunnels connecting its tyrosine-binding pocket with the external medium and the C-terminal Fe4 S4 cluster-containing region. A comparison with a tryptophan-bound NosL structure suggests that substrate binding causes the closing of the first tunnel and, along with mutagenesis studies, that tyrosine binds to HydG with its amino group well positioned for H-abstraction by SAM. In this orientation the dehydroglycine (DHG) fragment caused by tyrosine Cα-Cβ bond scission can readily migrate through the second tunnel towards the C-terminal domain where both CN(-) and CO are synthesized. Our HydG structure appears to be in a relaxed state with its C-terminal cluster CysX2 CysX22 Cys motif exposed to solvent. A rotation of this domain coupled to Fe4 S4 cluster assembly would bury its putatively reactive unique Fe ion thereby allowing it to interact with DHG.


    Organizational Affiliation

    Metalloproteins Unit, Institut de Biologie Structurale, UMR5075, CEA, CNRS, Université Grenoble Alpes, 71, Avenue des Martyrs, CS 10090, 38044 Grenoble cedex 9 (France). yvain.nicolet@ibs.fr.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HydG protein
A
477Carboxydothermus hydrogenoformans (strain ATCC BAA-161 / DSM 6008 / Z-2901)Mutation(s): 0 
Find proteins for Q3ABV3 (Carboxydothermus hydrogenoformans (strain ATCC BAA-161 / DSM 6008 / Z-2901))
Go to UniProtKB:  Q3ABV3
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

Download SDF File 
Download CCD File 
A
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
SAM
Query on SAM

Download SDF File 
Download CCD File 
A
S-ADENOSYLMETHIONINE
C15 H22 N6 O5 S
MEFKEPWMEQBLKI-FCKMPRQPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.79 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.223 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 92.230α = 90.00
b = 92.230β = 90.00
c = 167.600γ = 90.00
Software Package:
Software NamePurpose
ADSCdata collection
XDSdata scaling
PHASERphasing
PHENIXrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-01-28
    Type: Initial release
  • Version 1.1: 2015-02-25
    Type: Database references