1EHK
CRYSTAL STRUCTURE OF THE ABERRANT BA3-CYTOCHROME-C OXIDASE FROM THERMUS THERMOPHILUS
External Resource: Annotation
- Domain Annotation: SCOP/SCOPe Classification
- Domain Annotation: SCOP2 Classification
- Domain Annotation: ECOD Classification
- Domain Annotation: CATH
- Protein Family Annotation
- Gene Ontology: Gene Product Annotation
- InterPro: Protein Family Classification
- Membrane Protein Annotation: PDBTM
- Membrane Protein Annotation: MemProtMD
- Membrane Protein Annotation: mpstruc
- Structure Motif: Primary M-CSA Annotation
Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage
Domain Annotation: SCOP2 Classification SCOP2 Database Homepage
Chains | Type | Family Name | Domain Identifier | Family Identifier | Provenance Source (Version) |
---|---|---|---|---|---|
A | SCOP2B Superfamily | Cytochrome c oxidase subunit I-like | 8033796 | 3000653 | SCOP2B (2022-06-29) |
B | SCOP2B Superfamily | Cytochrome c oxidase subunit II-like, transmembrane region | 8033798 | 3000692 | SCOP2B (2022-06-29) |
B | SCOP2B Superfamily | Cupredoxins | 8040581 | 3000886 | SCOP2B (2022-06-29) |
C | SCOP2B Superfamily | Bacterial ba3 type cytochrome c oxidase subunit IIa | 8033799 | 3000717 | SCOP2B (2022-06-29) |
Domain Annotation: ECOD Classification ECOD Database Homepage
Chains | Family Name | Domain Identifier | Architecture | Possible Homology | Homology | Topology | Family | Provenance Source (Version) |
---|---|---|---|---|---|---|---|---|
A | COX1 | e1ehkA1 | A: alpha superhelices | X: Cytochrome c oxidase subunit I-like | H: Cytochrome c oxidase subunit I-like (From Topology) | T: Cytochrome c oxidase subunit I-like | F: COX1 | ECOD (1.6) |
B | COX2 | e1ehkB1 | A: beta sandwiches | X: Cupredoxin-like | H: Cupredoxin-related (From Topology) | T: Cupredoxin-related | F: COX2 | ECOD (1.6) |
B | COX2-transmemb | e1ehkB2 | A: extended segments | X: Cytochrome c oxidase subunit II-like, transmembrane region (From Topology) | H: Cytochrome c oxidase subunit II-like, transmembrane region (From Topology) | T: Cytochrome c oxidase subunit II-like, transmembrane region | F: COX2-transmemb | ECOD (1.6) |
C | CoxIIa | e1ehkC1 | A: extended segments | X: Bacterial ba3 type cytochrome c oxidase subunit IIa (From Topology) | H: Bacterial ba3 type cytochrome c oxidase subunit IIa (From Topology) | T: Bacterial ba3 type cytochrome c oxidase subunit IIa | F: CoxIIa | ECOD (1.6) |
Domain Annotation: CATH CATH Database Homepage
Chain | Domain | Class | Architecture | Topology | Homology | Provenance Source (Version) |
---|---|---|---|---|---|---|
A | 1.20.210.10 | Mainly Alpha | Up-down Bundle | Cytochrome C Oxidase | Chain A | CATH (4.3.0) |
B | 1.20.1070.10 | Mainly Alpha | Up-down Bundle | Rhopdopsin 7-helix transmembrane proteins | Rhodopsin 7-helix transmembrane proteins | CATH (4.3.0) |
B | 2.60.40.420 | Mainly Beta | Sandwich | Immunoglobulin-like | Cupredoxins - blue copper proteins | CATH (4.3.0) |
Protein Family Annotation Pfam Database Homepage
Chains | Accession | Name | Description | Comments | Source |
---|---|---|---|---|---|
PF00115 | Cytochrome C and Quinol oxidase polypeptide I (COX1) | Cytochrome C and Quinol oxidase polypeptide I | - | Family | |
PF00116 | Cytochrome C oxidase subunit II, periplasmic domain (COX2) | Cytochrome C oxidase subunit II, periplasmic domain | - | Domain | |
PF09125 | Cytochrome C oxidase subunit II, transmembrane (COX2-transmemb) | Cytochrome C oxidase subunit II, transmembrane | Members of this family adopt a tertiary structure consisting of two antiparallel transmembrane helices, in a transmembrane helix hairpin fold [1]. | Domain | |
PF08113 | Cytochrome c oxidase subunit IIa family (CoxIIa) | Cytochrome c oxidase subunit IIa family | - | Family |
Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage
InterPro: Protein Family Classification InterPro Database Homepage
Chains | Accession | Name | Type |
---|---|---|---|
IPR036927 | Cytochrome c oxidase-like, subunit I superfamily | Homologous Superfamily | |
IPR000883 | Cytochrome c oxidase subunit I | Family | |
IPR023615 | Cytochrome c oxidase, subunit I, copper-binding site | Binding Site | |
IPR023616 | Cytochrome c oxidase-like, subunit I domain | Domain | |
IPR033943 | Ba3-like heme-copper oxidase subunit I | Family | |
IPR015209 | Cytochrome C oxidase subunit IIa, transmembrane domain | Domain | |
IPR002429 | Cytochrome c oxidase subunit II-like C-terminal | Domain | |
IPR036257 | Cytochrome C oxidase subunit II, transmembrane domain superfamily | Homologous Superfamily | |
IPR008972 | Cupredoxin | Homologous Superfamily | |
IPR001505 | Copper centre Cu(A) | Binding Site | |
IPR034214 | Ba3-like heme-copper oxidase subunit II, C-terminal | Domain | |
IPR051403 | NosZ/Cytochrome c oxidase subunit 2 | Family | |
IPR012538 | Cytochrome c oxidase polypeptide 2A | Family | |
IPR036246 | Cytochrome c oxidase polypeptide 2A, ba3 type | Homologous Superfamily |
Membrane Protein Annotation: PDBTM PDBTM Database Homepage
Chains | External Link | Comment |
---|---|---|
PDBTM | Annotated as membrane protein by PDBTM |
Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage
Chains | External Link | Comment |
---|---|---|
MemProtMD | Annotated as membrane protein by MemProtMD |
Membrane Protein Annotation: mpstruc mpstruc Database Homepage
Chains | Resource Link | Group | Subgroup | Protein |
---|---|---|---|---|
mpstruc | TRANSMEMBRANE PROTEINS: ALPHA-HELICAL | Electron Transport Chain Complexes: Complex IV (Cytochrome C Oxidase) | Cytochrome ba3 |
Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage
Chains | Enzyme Name | Description | Catalytic Residues |
---|---|---|---|
cytochrome-c oxidase (BA3 type) M-CSA #735 | Cytochrome c oxidase (COX) is a multi-unit, membrane-bound enzyme, reducing molecular oxygen to water, coupling this to the creation of a proton and charge gradient across the membrane that is essential to respiratory pathways in mitochondria and aerobic bacteria. The exact catalytic mechanisms are not definitely known, and different COXs may or may not work via subtly different mechanisms, or via different combinations of several possible pathways. The ba3-type COX fromThermus thermophilus is a two subunit oxidase and expressed under limited oxygen supply; it shows similarity to archaeal oxidases (SoxB type) rather than most other eubacterial oxidases (SoxM type). Compared to other COXs it has reduced proton pumping efficiency. | Defined by 9 residues: HIS:A-233TYR:A-237HIS:A-384PHE:A-385HIS:A-386ARG:A-449ARG:A-450PHE:B-86PHE:B-88 | EC: 1.9.3.1 (PDB Primary Data) |