3zfs Summary

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Cryo-EM structure of the F420-reducing NiFe-hydrogenase from a methanogenic archaeon with bound substrate

The structure was published by Mills, D.J., Vitt, S., Strauss, M., Shima, S., and Vonck, J., in 2013 in a paper entitled "De Novo Modeling of the F420-Reducing [Nife]-Hydrogenase from a Methanogenic Archaeon by Cryo-Electron Microscopy" (abstract).

The structure was determined using Electron microscopy at a resolution of 4.0 Å and deposited in 2012.

The experimental data on which the structure is based was deposited separately in EMDB as entry 2097.

This PDB entry contains a complex of 3 biomacromolecules, namely F420-REDUCING HYDROGENASE, SUBUNIT ALPHA, F420-REDUCING HYDROGENASE, SUBUNIT GAMMA, and F420-REDUCING HYDROGENASE, SUBUNIT BETA.

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 heterotrimers.

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 F420-REDUCING HYDROGENASE, SUBUNIT ALPHA D9PYF9 (1-405) (D9PYF9_METTM)search Methanothermobacter marburgensis str. Marburgsearch 95% 405 95%
B F420-REDUCING HYDROGENASE, SUBUNIT GAMMA D9PYF7 (1-275) (D9PYF7_METTM)search Methanothermobacter marburgensis str. Marburgsearch 100% 275 78%
C F420-REDUCING HYDROGENASE, SUBUNIT BETA D9PYF6 (1-281) (D9PYF6_METTM)search Methanothermobacter marburgensis str. Marburgsearch 100% 281 98%


This entry contains 3 unique UniProt proteins:

UniProt accession Name Organism PDB
D9PYF9 (1 - 405) F420-REDUCING HYDROGENASE, SUBUNIT ALPHA Methanothermobacter marburgensis
D9PYF7 (1 - 275) F420-REDUCING HYDROGENASE, SUBUNIT GAMMA Methanothermobacter marburgensis
D9PYF6 (1 - 281) F420-REDUCING HYDROGENASE, SUBUNIT BETA Methanothermobacter marburgensis

Chain Sequence family (Pfam)
A (D9PYF9) PF00374: Nickel-dependent hydrogenasesearch
B (D9PYF7) PF01058: NADH ubiquinone oxidoreductase, 20 Kd subunitsearch, PF13237: 4Fe-4S dicluster domainsearch
C (D9PYF6) PF04422: Coenzyme F420 hydrogenase/dehydrogenase, beta subunit N-termsearch, PF04432: Coenzyme F420 hydrogenase/dehydrogenase, beta subunit C terminussearch

Chain ID Molecular function (GO) Biological process (GO)
A (D9PYF9) nickel cation bindingsearch iron-sulfur cluster bindingsearch coenzyme F420 hydrogenase activitysearch flavin adenine dinucleotide bindingsearch oxidoreductase activitysearch metal ion bindingsearch ferredoxin hydrogenase activitysearch oxidation-reduction processsearch
B (D9PYF7) 4 iron, 4 sulfur cluster bindingsearch electron carrier activitysearch oxidoreductase activity, acting on NAD(P)Hsearch nickel cation bindingsearch iron-sulfur cluster bindingsearch coenzyme F420 hydrogenase activitysearch oxidoreductase activitysearch flavin adenine dinucleotide bindingsearch oxidation-reduction processsearch
C (D9PYF6) nickel cation bindingsearch iron-sulfur cluster bindingsearch coenzyme F420 hydrogenase activitysearch flavin adenine dinucleotide bindingsearch oxidoreductase activitysearch oxidation-reduction processsearch

Chain InterPro annotation
A Nickel-dependent hydrogenase, large subunitsearch Coenzyme F420 hydrogenase, subunit alphasearch Nickel-dependent hydrogenase, large subunit, nickel binding sitesearch
B NADH:ubiquinone oxidoreductase-like, 20kDa subunitsearch [NiFe]-hydrogenase-3-type complex, small subunit/NADH:quinone oxidoreductase, subunit NuoBsearch Coenzyme F420 hydrogenase, subunit gammasearch 4Fe-4S ferredoxin-type, iron-sulpur binding domainsearch 4Fe-4S ferredoxin, iron-sulphur binding, conserved sitesearch
C Coenzyme F420 hydrogenase/dehydrogenase beta subunit, N-terminalsearch Coenzyme F420 hydrogenase/dehydrogenase beta subunit, C-terminalsearch Coenzyme F420 hydrogenase, subunit betasearch