1h2r Summary

pdbe.org/1h2r
spacer

THREE-DIMENSIONAL STRUCTURE OF NI-FE HYDROGENASE FROM DESULFIVIBRIO VULGARIS MIYAZAKI F IN THE REDUCED FORM AT 1.4 A RESOLUTION

The structure was published by Higuchi, Y., Ogata, H., Miki, K., Yasuoka, N., and Yagi, T., in 1999 in a paper entitled "Removal of the bridging ligand atom at the Ni-Fe active site of [NiFe] hydrogenase upon reduction with H2, as revealed by X-ray structure analysis at 1.4 A resolution." (abstract).

This crystal structure was determined using X-ray diffraction at a resolution of 1.4 Å and deposited in 1999.

The experimental data on which the structure is based was not deposited.

This PDB entry contains a complex of 2 biomacromolecules, namely PROTEIN (PERIPLASMIC [NIFE] HYDROGENASE SMALL SUBUNIT) and PROTEIN (PERIPLASMIC [NIFE] HYDROGENASE LARGE SUBUNIT).

It also contains one or more heterogenic compounds (e.g., ligands, co-factors, ions, modified amino acids, etc.); see here for a complete list.

The molecule most likely forms heterodimers.

The following tables show cross-reference information to other databases (to obtain a list of all PDB entries sharing the same property or classification, click on the magnifying glass icon):


Chain Name UniProt Name of source organism % of UniProt sequence present in the sample Residues in the sample molecules % of residues observed
S PROTEIN (PERIPLASMIC [NIFE] HYDROGENASE SMALL SUBUNIT) P21853 (51-317) (PHNS_DESVM)search Desulfovibrio vulgaris str. 'Miyazaki F'search 100% 267 100%
L PROTEIN (PERIPLASMIC [NIFE] HYDROGENASE LARGE SUBUNIT) P21852 (19-552) (PHNL_DESVM)search Desulfovibrio vulgaris str. 'Miyazaki F'search 94% 534 100%


This entry contains 2 unique UniProt proteins:

UniProt accession Name Organism PDB
P21853 (51 - 317) PROTEIN (PERIPLASMIC [NIFE] HYDROGENASE SMALL SUBUNIT) Desulfovibrio vulgaris str. 'Miyazaki F'
P21852 (19 - 552) PROTEIN (PERIPLASMIC [NIFE] HYDROGENASE LARGE SUBUNIT) Desulfovibrio vulgaris str. 'Miyazaki F'

Chain Structural classification (SCOP) Structural classification (CATH) Sequence family (Pfam)
S (P21853) Nickel-iron hydrogenase, small subunitsearch Rossmann foldsearch, Cytochrome-c3 Hydrogenase, chain A, domain 2search PF01058: NADH ubiquinone oxidoreductase, 20 Kd subunitsearch, PF14720: NiFe/NiFeSe hydrogenase small subunit C-terminalsearch
L (P21852) Nickel-iron hydrogenase, large subunitsearch Cytochrome-c3 Hydrogenase, chain Bsearch PF00374: Nickel-dependent hydrogenasesearch

Chain ID Molecular function (GO) Biological process (GO) Cellular component (GO)
S (P21853) ferredoxin hydrogenase activitysearch iron-sulfur cluster bindingsearch oxidoreductase activitysearch cytochrome-c3 hydrogenase activitysearch 3 iron, 4 sulfur cluster bindingsearch 4 iron, 4 sulfur cluster bindingsearch metal ion bindingsearch oxidation-reduction processsearch ferredoxin hydrogenase complexsearch periplasmic spacesearch
L (P21852) metal ion bindingsearch nickel cation bindingsearch ferredoxin hydrogenase activitysearch oxidoreductase activitysearch cytochrome-c3 hydrogenase activitysearch oxidation-reduction processsearch periplasmic spacesearch

Chain InterPro annotation
S [NiFe]-hydrogenase, small subunitsearch NADH:ubiquinone oxidoreductase-like, 20kDa subunitsearch Cytochrome-c3 hydrogenase, C-terminalsearch
L Nickel-dependent hydrogenase, large subunitsearch Nickel-dependent hydrogenase, large subunit, nickel binding sitesearch NiFe hydrogenase-likesearch