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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1ehka_	Membrane and cell surface proteins and peptides	Cytochrome c oxidase subunit I-like	Cytochrome c oxidase subunit I-like	Cytochrome c oxidase subunit I-like	Bacterial ba3 type cytochrome c oxidase subunit I	(Thermus thermophilus HB8 ) [TaxId: 300852 ],	SCOPe (2.08)
B	d1ehkb1	All beta proteins	Cupredoxin-like	Cupredoxins	Periplasmic domain of cytochrome c oxidase subunit II	Cytochrome c oxidase	(Thermus thermophilus HB8 ) [TaxId: 300852 ],	SCOPe (2.08)
B	d1ehkb2	Membrane and cell surface proteins and peptides	Transmembrane helix hairpin	Cytochrome c oxidase subunit II-like, transmembrane region	Cytochrome c oxidase subunit II-like, transmembrane region	Bacterial ba3 type cytochrome c oxidase subunit II	(Thermus thermophilus HB8 ) [TaxId: 300852 ],	SCOPe (2.08)
C	d1ehkc_	Membrane and cell surface proteins and peptides	Single transmembrane helix	Bacterial ba3 type cytochrome c oxidase subunit IIa	Bacterial ba3 type cytochrome c oxidase subunit IIa	Bacterial ba3 type cytochrome c oxidase subunit IIa	(Thermus thermophilus HB8 ) [TaxId: 300852 ],	SCOPe (2.08)

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
A	PF00115	Cytochrome C and Quinol oxidase polypeptide I (COX1)	Cytochrome C and Quinol oxidase polypeptide I	-	Family
B	PF00116	Cytochrome C oxidase subunit II, periplasmic domain (COX2)	Cytochrome C oxidase subunit II, periplasmic domain	-	Domain
B	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
C	PF08113	Cytochrome c oxidase subunit IIa family (CoxIIa)	Cytochrome c oxidase subunit IIa family	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	BA3-TYPE CYTOCHROME-C OXIDASE	monoatomic cation transmembrane transporter activity proton transmembrane transporter activity primary active transmembrane transporter activity cytochrome-c oxidase activity electron transfer activity active monoatomic ion transmembrane transporter activity oxidoreductase activity oxidoreduction-driven active transmembrane transporter activity active transmembrane transporter activity inorganic molecular entity transmembrane transporter activity oxidoreductase activity, acting on a heme group of donors inorganic cation transmembrane transporter activity monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity monoatomic cation transmembrane transporter activity proton transmembrane transporter activity primary active transmembrane transporter activity cytochrome-c oxidase activity electron transfer activity active monoatomic ion transmembrane transporter activity oxidoreductase activity oxidoreduction-driven active transmembrane transporter activity active transmembrane transporter activity inorganic molecular entity transmembrane transporter activity oxidoreductase activity, acting on a heme group of donors inorganic cation transmembrane transporter activity monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity catalytic activity binding organic cyclic compound binding tetrapyrrole binding heme binding cation binding ion binding metal ion binding small molecule binding	aerobic respiration cellular respiration oxidative phosphorylation energy derivation by oxidation of organic compounds cellular metabolic process metabolic process cellular process generation of precursor metabolites and energy	cell periphery plasma membrane membrane cellular anatomical entity respirasome
B	BA3-TYPE CYTOCHROME-C OXIDASE	cation binding transition metal ion binding copper ion binding ion binding binding metal ion binding small molecule binding monoatomic cation transmembrane transporter activity proton transmembrane transporter activity primary active transmembrane transporter activity cytochrome-c oxidase activity electron transfer activity active monoatomic ion transmembrane transporter activity oxidoreductase activity cation binding transition metal ion binding copper ion binding ion binding binding metal ion binding small molecule binding monoatomic cation transmembrane transporter activity proton transmembrane transporter activity primary active transmembrane transporter activity cytochrome-c oxidase activity electron transfer activity active monoatomic ion transmembrane transporter activity oxidoreductase activity oxidoreduction-driven active transmembrane transporter activity active transmembrane transporter activity inorganic molecular entity transmembrane transporter activity oxidoreductase activity, acting on a heme group of donors inorganic cation transmembrane transporter activity monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity catalytic activity	-	cell periphery plasma membrane membrane cellular anatomical entity respirasome
C	BA3-TYPE CYTOCHROME-C OXIDASE	monoatomic cation transmembrane transporter activity proton transmembrane transporter activity primary active transmembrane transporter activity cytochrome-c oxidase activity electron transfer activity active monoatomic ion transmembrane transporter activity oxidoreductase activity oxidoreduction-driven active transmembrane transporter activity active transmembrane transporter activity inorganic molecular entity transmembrane transporter activity oxidoreductase activity, acting on a heme group of donors inorganic cation transmembrane transporter activity monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity monoatomic cation transmembrane transporter activity proton transmembrane transporter activity primary active transmembrane transporter activity cytochrome-c oxidase activity electron transfer activity active monoatomic ion transmembrane transporter activity oxidoreductase activity oxidoreduction-driven active transmembrane transporter activity active transmembrane transporter activity inorganic molecular entity transmembrane transporter activity oxidoreductase activity, acting on a heme group of donors inorganic cation transmembrane transporter activity monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity catalytic activity	-	cell periphery plasma membrane membrane cellular anatomical entity respirasome

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR036927	Cytochrome c oxidase-like, subunit I superfamily	Homologous Superfamily
A	IPR000883	Cytochrome c oxidase subunit I	Family
A	IPR023615	Cytochrome c oxidase, subunit I, copper-binding site	Binding Site
A	IPR023616	Cytochrome c oxidase-like, subunit I domain	Domain
A	IPR033943	Ba3-like heme-copper oxidase subunit I	Family
B	IPR015209	Cytochrome C oxidase subunit IIa, transmembrane domain	Domain
B	IPR002429	Cytochrome c oxidase subunit II-like C-terminal	Domain
B	IPR036257	Cytochrome C oxidase subunit II, transmembrane domain superfamily	Homologous Superfamily
B	IPR008972	Cupredoxin	Homologous Superfamily
B	IPR001505	Copper centre Cu(A)	Binding Site
B	IPR034214	Ba3-like heme-copper oxidase subunit II, C-terminal	Domain
C	IPR012538	Cytochrome c oxidase polypeptide 2A	Family
C	IPR036246	Cytochrome c oxidase polypeptide 2A, ba3 type	Homologous Superfamily

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

Chains	External Link	Comment
A, B, C	PDBTM	Annotated as membrane protein by PDBTM

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage

Chains	External Link	Comment
A, B, C	MemProtMD	Annotated as membrane protein by MemProtMD

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A, B, C	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
A, B	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 \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 1.9.3.1 (PDB Primary Data) Search M-CSA Motif + EC 1.9.3.1

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.