6WTI

The Cryo-EM structure of the ubiquinol oxidase from Escherichia coli

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0004129	molecular_function	cytochrome-c oxidase activity
A	0005507	molecular_function	copper ion binding
A	0005515	molecular_function	protein binding
A	0005886	cellular_component	plasma membrane
A	0009055	molecular_function	electron transfer activity
A	0009060	biological_process	aerobic respiration
A	0009319	cellular_component	cytochrome o ubiquinol oxidase complex
A	0009486	molecular_function	cytochrome bo3 ubiquinol oxidase activity
A	0015078	molecular_function	proton transmembrane transporter activity
A	0015453	molecular_function	oxidoreduction-driven active transmembrane transporter activity
A	0015990	biological_process	electron transport coupled proton transport
A	0016020	cellular_component	membrane
A	0016682	molecular_function	oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor
A	0019646	biological_process	aerobic electron transport chain
A	0020037	molecular_function	heme binding
A	0022904	biological_process	respiratory electron transport chain
A	0046872	molecular_function	metal ion binding
A	0048039	molecular_function	ubiquinone binding
A	0070469	cellular_component	respirasome
A	1902600	biological_process	proton transmembrane transport
B	0004129	molecular_function	cytochrome-c oxidase activity
B	0005507	molecular_function	copper ion binding
B	0009486	molecular_function	cytochrome bo3 ubiquinol oxidase activity
B	0016020	cellular_component	membrane
B	0016682	molecular_function	oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor
B	0022900	biological_process	electron transport chain
C	0004129	molecular_function	cytochrome-c oxidase activity
C	0005515	molecular_function	protein binding
C	0005886	cellular_component	plasma membrane
C	0009055	molecular_function	electron transfer activity
C	0009060	biological_process	aerobic respiration
C	0009319	cellular_component	cytochrome o ubiquinol oxidase complex
C	0009486	molecular_function	cytochrome bo3 ubiquinol oxidase activity
C	0015078	molecular_function	proton transmembrane transporter activity
C	0015453	molecular_function	oxidoreduction-driven active transmembrane transporter activity
C	0015990	biological_process	electron transport coupled proton transport
C	0016020	cellular_component	membrane
C	0016491	molecular_function	oxidoreductase activity
C	0019646	biological_process	aerobic electron transport chain
C	0022904	biological_process	respiratory electron transport chain
D	0005515	molecular_function	protein binding
D	0005886	cellular_component	plasma membrane
D	0009055	molecular_function	electron transfer activity
D	0009060	biological_process	aerobic respiration
D	0009319	cellular_component	cytochrome o ubiquinol oxidase complex
D	0009486	molecular_function	cytochrome bo3 ubiquinol oxidase activity
D	0015078	molecular_function	proton transmembrane transporter activity
D	0015453	molecular_function	oxidoreduction-driven active transmembrane transporter activity
D	0015990	biological_process	electron transport coupled proton transport
D	0016020	cellular_component	membrane
D	0016491	molecular_function	oxidoreductase activity
D	0019646	biological_process	aerobic electron transport chain

Functional Information from PDB Data

site_id	AC1
Number of Residues	15
Details	binding site for residue HEM A 1001

Chain	Residue
A	PHE73
A	HIS421
A	ILE424
A	VAL429
A	PHE468
A	ARG481
A	ARG482
A	MET79
A	PHE103
A	HIS106
A	GLY107
A	MET110
A	ILE111
A	TRP170
A	ILE417

---

site_id	AC2
Number of Residues	26
Details	binding site for residue HEO A 1002

Chain	Residue
A	TRP170
A	VAL287
A	TYR288
A	ILE291
A	HIS333
A	HIS334
A	ILE355
A	ALA356
A	THR359
A	GLY395
A	GLY398
A	VAL399
A	LEU401
A	ALA402
A	ASP407
A	HIS411
A	LEU416
A	HIS419
A	PHE420
A	VAL423
A	ILE424
A	ARG481
B	MET51
B	VAL54
B	VAL55
B	ILE100

---

site_id	AC3
Number of Residues	3
Details	binding site for residue CU A 1003

Chain	Residue
A	HIS284
A	HIS333
A	HIS334

---

site_id	AC4
Number of Residues	13
Details	binding site for residue UQ8 A 1004

Chain	Residue
A	ILE16
A	VAL17
A	THR20
A	LEU70
A	ARG71
A	ALA74
A	ASP75
A	MET78
A	HIS98
A	GLN101
A	ILE102
A	ASN157
A	LEU160

---

site_id	AC5
Number of Residues	13
Details	binding site for residue 3PE A 1005

Chain	Residue
A	PHE138
A	PRO139
A	PHE140
A	LEU141
A	GLN195
A	PHE602
A	TRP625
A	LYS628
C	LYS25
C	GLY28
C	PHE29
C	TYR32
C	3PE401

---

site_id	AC6
Number of Residues	3
Details	binding site for residue 3PE A 1006

Chain	Residue
A	ALA251
A	TRP611
A	3PE1007

---

site_id	AC7
Number of Residues	1
Details	binding site for residue 3PE A 1007

Chain	Residue
A	3PE1006

---

site_id	AC8
Number of Residues	9
Details	binding site for residue U9V A 1008

Chain	Residue
A	TRP48
A	ILE62
A	ILE63
A	VAL150
A	TRP439
A	TRP440
A	PHE444
A	ARG523
A	3PE1009

---

site_id	AC9
Number of Residues	4
Details	binding site for residue 3PE A 1009

Chain	Residue
A	TYR517
A	ARG521
A	ARG523
A	U9V1008

---

site_id	AD1
Number of Residues	4
Details	binding site for residue 3PE B 401

Chain	Residue
A	ILE350
A	ILE354
B	ILE101
B	TRP108

---

site_id	AD2
Number of Residues	11
Details	binding site for residue 3PE C 401

Chain	Residue
C	SER152
C	TRP156
C	ARG176
A	VAL248
A	ALA251
A	PHE618
A	TRP625
A	3PE1005
C	LYS25
C	TYR32
C	HIS149

---

site_id	AD3
Number of Residues	6
Details	binding site for residue 3PE C 402

Chain	Residue
C	PHE120
C	HIS121
C	ILE124
C	ALA141
C	GLY144
C	THR145

---

site_id	AD4
Number of Residues	6
Details	binding site for residue 3PE D 201

Chain	Residue
C	PHE44
C	ALA48
C	MET201
D	VAL85
D	ILE88
D	VAL93

---

site_id	AD5
Number of Residues	4
Details	binding site for residue 3PE D 202

Chain	Residue
A	MET222
A	TRP230
A	ILE240
D	PHE83

---

Functional Information from PROSITE/UniProt

site_id	PS00077
Number of Residues	55
Details	COX1_CUB Heme-copper oxidase catalytic subunit, copper B binding region signature. WAWGHPeVyililpvfgvfseiaatfsrkrlfgytslvwatvcitvlsfivwl..HH

Chain	Residue	Details
A	TRP280-HIS334

---

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	31
Details	TOPO_DOM: Cytoplasmic => ECO:0000305

Chain	Residue	Details
D	MET1-THR17
D	PHE65-ALA80
C	VAL162-TRP184
A	THR261-GLY270
A	SER327-ALA340
A	LEU410-ASN412
A	GLY478-PRO489
A	ILE607-LEU613

---

site_id	SWS_FT_FI2
Number of Residues	54
Details	TRANSMEM: Helical => ECO:0000305

Chain	Residue	Details
D	TYR18-VAL36
D	ILE46-CYS64
D	PHE81-MET99
C	VAL143-MET161
C	HIS185-ALA203

---

site_id	SWS_FT_FI3
Number of Residues	17
Details	TOPO_DOM: Periplasmic => ECO:0000305

Chain	Residue	Details
D	MET37-VAL45
D	TRP100-HIS109
C	MET204
A	LYS308-PHE311
A	MET370-PHE377
A	PHE446-LEU448
A	ASP522-LYS587
A	ASP633-ASN663

---

site_id	SWS_FT_FI4
Number of Residues	1
Details	LIPID: S-diacylglycerol cysteine => ECO:0000255|PROSITE-ProRule:PRU00303

Chain	Residue	Details
B	CYS25

---

site_id	SWS_FT_FI5
Number of Residues	36
Details	TRANSMEM: Helical; Name=III

Chain	Residue	Details
A	PRO96-GLY132

---

site_id	SWS_FT_FI6
Number of Residues	23
Details	TRANSMEM: Helical; Name=IV

Chain	Residue	Details
A	PHE138-GLY161

---

site_id	SWS_FT_FI7
Number of Residues	30
Details	TRANSMEM: Helical; Name=V

Chain	Residue	Details
A	VAL185-MET215

---

site_id	SWS_FT_FI8
Number of Residues	35
Details	TRANSMEM: Helical; Name=VI

Chain	Residue	Details
A	MET225-GLY260

---

site_id	SWS_FT_FI9
Number of Residues	36
Details	TRANSMEM: Helical; Name=VII

Chain	Residue	Details
A	ASN271-ARG307

---

site_id	SWS_FT_FI10
Number of Residues	14
Details	TRANSMEM: Helical; Name=VIII

Chain	Residue	Details
A	GLY312-LEU326

---

site_id	SWS_FT_FI11
Number of Residues	28
Details	TRANSMEM: Helical; Name=IX

Chain	Residue	Details
A	GLY341-THR369

---

site_id	SWS_FT_FI12
Number of Residues	31
Details	TRANSMEM: Helical; Name=X

Chain	Residue	Details
A	HIS378-VAL409

---

site_id	SWS_FT_FI13
Number of Residues	32
Details	TRANSMEM: Helical; Name=XI

Chain	Residue	Details
A	SER413-GLY445

---

site_id	SWS_FT_FI14
Number of Residues	28
Details	TRANSMEM: Helical; Name=XII

Chain	Residue	Details
A	ASN449-MET477

---

site_id	SWS_FT_FI15
Number of Residues	31
Details	TRANSMEM: Helical; Name=XIII

Chain	Residue	Details
A	GLN490-ARG521

---

site_id	SWS_FT_FI16
Number of Residues	18
Details	TRANSMEM: Helical; Name=XIV

Chain	Residue	Details
A	ASN588-MET606

---

site_id	SWS_FT_FI17
Number of Residues	18
Details	TRANSMEM: Helical; Name=XV

Chain	Residue	Details
A	ALA614-GLU632

---

site_id	SWS_FT_FI18
Number of Residues	1
Details	BINDING: BINDING => ECO:0000269|PubMed:33408407, ECO:0000269|PubMed:34417297, ECO:0007744|PDB:6WTI, ECO:0007744|PDB:7CUB, ECO:0007744|PDB:7CUW, ECO:0007744|PDB:7N9Z

Chain	Residue	Details
A	ARG71

---

site_id	SWS_FT_FI19
Number of Residues	1
Details	BINDING: BINDING => ECO:0000269|PubMed:34417297, ECO:0007744|PDB:7CUW

Chain	Residue	Details
A	ASP75

---

site_id	SWS_FT_FI20
Number of Residues	1
Details	BINDING: BINDING => ECO:0000269|PubMed:34417297, ECO:0007744|PDB:7CUB, ECO:0007744|PDB:7CUW, ECO:0007744|PDB:7N9Z

Chain	Residue	Details
A	HIS98

---

site_id	SWS_FT_FI21
Number of Residues	3
Details	BINDING: axial binding residue => ECO:0000269|PubMed:11017202, ECO:0000269|PubMed:33408407, ECO:0007744|PDB:1FFT, ECO:0007744|PDB:6WTI

Chain	Residue	Details
A	HIS106
A	HIS419
A	HIS421

---

site_id	SWS_FT_FI22
Number of Residues	1
Details	BINDING: BINDING => ECO:0000269|PubMed:11017202, ECO:0007744|PDB:1FFT

Chain	Residue	Details
A	TRP170

---

site_id	SWS_FT_FI23
Number of Residues	5
Details	BINDING: BINDING => ECO:0000269|PubMed:11017202, ECO:0000269|PubMed:33408407, ECO:0007744|PDB:1FFT, ECO:0007744|PDB:6WTI

Chain	Residue	Details
A	HIS284
A	HIS333
A	HIS334
A	HIS411
A	ARG482

---

site_id	SWS_FT_FI24
Number of Residues	2
Details	BINDING: BINDING => ECO:0000269|PubMed:33408407, ECO:0007744|PDB:6WTI

Chain	Residue	Details
A	TYR288
A	ARG481

---

site_id	SWS_FT_FI25
Number of Residues	2
Details	CROSSLNK: 1'-histidyl-3'-tyrosine (His-Tyr) => ECO:0000269|PubMed:34417297

Chain	Residue	Details
A	HIS284
A	TYR288

---

Catalytic Information from CSA

site_id	MCSA1
Number of Residues	23
Details	M-CSA 714

Chain	Residue	Details
A	TYR61	proton shuttle (general acid/base)
A	THR149	proton shuttle (general acid/base)
A	THR201	proton shuttle (general acid/base)
A	THR204	proton shuttle (general acid/base)
A	THR211	proton shuttle (general acid/base)
A	HIS284	metal ligand, modifies pKa
A	GLU286	proton shuttle (general acid/base)
A	TYR288	electron shuttle, proton shuttle (general acid/base)
A	SER299	proton shuttle (general acid/base)
A	SER315	proton shuttle (general acid/base)
A	THR359	proton shuttle (general acid/base)
A	ARG71	electrostatic stabiliser
A	LYS362	proton shuttle (general acid/base)
A	HIS419	electron shuttle
A	PHE420	electron shuttle
A	HIS421	electron shuttle
A	ASP75	electrostatic stabiliser
A	MET79	electron shuttle
A	PHE103	electron shuttle
A	ASN124	proton shuttle (general acid/base)
A	ASP135	proton shuttle (general acid/base)
A	ASN142	proton shuttle (general acid/base)
A	SER145	proton shuttle (general acid/base)

---