7Z0T | pdb_00007z0t

Structure of the Escherichia coli formate hydrogenlyase complex (aerobic preparation, composite structure)


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
G [auth A]SCOP2B SuperfamilyADC-like 8042869 3001132 SCOP2B (2022-06-29)
G [auth A]SCOP2B SuperfamilyFormate dehydrogenase/DMSO reductase, domains 1-3 8042870 3001453 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
A [auth C]Proton_antipo_Me7z0tC1 A: alpha complex topologyX: Sodium/proton antiporter subunits-like (From Homology)H: Sodium/proton antiporter subunits-likeT: NADH-quinone oxidoreductase subunit L (NuoL)-relatedF: Proton_antipo_MECOD (1.6)
F [auth D]NADHdhe7z0tD1 A: alpha complex topologyX: Sodium/proton antiporter subunits-like (From Homology)H: Sodium/proton antiporter subunits-likeT: NADH-quinone oxidoreductase subunit 8 (Nqo8)-relatedF: NADHdhECOD (1.6)
G [auth A]Molydop_bindinge7z0tA3 A: beta barrelsX: cradle loop barrelH: RIFT-relatedT: double psiF: Molydop_bindingECOD (1.6)
G [auth A]Molybdop_Fe4S4e7z0tA2 A: a+b two layersX: Formate dehydrogenase/DMSO reductase, domain 1 (From Topology)H: Formate dehydrogenase/DMSO reductase, domain 1 (From Topology)T: Formate dehydrogenase/DMSO reductase, domain 1F: Molybdop_Fe4S4ECOD (1.6)
G [auth A]Molybdopterin_2nde7z0tA4 A: a/b three-layered sandwichesX: Rossmann-likeH: Formate dehydrogenase/DMSO reductase, domains 2 and 3 (From Topology)T: Formate dehydrogenase/DMSO reductase, domains 2 and 3F: Molybdopterin_2ndECOD (1.6)
G [auth A]Molybdopterin_1st_1e7z0tA1 A: a/b three-layered sandwichesX: Rossmann-likeH: Formate dehydrogenase/DMSO reductase, domains 2 and 3 (From Topology)T: Formate dehydrogenase/DMSO reductase, domains 2 and 3F: Molybdopterin_1st_1ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
A [auth C]PF00361NADH:quinone oxidoreductase/Mrp antiporter, TM (Proton_antipo_M)NADH:quinone oxidoreductase/Mrp antiporter, TMThis entry includes membrane transporters and represents some 7 of potentially 14-16 TM regions. In many instances, its members forms part of complex I that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associa ...This entry includes membrane transporters and represents some 7 of potentially 14-16 TM regions. In many instances, its members forms part of complex I that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane, and in this context is a combination predominantly of subunits 2, 4, 5, 14, L, M and N [1]. In many bacterial species these proteins are probable stand-alone transporters not coupled with oxidoreduction [2].
Domain
B [auth E]PF00329Respiratory-chain NADH dehydrogenase, 30 Kd subunit (Complex1_30kDa)Respiratory-chain NADH dehydrogenase, 30 Kd subunitDomain
B [auth E]PF00374Nickel-dependent hydrogenase (NiFeSe_Hases)Nickel-dependent hydrogenase- Family
B [auth E]PF00346Respiratory-chain NADH dehydrogenase, 49 Kd subunit (Complex1_49kDa)Respiratory-chain NADH dehydrogenase, 49 Kd subunit- Family
C [auth B]PF000374Fe-4S binding domain (Fer4)4Fe-4S binding domainSuperfamily includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. Structure of the domain is an alpha-antiparallel beta sandwich. Domain
D [auth G]PF01058NADH ubiquinone oxidoreductase, 20 Kd subunit (Oxidored_q6)NADH ubiquinone oxidoreductase, 20 Kd subunitDomain
E [auth F]PF000374Fe-4S binding domain (Fer4)4Fe-4S binding domainSuperfamily includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. Structure of the domain is an alpha-antiparallel beta sandwich. Domain
F [auth D]PF00146NADH dehydrogenase (NADHdh)NADH dehydrogenase- Family
G [auth A]PF01568Molydopterin dinucleotide binding domain (Molydop_binding)Molydopterin dinucleotide binding domainThis domain is found in various molybdopterin - containing oxidoreductases and tungsten formylmethanofuran dehydrogenase subunit d (FwdD) and molybdenum formylmethanofuran dehydrogenase subunit (FmdD); where the domain constitutes almost the entire s ...This domain is found in various molybdopterin - containing oxidoreductases and tungsten formylmethanofuran dehydrogenase subunit d (FwdD) and molybdenum formylmethanofuran dehydrogenase subunit (FmdD); where the domain constitutes almost the entire subunit. The formylmethanofuran dehydrogenase catalyses the first step in methane formation from CO2 in methanogenic archaea and has a molybdopterin dinucleotide cofactor [1]. This domain corresponds to the C-terminal domain IV in dimethyl sulfoxide (DMSO)reductase which interacts with the 2-amino pyrimidone ring of both molybdopterin guanine dinucleotide molecules [2].
Domain
G [auth A]PF04879Molybdopterin oxidoreductase Fe4S4 domain (Molybdop_Fe4S4)Molybdopterin oxidoreductase Fe4S4 domainThis domain is found in formate dehydrogenase H for which the structure is known. This first domain (residues 1 to 60) of PDB:1aa6 is an Fe4S4 cluster just below the protein surface [1]. Domain
G [auth A]PF00384Molybdopterin oxidoreductase (Molybdopterin)Molybdopterin oxidoreductaseDomain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
A [auth C]Formate hydrogenlyase subunit 3
B [auth E]Formate hydrogenlyase subunit 5
C [auth B]Formate hydrogenlyase subunit 2
D [auth G]Formate hydrogenlyase subunit 7
E [auth F]Formate hydrogenlyase subunit 6
F [auth D]Formate hydrogenlyase subunit 4
G [auth A]Formate dehydrogenase H

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
A [auth C]IPR052175Complex I-like Hydrogenase ComponentFamily
A [auth C]IPR003918NADH:ubiquinone oxidoreductaseFamily
A [auth C]IPR001750NADH:quinone oxidoreductase/Mrp antiporter, transmembrane domainDomain
B [auth E]IPR037232NADH:ubiquinone oxidoreductase, 30kDa subunit superfamilyHomologous Superfamily
B [auth E]IPR001501Nickel-dependent hydrogenase, large subunitFamily
B [auth E]IPR014029NADH:ubiquinone oxidoreductase, 49kDa subunit, conserved siteConserved Site
B [auth E]IPR029014[NiFe]-hydrogenase, large subunitHomologous Superfamily
B [auth E]IPR052197Complex I 49 kDa subunit-likeFamily
B [auth E]IPR001268NADH:ubiquinone oxidoreductase, 30kDa subunitDomain
B [auth E]IPR001135NADH-quinone oxidoreductase, subunit DDomain
C [auth B]IPR0179004Fe-4S ferredoxin, iron-sulphur binding, conserved siteConserved Site
C [auth B]IPR0178964Fe-4S ferredoxin-type, iron-sulphur binding domainDomain
C [auth B]IPR050294Ion-translocating oxidoreductase complex subunit BFamily
D [auth G]IPR052375Complex I 20 kDa subunit-likeFamily
D [auth G]IPR006138NADH-ubiquinone oxidoreductase, 20 Kd subunitFamily
D [auth G]IPR006137NADH:ubiquinone oxidoreductase-like, 20kDa subunitDomain
E [auth F]IPR010226NADH-quinone oxidoreductase, chain IFamily
E [auth F]IPR0179004Fe-4S ferredoxin, iron-sulphur binding, conserved siteConserved Site
E [auth F]IPR0178964Fe-4S ferredoxin-type, iron-sulphur binding domainDomain
F [auth D]IPR001694NADH:ubiquinone oxidoreductase, subunit 1/F420H2 oxidoreductase subunit HFamily
F [auth D]IPR052561Complex I Subunit 1Family
F [auth D]IPR018086NADH:ubiquinone oxidoreductase, subunit 1, conserved siteConserved Site
G [auth A]IPR006963Molybdopterin oxidoreductase, 4Fe-4S domainDomain
G [auth A]IPR006657Molybdopterin dinucleotide-binding domainDomain
G [auth A]IPR006656Molybdopterin oxidoreductaseDomain
G [auth A]IPR009010Aspartate decarboxylase-like domain superfamilyHomologous Superfamily
G [auth A]IPR006655Molybdopterin oxidoreductase, prokaryotic, conserved siteConserved Site
G [auth A]IPR041924Formate dehydrogenase H, N-terminalDomain
G [auth A]IPR050123Prokaryotic molybdopterin-containing oxidoreductaseFamily
G [auth A]IPR027467Molybdopterin oxidoreductase, molybdopterin cofactor binding siteBinding Site
G [auth A]IPR041925Formate dehydrogenase H, molybdopterin-binding domainDomain
G [auth A]IPR006478Formate dehydrogenase, alpha subunitFamily