6CFW | pdb_00006cfw

cryoEM structure of a respiratory membrane-bound hydrogenase


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
A [auth H]SCOP2 FamilyND4 antiporter-like subunits 8059301 4005749 SCOP2 (2022-06-29)
A [auth H]SCOP2 SuperfamilyAntiporter subunits half-channel-like 8093345 3002280 SCOP2 (2022-06-29)
A [auth H]SCOP2 SuperfamilyAntiporter subunits half-channel-like 8059302 3002280 SCOP2 (2022-06-29)
B [auth G]SCOP2 FamilyNADH-quinone oxidoreductase NDH subunit 11-like 8093352 4005793 SCOP2 (2022-06-29)
B [auth G]SCOP2 SuperfamilyNADH-quinone oxidoreductase, subunit 11-like 8093353 3002200 SCOP2 (2022-06-29)
C [auth D]SCOP2 FamilyNADH-quinone oxidoreductase NDH subunit 10-like 8093354 4005844 SCOP2 (2022-06-29)
C [auth D]SCOP2 SuperfamilyNADH-quinone oxidoreductase, subunit 11-like 8093355 3002200 SCOP2 (2022-06-29)
E [auth M]SCOP2 FamilyNADH-quinone oxidoreductase subunit 8-like 8067554 4005664 SCOP2 (2022-06-29)
E [auth M]SCOP2 SuperfamilyAntiporter subunits half-channel-like 8067555 3002280 SCOP2 (2022-06-29)
I [auth C]SCOP2 FamilyMonovalent cation/H+ antiporter MBH, subunit G 8093343 4007805 SCOP2 (2022-06-29)
I [auth C]SCOP2 SuperfamilyNADH-quinone oxidoreductase, subunit 11-like 8093344 3002200 SCOP2 (2022-06-29)
J [auth B]SCOP2 FamilyMonovalent cation/H+ antiporter MBH, subunit F 8093341 4007804 SCOP2 (2022-06-29)
J [auth B]SCOP2 SuperfamilyNADH-quinone oxidoreductase, subunit 11-like 8093342 3002200 SCOP2 (2022-06-29)
K [auth J]SCOP2 FamilyNq06/HydA N-terminal domain-like 8085730 4007641 SCOP2 (2022-06-29)
K [auth J]SCOP2 SuperfamilyNqo6/HydA N-terminal domain-like 8085731 3002291 SCOP2 (2022-06-29)
M [auth L]SCOP2 FamilyNqo4-like 8085742 4000433 SCOP2 (2022-06-29)
M [auth L]SCOP2 SuperfamilyHydB/Nqo4-like 8085743 3001849 SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
A [auth H]Proton_antipo_Me6cfwH1 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)
B [auth G]Oxidored_q2e6cfwG1 A: alpha complex topologyX: NADH-quinone oxidoreductase subunit K (From Topology)H: NADH-quinone oxidoreductase subunit K (From Topology)T: NADH-quinone oxidoreductase subunit KF: Oxidored_q2ECOD (1.6)
E [auth M]NADHdhe6cfwM1 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)
K [auth J]Oxidored_q6e6cfwJ1 A: a/b three-layered sandwichesX: Flavodoxin-likeH: Class I glutamine amidotransferase-likeT: CheY-likeF: Oxidored_q6ECOD (1.6)
L [auth K]Complex1_30kDae6cfwK1 A: a+b two layersX: Nqo5-likeH: Nqo5-like (From Topology)T: Nqo5-likeF: Complex1_30kDaECOD (1.6)
M [auth L]Complex1_49kDa_1ste6cfwL1 A: alpha complex topologyX: alpha-helical domain in nickel-iron hydrogenase, large subunit (From Topology)H: alpha-helical domain in nickel-iron hydrogenase, large subunit (From Topology)T: alpha-helical domain in nickel-iron hydrogenase, large subunitF: Complex1_49kDa_1stECOD (1.6)
M [auth L]NuoDe6cfwL2 A: a+b two layersX: FAD-linked reductases, C-terminal domain-likeH: Ni-Fe binding domain in nickel-iron hydrogenase large subunit (From Topology)T: Ni-Fe binding domain in nickel-iron hydrogenase large subunitF: NuoDECOD (1.6)
M [auth L]NiFeSe_Hases_3rd_1e6cfwL3 A: a+b two layersX: FAD-linked reductases, C-terminal domain-likeH: Ni-Fe binding domain in nickel-iron hydrogenase large subunit (From Topology)T: Ni-Fe binding domain in nickel-iron hydrogenase large subunitF: NiFeSe_Hases_3rd_1ECOD (1.6)
NFer4_21_1e6cfwN1 A: a+b two layersX: 4Fe-4S ferredoxin (From Topology)H: 4Fe-4S ferredoxin (From Topology)T: 4Fe-4S ferredoxinF: Fer4_21_1ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

ChainDomainClassArchitectureTopologyHomologyProvenance Source (Version)
K [auth J]3.40.50.12280 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold CATH (utative)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
A [auth H]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
A [auth H]PF00662NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus (Proton_antipo_N)NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminusThis entry represents an amino terminal extension of Pfam:PF00361. Only NADH-Ubiquinone chain 5 and eubacterial chain L are in this family. This sub-family is part of complex I which catalyses the transfer of two electrons from NADH to ubiquinone in ...This entry represents an amino terminal extension of Pfam:PF00361. Only NADH-Ubiquinone chain 5 and eubacterial chain L are in this family. This sub-family is part of complex I which catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane.
Domain
B [auth G]PF00420NADH-ubiquinone/plastoquinone oxidoreductase chain 4L (Oxidored_q2)NADH-ubiquinone/plastoquinone oxidoreductase chain 4L- Family
C [auth D]PF13244MBH, subunit D (MbhD)MBH, subunit DHydrogen gas-evolving membrane-bound hydrogenase (MBH) is a respiratory complex homologous to the quinone-reducing Complex I. Like Complex I, MBH has peripheral and membrane arms. MBH is made of 14 subunits (MbhA-N). MbhJ, K, L, N and M form the Memb ...Hydrogen gas-evolving membrane-bound hydrogenase (MBH) is a respiratory complex homologous to the quinone-reducing Complex I. Like Complex I, MBH has peripheral and membrane arms. MBH is made of 14 subunits (MbhA-N). MbhJ, K, L, N and M form the Membrane-anchored hydrogenase module. MbhJ, K, L, N are predicted to be exposed to the cytoplasm and form the peripheral arm. The remaining 10 subunits are predicted to be integral membrane proteins forming the membrane arm, made of 44 transmembrane helices (TMH) [2, 3]. MbhA, B, C and F form the Sodium translocation module. MbhD, E, G and H form the Proton translocation module. MbhI is the linker between the hydrogenase module and the proton-translocating membrane module. It anchors the discontinuous TMH7 of MbhH via its middle lateral helix and the C-terminal of TMH2, found in MbhE. MbhD and MbhE together are equivalent to Nqo10 of Complex I [1]. MbhD has three TM helices.
Domain
E [auth M]PF00146NADH dehydrogenase (NADHdh)NADH dehydrogenase- Family
PF04039Domain related to MnhB subunit of Na+/H+ antiporter (MnhB)Domain related to MnhB subunit of Na+/H+ antiporter- Family
H [auth E]PF20501MBH, subunit E (MbhE)MBH, subunit EHydrogen gas-evolving membrane-bound hydrogenase (MBH) is a respiratory complex homologous to the quinone-reducing Complex I. Like Complex I, MBH has peripheral and membrane arms. MBH is made of 14 subunits (MbhA-N). MbhJ, K, L, N and M form the Memb ...Hydrogen gas-evolving membrane-bound hydrogenase (MBH) is a respiratory complex homologous to the quinone-reducing Complex I. Like Complex I, MBH has peripheral and membrane arms. MBH is made of 14 subunits (MbhA-N). MbhJ, K, L, N and M form the Membrane-anchored hydrogenase module. MbhJ, K, L, N are predicted to be exposed to the cytoplasm and form the peripheral arm. The remaining 10 subunits are predicted to be integral membrane proteins forming the membrane arm, made of 44 transmembrane helices (TMH) [2, 3]. MbhA, B, C and F form the Sodium translocation module. MbhD, E, G and H form the Proton translocation module. MbhI is the linker between the hydrogenase module and the proton-translocating membrane module. It anchors the discontinuous TMH7 of MbhH via its middle lateral helix and the C-terminal of TMH2, found in MbhE. MbhD and MbhE together are equivalent to Nqo10 of Complex I [1]. MbhE has two transmembrane helices: TMH1 and TMH2.
Domain
I [auth C]PF03334Na+/H+ antiporter subunit (PhaG_MnhG_YufB)Na+/H+ antiporter subunit- Family
J [auth B]PF04066Multiple resistance and pH regulation protein F (MrpF / PhaF) (MrpF_PhaF)Multiple resistance and pH regulation protein F (MrpF / PhaF)- Family
K [auth J]PF01058NADH ubiquinone oxidoreductase, 20 Kd subunit (Oxidored_q6)NADH ubiquinone oxidoreductase, 20 Kd subunitDomain
L [auth K]PF00329Respiratory-chain NADH dehydrogenase, 30 Kd subunit (Complex1_30kDa)Respiratory-chain NADH dehydrogenase, 30 Kd subunitDomain
M [auth L]PF00374Nickel-dependent hydrogenase (NiFeSe_Hases)Nickel-dependent hydrogenase- Family
M [auth L]PF00346Respiratory-chain NADH dehydrogenase, 49 Kd subunit (Complex1_49kDa)Respiratory-chain NADH dehydrogenase, 49 Kd subunit- Family
PF131874Fe-4S dicluster domain (Fer4_9)4Fe-4S dicluster domain- Family
G [auth A]PF01899Na+/H+ ion antiporter subunit (MNHE)Na+/H+ ion antiporter subunit- Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
A [auth H]Monovalent cation/H+ antiporter subunit D- -
B [auth G]Monovalent cation/H+ antiporter subunit C- -
C [auth D]MBH subunit- -
E [auth M]Mbh13 NADH dehydrogenase subunit- -
Monovalent cation/H+ antiporter subunit B- -
H [auth E]MBH subunit- -
I [auth C]Monovalent cation/H+ antiporter subunit G -
J [auth B]Monovalent cation/H+ antiporter subunit F -
K [auth J]Probable membrane-bound hydrogenase subunit mbhJ
L [auth K]Membrane-bound hydrogenase subunit beta
M [auth L]Membrane-bound hydrogenase subunit alpha
NADH-plastoquinone oxidoreductase subunit -
G [auth A]Monovalent cation/H+ antiporter subunit E -
D [auth I]MBH subunit- -

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
A [auth H]IPR050586CPA3 Na+/H+ Antiporter Subunit DFamily
A [auth H]IPR001516NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminalDomain
A [auth H]IPR001750NADH:quinone oxidoreductase/Mrp antiporter, transmembrane domainDomain
B [auth G]IPR039428NADH-ubiquinone oxidoreductase chain 4L/Mnh complex subunit C1-likeFamily
B [auth G]IPR050601CPA3 antiporter subunit CFamily
C [auth D]IPR025383MrpA C-terminal/MbhDDomain
C [auth D]IPR042106NADH-ubiquinone/plastoquinone oxidoreductase chain 6, subunit NuoJHomologous Superfamily
E [auth M]IPR001694NADH:ubiquinone oxidoreductase, subunit 1/F420H2 oxidoreductase subunit HFamily
E [auth M]IPR052561Complex I Subunit 1Family
IPR050622CPA3 Na(+)/H(+) Antiporter Subunit BFamily
IPR007182Na+/H+ antiporter MnhB subunit-related proteinDomain
H [auth E]IPR046806MrpA C-terminal/MbhEDomain
I [auth C]IPR005133Na+/H+ antiporter subunit GFamily
J [auth B]IPR007208Na(+)/H(+) antiporter subunit F-likeFamily
K [auth J]IPR052375Complex I 20 kDa subunit-likeFamily
K [auth J]IPR006137NADH:ubiquinone oxidoreductase-like, 20kDa subunitDomain
L [auth K]IPR037232NADH:ubiquinone oxidoreductase, 30kDa subunit superfamilyHomologous Superfamily
L [auth K]IPR001268NADH:ubiquinone oxidoreductase, 30kDa subunitDomain
M [auth L]IPR052197Complex I 49 kDa subunit-likeFamily
M [auth L]IPR001501Nickel-dependent hydrogenase, large subunitFamily
M [auth L]IPR029014[NiFe]-hydrogenase, large subunitHomologous Superfamily
M [auth L]IPR001135NADH-quinone oxidoreductase, subunit DDomain
IPR0179004Fe-4S ferredoxin, iron-sulphur binding, conserved siteConserved Site
IPR0178964Fe-4S ferredoxin-type, iron-sulphur binding domainDomain
IPR010226NADH-quinone oxidoreductase, chain IFamily
G [auth A]IPR002758Na+/H+ antiporter subunit EFamily