1YRQ: Structure Of The Ready Oxidized Form Of [nife]-hydrogenase

Citation:
Abstract
[NiFe] hydrogenases catalyze the reversible heterolytic cleavage of molecular hydrogen. Several oxidized, inactive states of these enzymes are known that are distinguishable by their very different activation properties. So far, the structural basis for this difference has not been understood because of lack of relevant crystallographic data. Here, we present the crystal structure of the ready Ni-B state of Desulfovibrio fructosovorans [NiFe] hydrogenase and show it to have a putative mu-hydroxo Ni-Fe bridging ligand at the active site. On the other hand, a new, improved refinement procedure of the X-ray diffraction data obtained for putative unready Ni-A/Ni-SU states resulted in a more elongated electron density for the bridging ligand, suggesting that it is a diatomic species. The slow activation of the Ni-A state, compared with the rapid activation of the Ni-B state, is therefore proposed to result from the different chemical nature of the ligands in the two oxidized species. Our results along with very recent electrochemical studies suggest that the diatomic ligand could be hydro-peroxide.
PDB ID: 1YRQDownload
MMDB ID: 32952
PDB Deposition Date: 2005/2/4
Updated in MMDB: 2017/11
Experimental Method:
x-ray diffraction
Resolution: 2.1  Å
Source Organism:
Similar Structures:
Biological Unit for 1YRQ: dimeric; determined by author and by software (PISA,PQS)
Molecular Components in 1YRQ
Label Count Molecule
Proteins (2 molecules)
1
Periplasmic [nife] Hydrogenase Small Subunit
Molecule annotation
1
Periplasmic [nife] Hydrogenase Large Subunit
Molecule annotation
Chemicals (6 molecules)
1
2
2
1
3
1
4
1
5
1
* Click molecule labels to explore molecular sequence information.

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