3C8Y: 1.39 Angstrom Crystal Structure Of Fe-Only Hydrogenase

Citation:
Abstract
An X-ray crystallographic refinement of the H-cluster of [FeFe]-hydrogenase from Clostridium pasteurianum has been carried out to close-to atomic resolution and is the highest resolution [FeFe]-hydrogenase presented to date. The 1.39 A, anisotropically refined [FeFe]-hydrogenase structure provides a basis for examining the outstanding issue of the composition of the unique nonprotein dithiolate ligand of the H-cluster. In addition to influencing the electronic structure of the H-cluster, the composition of the ligand has mechanistic implications due to the potential of the bridge-head gamma-group participating in proton transfer during catalysis. In this work, sequential density functional theory optimizations of the dithiolate ligand embedded in a 3.5-3.9 A protein environment provide an unbiased approach to examining the most likely composition of the ligand. Structural, conformational, and energetic considerations indicate a preference for dithiomethylether as an H-cluster ligand and strongly disfavor the dithiomethylammonium as a catalytic base for hydrogen production.
PDB ID: 3C8YDownload
MMDB ID: 64053
PDB Deposition Date: 2008/2/14
Updated in MMDB: 2012/09
Experimental Method:
x-ray diffraction
Resolution: 1.39  Å
Source Organism:
Similar Structures:
Biological Unit for 3C8Y: monomeric; determined by author and by software (PISA)
Molecular Components in 3C8Y
Label Count Molecule
Protein (1 molecule)
1
Iron Hydrogenase 1
Molecule annotation
Chemicals (9 molecules)
1
1
2
4
3
1
4
3
* Click molecule labels to explore molecular sequence information.

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