6RKW

CryoEM structure of the complete E. coli DNA Gyrase complex bound to a 130 bp DNA duplex

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0003677	molecular_function	DNA binding
A	0003916	molecular_function	DNA topoisomerase activity
A	0003918	molecular_function	DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity
A	0005515	molecular_function	protein binding
A	0005524	molecular_function	ATP binding
A	0005694	cellular_component	chromosome
A	0005737	cellular_component	cytoplasm
A	0005829	cellular_component	cytosol
A	0006259	biological_process	DNA metabolic process
A	0006261	biological_process	DNA-templated DNA replication
A	0006265	biological_process	DNA topological change
A	0006351	biological_process	DNA-templated transcription
A	0008094	molecular_function	ATP-dependent activity, acting on DNA
A	0009330	cellular_component	DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex
A	0009410	biological_process	response to xenobiotic stimulus
A	0016020	cellular_component	membrane
A	0034335	molecular_function	DNA negative supercoiling activity
A	0042802	molecular_function	identical protein binding
A	0046677	biological_process	response to antibiotic
A	0051276	biological_process	chromosome organization
A	2000104	biological_process	negative regulation of DNA-templated DNA replication
B	0003677	molecular_function	DNA binding
B	0003916	molecular_function	DNA topoisomerase activity
B	0003918	molecular_function	DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity
B	0005515	molecular_function	protein binding
B	0005524	molecular_function	ATP binding
B	0005694	cellular_component	chromosome
B	0005737	cellular_component	cytoplasm
B	0005829	cellular_component	cytosol
B	0006261	biological_process	DNA-templated DNA replication
B	0006265	biological_process	DNA topological change
B	0006351	biological_process	DNA-templated transcription
B	0008094	molecular_function	ATP-dependent activity, acting on DNA
B	0009330	cellular_component	DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex
B	0009410	biological_process	response to xenobiotic stimulus
B	0034335	molecular_function	DNA negative supercoiling activity
B	0046677	biological_process	response to antibiotic
B	0046872	molecular_function	metal ion binding
B	0051276	biological_process	chromosome organization
C	0003677	molecular_function	DNA binding
C	0003916	molecular_function	DNA topoisomerase activity
C	0003918	molecular_function	DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity
C	0005515	molecular_function	protein binding
C	0005524	molecular_function	ATP binding
C	0005694	cellular_component	chromosome
C	0005737	cellular_component	cytoplasm
C	0005829	cellular_component	cytosol
C	0006259	biological_process	DNA metabolic process
C	0006261	biological_process	DNA-templated DNA replication
C	0006265	biological_process	DNA topological change
C	0006351	biological_process	DNA-templated transcription
C	0008094	molecular_function	ATP-dependent activity, acting on DNA
C	0009330	cellular_component	DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex
C	0009410	biological_process	response to xenobiotic stimulus
C	0016020	cellular_component	membrane
C	0034335	molecular_function	DNA negative supercoiling activity
C	0042802	molecular_function	identical protein binding
C	0046677	biological_process	response to antibiotic
C	0051276	biological_process	chromosome organization
C	2000104	biological_process	negative regulation of DNA-templated DNA replication
D	0003677	molecular_function	DNA binding
D	0003916	molecular_function	DNA topoisomerase activity
D	0003918	molecular_function	DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity
D	0005515	molecular_function	protein binding
D	0005524	molecular_function	ATP binding
D	0005694	cellular_component	chromosome
D	0005737	cellular_component	cytoplasm
D	0005829	cellular_component	cytosol
D	0006261	biological_process	DNA-templated DNA replication
D	0006265	biological_process	DNA topological change
D	0006351	biological_process	DNA-templated transcription
D	0008094	molecular_function	ATP-dependent activity, acting on DNA
D	0009330	cellular_component	DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex
D	0009410	biological_process	response to xenobiotic stimulus
D	0034335	molecular_function	DNA negative supercoiling activity
D	0046677	biological_process	response to antibiotic
D	0046872	molecular_function	metal ion binding
D	0051276	biological_process	chromosome organization

Functional Information from PDB Data

site_id	AC1
Number of Residues	18
Details	binding site for residue ANP B 901

Chain	Residue
B	GLU42
B	GLY114
B	LEU115
B	HIS116
B	GLY117
B	VAL118
B	GLY119
B	VAL120
B	GLN335
D	ILE10
B	ASN46
B	ILE78
B	ILE94
B	ALA100
B	GLY101
B	GLY102
B	LYS103
B	TYR109

---

site_id	AC2
Number of Residues	19
Details	binding site for residue ANP D 901

Chain	Residue
B	TYR5
D	GLU42
D	ASN46
D	ALA47
D	GLU50
D	ASP73
D	ILE78
D	ILE94
D	ALA100
D	GLY102
D	LYS103
D	TYR109
D	GLY114
D	LEU115
D	HIS116
D	GLY117
D	VAL118
D	GLY119
D	VAL120

---

site_id	AC3
Number of Residues	10
Details	binding site for residue JHN G 101

Chain	Residue
A	ALA67
A	ASP82
A	MET120
C	ALA67
C	ASP82
C	MET120
G	DT2
G	DA3
H	DT2
H	DA3

---

Functional Information from PROSITE/UniProt

site_id	PS00177
Number of Residues	9
Details	TOPOISOMERASE_II DNA topoisomerase II signature. LVEGDSAGG

Chain	Residue	Details
B	LEU422-GLY430

---

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	2
Details	ACT_SITE: Proton acceptor (ATPase activity) => ECO:0000305|PubMed:10734094, ECO:0000305|PubMed:8248233

Chain	Residue	Details
B	GLU42
D	GLU42

---

site_id	SWS_FT_FI2
Number of Residues	2
Details	BINDING: BINDING => ECO:0000269|PubMed:25202966, ECO:0000269|PubMed:25849408, ECO:0000305|PubMed:10734094

Chain	Residue	Details
B	TYR5
D	TYR5

---

site_id	SWS_FT_FI3
Number of Residues	10
Details	BINDING: BINDING => ECO:0000269|PubMed:10734094, ECO:0000269|PubMed:25202966, ECO:0000269|PubMed:25849408

Chain	Residue	Details
B	ASN46
D	LEU115
B	ASP73
B	GLY102
B	TYR109
B	LEU115
D	ASN46
D	ASP73
D	GLY102
D	TYR109

---

site_id	SWS_FT_FI4
Number of Residues	14
Details	BINDING: BINDING => ECO:0000269|PubMed:25849408

Chain	Residue	Details
B	ILE94
D	ALA100
D	LYS103
D	ASP105
D	GLY117
D	SER121
B	VAL97
B	ALA100
B	LYS103
B	ASP105
B	GLY117
B	SER121
D	ILE94
D	VAL97

---

site_id	SWS_FT_FI5
Number of Residues	2
Details	BINDING: BINDING => ECO:0000269|PubMed:10734094, ECO:0000269|PubMed:25849408

Chain	Residue	Details
B	GLN335
D	GLN335

---

site_id	SWS_FT_FI6
Number of Residues	6
Details	BINDING: BINDING => ECO:0000255|HAMAP-Rule:MF_01898, ECO:0000305|PubMed:12051843, ECO:0000305|PubMed:18642932

Chain	Residue	Details
B	GLU424
B	ASP498
B	ASP500
D	GLU424
D	ASP498
D	ASP500

---

site_id	SWS_FT_FI7
Number of Residues	2
Details	SITE: Transition state stabilizer => ECO:0000305|PubMed:9657678

Chain	Residue	Details
B	LYS337
D	LYS337

---

site_id	SWS_FT_FI8
Number of Residues	4
Details	SITE: Interaction with DNA => ECO:0000255|HAMAP-Rule:MF_01898

Chain	Residue	Details
B	LYS449
B	ASN452
D	LYS449
D	ASN452

---

Catalytic Information from CSA

site_id	MCSA1
Number of Residues	3
Details	M-CSA 745

Chain	Residue	Details
A	ARG32	electrostatic stabiliser
A	HIS78	proton acceptor
A	TYR122	metal ligand, nucleofuge, nucleophile, proton acceptor, proton donor

---

site_id	MCSA2
Number of Residues	3
Details	M-CSA 745

Chain	Residue	Details
C	ARG32	electrostatic stabiliser
C	HIS78	proton acceptor
C	TYR122	metal ligand, nucleofuge, nucleophile, proton acceptor, proton donor

---