3f47 image
Deposition Date 2008-10-31
Release Date 2009-02-10
Last Version Date 2023-11-01
Entry Detail
PDB ID:
3F47
Keywords:
Title:
The Crystal Structure of [Fe]-Hydrogenase (Hmd) Holoenzyme from Methanocaldococcus jannaschii
Biological Source:
Source Organism:
Host Organism:
Method Details:
Experimental Method:
Resolution:
1.75 Å
R-Value Free:
0.20
R-Value Work:
0.17
R-Value Observed:
0.17
Space Group:
I 41 2 2
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:5,10-methenyltetrahydromethanopterin hydrogenase
Gene (Uniprot):hmd
Chain IDs:A
Chain Length:358
Number of Molecules:1
Biological Source:Methanocaldococcus jannaschii
Primary Citation
The crystal structure of C176A mutated [Fe]-hydrogenase suggests an acyl-iron ligation in the active site iron complex.
Febs Lett. 583 585 590 (2009)
PMID: 19162018 DOI: 10.1016/j.febslet.2009.01.017

Abstact

[Fe]-hydrogenase is one of three types of enzymes known to activate H(2). Crystal structure analysis recently revealed that its active site iron is ligated square-pyramidally by Cys176-sulfur, two CO, an "unknown" ligand and the sp(2)-hybridized nitrogen of a unique iron-guanylylpyridinol-cofactor. We report here on the structure of the C176A mutated enzyme crystallized in the presence of dithiothreitol (DTT). It suggests an iron center octahedrally coordinated by one DTT-sulfur and one DTT-oxygen, two CO, the 2-pyridinol's nitrogen and the 2-pyridinol's 6-formylmethyl group in an acyl-iron ligation. This result led to a re-interpretation of the iron ligation in the wild-type.

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Primary Citation of related structures