3DAG image
Deposition Date 2008-05-29
Release Date 2008-12-09
Last Version Date 2023-08-30
Entry Detail
PDB ID:
3DAG
Keywords:
Title:
The crystal structure of [Fe]-hydrogenase holoenzyme (HMD) from METHANOCALDOCOCCUS JANNASCHII
Biological Source:
Source Organism:
Host Organism:
Method Details:
Experimental Method:
Resolution:
1.75 Å
R-Value Free:
0.21
R-Value Work:
0.17
R-Value Observed:
0.18
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 [Fe]-hydrogenase reveals the geometry of the active site.
Science 321 572 575 (2008)
PMID: 18653896 DOI: 10.1126/science.1158978

Abstact

Biological formation and consumption of molecular hydrogen (H2) are catalyzed by hydrogenases, of which three phylogenetically unrelated types are known: [NiFe]-hydrogenases, [FeFe]-hydrogenases, and [Fe]-hydrogenase. We present a crystal structure of [Fe]-hydrogenase at 1.75 angstrom resolution, showing a mononuclear iron coordinated by the sulfur of cysteine 176, two carbon monoxide (CO) molecules, and the sp2-hybridized nitrogen of a 2-pyridinol compound with back-bonding properties similar to those of cyanide. The three-dimensional arrangement of the ligands is similar to that of thiolate, CO, and cyanide ligated to the low-spin iron in binuclear [NiFe]- and [FeFe]-hydrogenases, although the enzymes have evolved independently and the CO and cyanide ligands are not found in any other metalloenzyme. The related iron ligation pattern of hydrogenases exemplifies convergent evolution and presumably plays an essential role in H2 activation. This finding may stimulate the ongoing synthesis of catalysts that could substitute for platinum in applications such as fuel cells.

Legend

Protein

Chemical

Disease

Primary Citation of related structures