3ayz Summary

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Membrane-bound respiratory [NiFe] hydrogenase from Hydrogenovibrio marinus in an air-oxidized condition

The structure was published by Shomura, Y., Yoon, K.S., Nishihara, H., and Higuchi, Y., in 2011 in a paper entitled "Structural basis for a [4Fe-3S] cluster in the oxygen-tolerant membrane-bound [NiFe]-hydrogenase" (abstract).

This crystal structure was determined using X-ray diffraction at a resolution of 1.22 Å and deposited in 2011.

The experimental data on which the structure is based was also deposited.

This PDB entry contains a complex of 2 biomacromolecules, namely Membrane-bound hydrogenase large subunit and Membrane-bound hydrogenase small 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 heterotetramers.

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
A Membrane-bound hydrogenase large subunit F2Z6J6 (1-596) (F2Z6J6_HYDMR)search Hydrogenovibrio marinussearch 98% 596 99%
C Membrane-bound hydrogenase large subunit F2Z6J6 (1-596) (F2Z6J6_HYDMR)search Hydrogenovibrio marinussearch 98% 596 99%
B Membrane-bound hydrogenase small subunit F2Z6J5 (41-323) (F2Z6J5_HYDMR)search Hydrogenovibrio marinussearch < 90% 283 96%
D Membrane-bound hydrogenase small subunit F2Z6J5 (41-323) (F2Z6J5_HYDMR)search Hydrogenovibrio marinussearch < 90% 283 96%


This entry contains 2 unique UniProt proteins:

UniProt accession Name Organism PDB
F2Z6J6 (1 - 596) Membrane-bound hydrogenase large subunit Hydrogenovibrio marinus
F2Z6J5 (41 - 323) Membrane-bound hydrogenase small subunit Hydrogenovibrio marinus

Chain Sequence family (Pfam)
A, C (F2Z6J6) PF00374: Nickel-dependent hydrogenasesearch
B, D NADH ubiquinone oxidoreductase, 20 Kd subunitsearch, NiFe/NiFeSe hydrogenase small subunit C-terminalsearch

Chain ID Molecular function (GO) Biological process (GO) Cellular component (GO)
A, C (F2Z6J6) nickel cation bindingsearch ferredoxin hydrogenase activitysearch oxidoreductase activitysearch metal ion bindingsearch oxidation-reduction processsearch
B, D (F2Z6J5) ferredoxin hydrogenase activitysearch iron-sulfur cluster bindingsearch oxidation-reduction processsearch ferredoxin hydrogenase complexsearch

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