3C8Y

1.39 Angstrom crystal structure of Fe-only hydrogenase

Summary for 3C8Y

• Entry DOI: 10.2210/pdb3c8y/pdb
• Descriptor: Iron hydrogenase 1, 2 IRON/2 SULFUR/3 CARBONYL/2 CYANIDE/WATER/METHYLETHER CLUSTER, IRON/SULFUR CLUSTER, ... (6 entities in total)
• Functional Keywords: dithiomethylether, h-cluster, hydrogenase, iron, iron-sulfur, metal-binding, oxidoreductase
• Biological source: Clostridium pasteurianum
• Total number of polymer chains: 1
• Total formula weight: 66147.75

Authors

Pandey, A.S.,Lemon, B.J.,Peters, J.W. (deposition date: 2008-02-14, release date: 2008-04-22, Last modification date: 2023-08-30)

Primary citation

Pandey, A.S.,Harris, T.V.,Giles, L.J.,Peters, J.W.,Szilagyi, R.K.
Dithiomethylether as a ligand in the hydrogenase h-cluster.
J.Am.Chem.Soc., 130:4533-4540, 2008

PubMed 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.

PubMed: 18324814
DOI: 10.1021/ja711187e

Experimental method

X-RAY DIFFRACTION (1.39 Å)