1BHN

NUCLEOSIDE DIPHOSPHATE KINASE ISOFORM A FROM BOVINE RETINA

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000287	molecular_function	magnesium ion binding
A	0003677	molecular_function	DNA binding
A	0004520	molecular_function	DNA endonuclease activity
A	0004536	molecular_function	DNA nuclease activity
A	0004550	molecular_function	nucleoside diphosphate kinase activity
A	0004673	molecular_function	protein histidine kinase activity
A	0004674	molecular_function	protein serine/threonine kinase activity
A	0005634	cellular_component	nucleus
A	0005737	cellular_component	cytoplasm
A	0005739	cellular_component	mitochondrion
A	0005769	cellular_component	early endosome
A	0005829	cellular_component	cytosol
A	0005886	cellular_component	plasma membrane
A	0006183	biological_process	GTP biosynthetic process
A	0006228	biological_process	UTP biosynthetic process
A	0006241	biological_process	CTP biosynthetic process
A	0006308	biological_process	DNA catabolic process
A	0006309	biological_process	apoptotic DNA fragmentation
A	0006720	biological_process	isoprenoid metabolic process
A	0006753	biological_process	nucleoside phosphate metabolic process
A	0008296	molecular_function	3'-5'-DNA exonuclease activity
A	0009132	biological_process	nucleoside diphosphate metabolic process
A	0009142	biological_process	nucleoside triphosphate biosynthetic process
A	0016301	molecular_function	kinase activity
A	0016776	molecular_function	phosphotransferase activity, phosphate group as acceptor
A	0019003	molecular_function	GDP binding
A	0032587	cellular_component	ruffle membrane
A	0034214	biological_process	protein hexamerization
A	0042304	biological_process	regulation of fatty acid biosynthetic process
A	0042802	molecular_function	identical protein binding
A	0043024	molecular_function	ribosomal small subunit binding
A	0043531	molecular_function	ADP binding
A	0046042	biological_process	ITP biosynthetic process
A	0046356	biological_process	acetyl-CoA catabolic process
A	0047887	molecular_function	farnesyl diphosphate kinase activity
A	0050679	biological_process	positive regulation of epithelial cell proliferation
A	0072521	biological_process	purine-containing compound metabolic process
A	0106310	molecular_function	protein serine kinase activity
A	0120225	molecular_function	coenzyme A binding
A	0120226	molecular_function	succinyl-CoA binding
A	1905502	molecular_function	acetyl-CoA binding
B	0000287	molecular_function	magnesium ion binding
B	0003677	molecular_function	DNA binding
B	0004520	molecular_function	DNA endonuclease activity
B	0004536	molecular_function	DNA nuclease activity
B	0004550	molecular_function	nucleoside diphosphate kinase activity
B	0004673	molecular_function	protein histidine kinase activity
B	0004674	molecular_function	protein serine/threonine kinase activity
B	0005634	cellular_component	nucleus
B	0005737	cellular_component	cytoplasm
B	0005739	cellular_component	mitochondrion
B	0005769	cellular_component	early endosome
B	0005829	cellular_component	cytosol
B	0005886	cellular_component	plasma membrane
B	0006183	biological_process	GTP biosynthetic process
B	0006228	biological_process	UTP biosynthetic process
B	0006241	biological_process	CTP biosynthetic process
B	0006308	biological_process	DNA catabolic process
B	0006309	biological_process	apoptotic DNA fragmentation
B	0006720	biological_process	isoprenoid metabolic process
B	0006753	biological_process	nucleoside phosphate metabolic process
B	0008296	molecular_function	3'-5'-DNA exonuclease activity
B	0009132	biological_process	nucleoside diphosphate metabolic process
B	0009142	biological_process	nucleoside triphosphate biosynthetic process
B	0016301	molecular_function	kinase activity
B	0016776	molecular_function	phosphotransferase activity, phosphate group as acceptor
B	0019003	molecular_function	GDP binding
B	0032587	cellular_component	ruffle membrane
B	0034214	biological_process	protein hexamerization
B	0042304	biological_process	regulation of fatty acid biosynthetic process
B	0042802	molecular_function	identical protein binding
B	0043024	molecular_function	ribosomal small subunit binding
B	0043531	molecular_function	ADP binding
B	0046042	biological_process	ITP biosynthetic process
B	0046356	biological_process	acetyl-CoA catabolic process
B	0047887	molecular_function	farnesyl diphosphate kinase activity
B	0050679	biological_process	positive regulation of epithelial cell proliferation
B	0072521	biological_process	purine-containing compound metabolic process
B	0106310	molecular_function	protein serine kinase activity
B	0120225	molecular_function	coenzyme A binding
B	0120226	molecular_function	succinyl-CoA binding
B	1905502	molecular_function	acetyl-CoA binding
C	0000287	molecular_function	magnesium ion binding
C	0003677	molecular_function	DNA binding
C	0004520	molecular_function	DNA endonuclease activity
C	0004536	molecular_function	DNA nuclease activity
C	0004550	molecular_function	nucleoside diphosphate kinase activity
C	0004673	molecular_function	protein histidine kinase activity
C	0004674	molecular_function	protein serine/threonine kinase activity
C	0005634	cellular_component	nucleus
C	0005737	cellular_component	cytoplasm
C	0005739	cellular_component	mitochondrion
C	0005769	cellular_component	early endosome
C	0005829	cellular_component	cytosol
C	0005886	cellular_component	plasma membrane
C	0006183	biological_process	GTP biosynthetic process
C	0006228	biological_process	UTP biosynthetic process
C	0006241	biological_process	CTP biosynthetic process
C	0006308	biological_process	DNA catabolic process
C	0006309	biological_process	apoptotic DNA fragmentation
C	0006720	biological_process	isoprenoid metabolic process
C	0006753	biological_process	nucleoside phosphate metabolic process
C	0008296	molecular_function	3'-5'-DNA exonuclease activity
C	0009132	biological_process	nucleoside diphosphate metabolic process
C	0009142	biological_process	nucleoside triphosphate biosynthetic process
C	0016301	molecular_function	kinase activity
C	0016776	molecular_function	phosphotransferase activity, phosphate group as acceptor
C	0019003	molecular_function	GDP binding
C	0032587	cellular_component	ruffle membrane
C	0034214	biological_process	protein hexamerization
C	0042304	biological_process	regulation of fatty acid biosynthetic process
C	0042802	molecular_function	identical protein binding
C	0043024	molecular_function	ribosomal small subunit binding
C	0043531	molecular_function	ADP binding
C	0046042	biological_process	ITP biosynthetic process
C	0046356	biological_process	acetyl-CoA catabolic process
C	0047887	molecular_function	farnesyl diphosphate kinase activity
C	0050679	biological_process	positive regulation of epithelial cell proliferation
C	0072521	biological_process	purine-containing compound metabolic process
C	0106310	molecular_function	protein serine kinase activity
C	0120225	molecular_function	coenzyme A binding
C	0120226	molecular_function	succinyl-CoA binding
C	1905502	molecular_function	acetyl-CoA binding
D	0000287	molecular_function	magnesium ion binding
D	0003677	molecular_function	DNA binding
D	0004520	molecular_function	DNA endonuclease activity
D	0004536	molecular_function	DNA nuclease activity
D	0004550	molecular_function	nucleoside diphosphate kinase activity
D	0004673	molecular_function	protein histidine kinase activity
D	0004674	molecular_function	protein serine/threonine kinase activity
D	0005634	cellular_component	nucleus
D	0005737	cellular_component	cytoplasm
D	0005739	cellular_component	mitochondrion
D	0005769	cellular_component	early endosome
D	0005829	cellular_component	cytosol
D	0005886	cellular_component	plasma membrane
D	0006183	biological_process	GTP biosynthetic process
D	0006228	biological_process	UTP biosynthetic process
D	0006241	biological_process	CTP biosynthetic process
D	0006308	biological_process	DNA catabolic process
D	0006309	biological_process	apoptotic DNA fragmentation
D	0006720	biological_process	isoprenoid metabolic process
D	0006753	biological_process	nucleoside phosphate metabolic process
D	0008296	molecular_function	3'-5'-DNA exonuclease activity
D	0009132	biological_process	nucleoside diphosphate metabolic process
D	0009142	biological_process	nucleoside triphosphate biosynthetic process
D	0016301	molecular_function	kinase activity
D	0016776	molecular_function	phosphotransferase activity, phosphate group as acceptor
D	0019003	molecular_function	GDP binding
D	0032587	cellular_component	ruffle membrane
D	0034214	biological_process	protein hexamerization
D	0042304	biological_process	regulation of fatty acid biosynthetic process
D	0042802	molecular_function	identical protein binding
D	0043024	molecular_function	ribosomal small subunit binding
D	0043531	molecular_function	ADP binding
D	0046042	biological_process	ITP biosynthetic process
D	0046356	biological_process	acetyl-CoA catabolic process
D	0047887	molecular_function	farnesyl diphosphate kinase activity
D	0050679	biological_process	positive regulation of epithelial cell proliferation
D	0072521	biological_process	purine-containing compound metabolic process
D	0106310	molecular_function	protein serine kinase activity
D	0120225	molecular_function	coenzyme A binding
D	0120226	molecular_function	succinyl-CoA binding
D	1905502	molecular_function	acetyl-CoA binding
E	0000287	molecular_function	magnesium ion binding
E	0003677	molecular_function	DNA binding
E	0004520	molecular_function	DNA endonuclease activity
E	0004536	molecular_function	DNA nuclease activity
E	0004550	molecular_function	nucleoside diphosphate kinase activity
E	0004673	molecular_function	protein histidine kinase activity
E	0004674	molecular_function	protein serine/threonine kinase activity
E	0005634	cellular_component	nucleus
E	0005737	cellular_component	cytoplasm
E	0005739	cellular_component	mitochondrion
E	0005769	cellular_component	early endosome
E	0005829	cellular_component	cytosol
E	0005886	cellular_component	plasma membrane
E	0006183	biological_process	GTP biosynthetic process
E	0006228	biological_process	UTP biosynthetic process
E	0006241	biological_process	CTP biosynthetic process
E	0006308	biological_process	DNA catabolic process
E	0006309	biological_process	apoptotic DNA fragmentation
E	0006720	biological_process	isoprenoid metabolic process
E	0006753	biological_process	nucleoside phosphate metabolic process
E	0008296	molecular_function	3'-5'-DNA exonuclease activity
E	0009132	biological_process	nucleoside diphosphate metabolic process
E	0009142	biological_process	nucleoside triphosphate biosynthetic process
E	0016301	molecular_function	kinase activity
E	0016776	molecular_function	phosphotransferase activity, phosphate group as acceptor
E	0019003	molecular_function	GDP binding
E	0032587	cellular_component	ruffle membrane
E	0034214	biological_process	protein hexamerization
E	0042304	biological_process	regulation of fatty acid biosynthetic process
E	0042802	molecular_function	identical protein binding
E	0043024	molecular_function	ribosomal small subunit binding
E	0043531	molecular_function	ADP binding
E	0046042	biological_process	ITP biosynthetic process
E	0046356	biological_process	acetyl-CoA catabolic process
E	0047887	molecular_function	farnesyl diphosphate kinase activity
E	0050679	biological_process	positive regulation of epithelial cell proliferation
E	0072521	biological_process	purine-containing compound metabolic process
E	0106310	molecular_function	protein serine kinase activity
E	0120225	molecular_function	coenzyme A binding
E	0120226	molecular_function	succinyl-CoA binding
E	1905502	molecular_function	acetyl-CoA binding
F	0000287	molecular_function	magnesium ion binding
F	0003677	molecular_function	DNA binding
F	0004520	molecular_function	DNA endonuclease activity
F	0004536	molecular_function	DNA nuclease activity
F	0004550	molecular_function	nucleoside diphosphate kinase activity
F	0004673	molecular_function	protein histidine kinase activity
F	0004674	molecular_function	protein serine/threonine kinase activity
F	0005634	cellular_component	nucleus
F	0005737	cellular_component	cytoplasm
F	0005739	cellular_component	mitochondrion
F	0005769	cellular_component	early endosome
F	0005829	cellular_component	cytosol
F	0005886	cellular_component	plasma membrane
F	0006183	biological_process	GTP biosynthetic process
F	0006228	biological_process	UTP biosynthetic process
F	0006241	biological_process	CTP biosynthetic process
F	0006308	biological_process	DNA catabolic process
F	0006309	biological_process	apoptotic DNA fragmentation
F	0006720	biological_process	isoprenoid metabolic process
F	0006753	biological_process	nucleoside phosphate metabolic process
F	0008296	molecular_function	3'-5'-DNA exonuclease activity
F	0009132	biological_process	nucleoside diphosphate metabolic process
F	0009142	biological_process	nucleoside triphosphate biosynthetic process
F	0016301	molecular_function	kinase activity
F	0016776	molecular_function	phosphotransferase activity, phosphate group as acceptor
F	0019003	molecular_function	GDP binding
F	0032587	cellular_component	ruffle membrane
F	0034214	biological_process	protein hexamerization
F	0042304	biological_process	regulation of fatty acid biosynthetic process
F	0042802	molecular_function	identical protein binding
F	0043024	molecular_function	ribosomal small subunit binding
F	0043531	molecular_function	ADP binding
F	0046042	biological_process	ITP biosynthetic process
F	0046356	biological_process	acetyl-CoA catabolic process
F	0047887	molecular_function	farnesyl diphosphate kinase activity
F	0050679	biological_process	positive regulation of epithelial cell proliferation
F	0072521	biological_process	purine-containing compound metabolic process
F	0106310	molecular_function	protein serine kinase activity
F	0120225	molecular_function	coenzyme A binding
F	0120226	molecular_function	succinyl-CoA binding
F	1905502	molecular_function	acetyl-CoA binding

Functional Information from PDB Data

site_id	A
Number of Residues	6
Details	C-GMP AND GDP ARE FOUND (EACH WITH HALF OCCUPANCY) IN THE NUCLEOTIDE BINDING SITE.

Chain	Residue
A	LYS12
A	TYR52
A	VAL112
A	ASN115
A	HIS118
A	GLU152

---

site_id	AC1
Number of Residues	9
Details	BINDING SITE FOR RESIDUE 35G A 160

Chain	Residue
A	LYS12
A	TYR52
A	PHE60
A	ARG105
A	VAL112
A	ASN115
A	HIS118
A	GDP161
A	HOH502

---

site_id	AC2
Number of Residues	12
Details	BINDING SITE FOR RESIDUE GDP A 161

Chain	Residue
A	LYS12
A	PHE60
A	ARG88
A	THR94
A	ARG105
A	VAL112
A	GLY113
A	ASN115
A	HIS118
A	35G160
A	HOH502
B	GLU152

---

site_id	AC3
Number of Residues	11
Details	BINDING SITE FOR RESIDUE 35G B 160

Chain	Residue
B	LYS12
B	TYR52
B	PHE60
B	ARG105
B	VAL112
B	ASN115
B	HIS118
B	GDP161
B	HOH372
B	HOH503
C	GLU152

---

site_id	AC4
Number of Residues	15
Details	BINDING SITE FOR RESIDUE GDP B 161

Chain	Residue
B	LYS12
B	TYR52
B	LEU55
B	PHE60
B	LEU64
B	ARG88
B	VAL112
B	ASN115
B	HIS118
B	GLY119
B	35G160
B	HOH204
B	HOH372
B	HOH503
C	GLU152

---

site_id	AC5
Number of Residues	10
Details	BINDING SITE FOR RESIDUE 35G C 160

Chain	Residue
C	LYS12
C	TYR52
C	PHE60
C	LEU64
C	THR94
C	ASN115
C	HIS118
C	GDP161
C	HOH238
C	HOH505

---

site_id	AC6
Number of Residues	12
Details	BINDING SITE FOR RESIDUE GDP C 161

Chain	Residue
C	ARG105
C	VAL112
C	ASN115
C	35G160
C	HOH497
C	HOH505
A	GLU152
C	LYS12
C	PHE60
C	LEU64
C	ARG88
C	THR94

---

site_id	AC7
Number of Residues	9
Details	BINDING SITE FOR RESIDUE 35G D 160

Chain	Residue
D	LYS12
D	TYR52
D	PHE60
D	LEU64
D	VAL112
D	GLY113
D	ASN115
D	HIS118
D	GDP161

---

site_id	AC8
Number of Residues	12
Details	BINDING SITE FOR RESIDUE GDP D 161

Chain	Residue
D	LYS12
D	LEU55
D	PHE60
D	LEU64
D	ARG88
D	THR94
D	ARG105
D	VAL112
D	ASN115
D	35G160
D	HOH285
D	HOH507

---

site_id	AC9
Number of Residues	8
Details	BINDING SITE FOR RESIDUE 35G E 160

Chain	Residue
E	LYS12
E	PHE60
E	THR94
E	ASN115
E	HIS118
E	GDP161
E	HOH221
F	GLU152

---

site_id	B
Number of Residues	6
Details	C-GMP AND GDP ARE FOUND (EACH WITH HALF OCCUPANCY) IN THE NUCLEOTIDE BINDING SITE.

Chain	Residue
B	ASN115
B	HIS118
B	GLU152
B	LYS12
B	TYR52
B	VAL112

---

site_id	BC1
Number of Residues	11
Details	BINDING SITE FOR RESIDUE GDP E 161

Chain	Residue
E	LYS12
E	PHE60
E	LEU64
E	ARG88
E	THR94
E	VAL112
E	ASN115
E	35G160
E	HOH221
E	HOH266
F	GLU152

---

site_id	BC2
Number of Residues	12
Details	BINDING SITE FOR RESIDUE 35G F 160

Chain	Residue
D	GLU152
F	LYS12
F	TYR52
F	PHE60
F	ARG105
F	VAL112
F	GLY113
F	ASN115
F	HIS118
F	GDP161
F	HOH377
F	HOH494

---

site_id	BC3
Number of Residues	14
Details	BINDING SITE FOR RESIDUE GDP F 161

Chain	Residue
D	GLU152
F	LYS12
F	LEU55
F	PHE60
F	LEU64
F	ARG88
F	THR94
F	VAL112
F	ASN115
F	HIS118
F	35G160
F	HOH377
F	HOH494
F	HOH495

---

site_id	C
Number of Residues	6
Details	C-GMP AND GDP ARE FOUND (EACH WITH HALF OCCUPANCY) IN THE NUCLEOTIDE BINDING SITE.

Chain	Residue
C	LYS12
C	TYR52
C	VAL112
C	ASN115
C	HIS118
C	GLU152

---

site_id	D
Number of Residues	6
Details	C-GMP AND GDP ARE FOUND (EACH WITH HALF OCCUPANCY) IN THE NUCLEOTIDE BINDING SITE.

Chain	Residue
D	LYS12
D	TYR52
D	VAL112
D	ASN115
D	HIS118
D	GLU152

---

site_id	E
Number of Residues	6
Details	C-GMP AND GDP ARE FOUND (EACH WITH HALF OCCUPANCY) IN THE NUCLEOTIDE BINDING SITE.

Chain	Residue
E	LYS12
E	TYR52
E	VAL112
E	ASN115
E	HIS118
E	GLU152

---

site_id	F
Number of Residues	6
Details	C-GMP AND GDP ARE FOUND (EACH WITH HALF OCCUPANCY) IN THE NUCLEOTIDE BINDING SITE.

Chain	Residue
F	LYS12
F	TYR52
F	VAL112
F	ASN115
F	HIS118
F	GLU152

---

Functional Information from PROSITE/UniProt

site_id	PS00469
Number of Residues	9
Details	NDPK Nucleoside diphosphate kinase (NDPK) active site signature. NiiHGSDSV

Chain	Residue	Details
A	ASN115-VAL123

---

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	6
Details	Active site: {"description":"Pros-phosphohistidine intermediate","evidences":[{"source":"UniProtKB","id":"P15531","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI2
Number of Residues	48
Details	Binding site: {"evidences":[{"source":"UniProtKB","id":"P15532","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI3
Number of Residues	6
Details	Binding site: {"evidences":[{"source":"PubMed","id":"10329774","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1BHN","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI4
Number of Residues	18
Details	Binding site: {"evidences":[{"source":"UniProtKB","id":"P15531","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI5
Number of Residues	6
Details	Modified residue: {"description":"L-cysteine coenzyme A disulfide; alternate","evidences":[{"source":"UniProtKB","id":"P15531","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI6
Number of Residues	18
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"UniProtKB","id":"P15531","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI7
Number of Residues	12
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"source":"UniProtKB","id":"P15531","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

Catalytic Information from CSA

site_id	CSA1
Number of Residues	2
Details	Annotated By Reference To The Literature 1nsp

Chain	Residue	Details
A	ASN115
A	LYS12

---

site_id	CSA10
Number of Residues	2
Details	Annotated By Reference To The Literature 1nsp

Chain	Residue	Details
D	TYR52
D	LYS12

---

site_id	CSA11
Number of Residues	2
Details	Annotated By Reference To The Literature 1nsp

Chain	Residue	Details
E	TYR52
E	LYS12

---

site_id	CSA12
Number of Residues	2
Details	Annotated By Reference To The Literature 1nsp

Chain	Residue	Details
F	TYR52
F	LYS12

---

site_id	CSA2
Number of Residues	2
Details	Annotated By Reference To The Literature 1nsp

Chain	Residue	Details
B	ASN115
B	LYS12

---

site_id	CSA3
Number of Residues	2
Details	Annotated By Reference To The Literature 1nsp

Chain	Residue	Details
C	ASN115
C	LYS12

---

site_id	CSA4
Number of Residues	2
Details	Annotated By Reference To The Literature 1nsp

Chain	Residue	Details
D	ASN115
D	LYS12

---

site_id	CSA5
Number of Residues	2
Details	Annotated By Reference To The Literature 1nsp

Chain	Residue	Details
E	ASN115
E	LYS12

---

site_id	CSA6
Number of Residues	2
Details	Annotated By Reference To The Literature 1nsp

Chain	Residue	Details
F	ASN115
F	LYS12

---

site_id	CSA7
Number of Residues	2
Details	Annotated By Reference To The Literature 1nsp

Chain	Residue	Details
A	TYR52
A	LYS12

---

site_id	CSA8
Number of Residues	2
Details	Annotated By Reference To The Literature 1nsp

Chain	Residue	Details
B	TYR52
B	LYS12

---

site_id	CSA9
Number of Residues	2
Details	Annotated By Reference To The Literature 1nsp

Chain	Residue	Details
C	TYR52
C	LYS12

---