Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

4G8J

X-ray Structure of Uridine Phosphorylease from Vibrio cholerae Complexed with Thymidine at 2.12 A Resolution

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0003824	molecular_function	catalytic activity
A	0004731	molecular_function	purine-nucleoside phosphorylase activity
A	0004850	molecular_function	uridine phosphorylase activity
A	0005737	cellular_component	cytoplasm
A	0005829	cellular_component	cytosol
A	0006152	biological_process	purine nucleoside catabolic process
A	0006218	biological_process	uridine catabolic process
A	0009116	biological_process	nucleoside metabolic process
A	0009164	biological_process	nucleoside catabolic process
A	0009166	biological_process	nucleotide catabolic process
A	0016757	molecular_function	glycosyltransferase activity
A	0016763	molecular_function	pentosyltransferase activity
A	0044206	biological_process	UMP salvage
A	0046872	molecular_function	metal ion binding
B	0003824	molecular_function	catalytic activity
B	0004731	molecular_function	purine-nucleoside phosphorylase activity
B	0004850	molecular_function	uridine phosphorylase activity
B	0005737	cellular_component	cytoplasm
B	0005829	cellular_component	cytosol
B	0006152	biological_process	purine nucleoside catabolic process
B	0006218	biological_process	uridine catabolic process
B	0009116	biological_process	nucleoside metabolic process
B	0009164	biological_process	nucleoside catabolic process
B	0009166	biological_process	nucleotide catabolic process
B	0016757	molecular_function	glycosyltransferase activity
B	0016763	molecular_function	pentosyltransferase activity
B	0044206	biological_process	UMP salvage
B	0046872	molecular_function	metal ion binding
C	0003824	molecular_function	catalytic activity
C	0004731	molecular_function	purine-nucleoside phosphorylase activity
C	0004850	molecular_function	uridine phosphorylase activity
C	0005737	cellular_component	cytoplasm
C	0005829	cellular_component	cytosol
C	0006152	biological_process	purine nucleoside catabolic process
C	0006218	biological_process	uridine catabolic process
C	0009116	biological_process	nucleoside metabolic process
C	0009164	biological_process	nucleoside catabolic process
C	0009166	biological_process	nucleotide catabolic process
C	0016757	molecular_function	glycosyltransferase activity
C	0016763	molecular_function	pentosyltransferase activity
C	0044206	biological_process	UMP salvage
C	0046872	molecular_function	metal ion binding
D	0003824	molecular_function	catalytic activity
D	0004731	molecular_function	purine-nucleoside phosphorylase activity
D	0004850	molecular_function	uridine phosphorylase activity
D	0005737	cellular_component	cytoplasm
D	0005829	cellular_component	cytosol
D	0006152	biological_process	purine nucleoside catabolic process
D	0006218	biological_process	uridine catabolic process
D	0009116	biological_process	nucleoside metabolic process
D	0009164	biological_process	nucleoside catabolic process
D	0009166	biological_process	nucleotide catabolic process
D	0016757	molecular_function	glycosyltransferase activity
D	0016763	molecular_function	pentosyltransferase activity
D	0044206	biological_process	UMP salvage
D	0046872	molecular_function	metal ion binding
E	0003824	molecular_function	catalytic activity
E	0004731	molecular_function	purine-nucleoside phosphorylase activity
E	0004850	molecular_function	uridine phosphorylase activity
E	0005737	cellular_component	cytoplasm
E	0005829	cellular_component	cytosol
E	0006152	biological_process	purine nucleoside catabolic process
E	0006218	biological_process	uridine catabolic process
E	0009116	biological_process	nucleoside metabolic process
E	0009164	biological_process	nucleoside catabolic process
E	0009166	biological_process	nucleotide catabolic process
E	0016757	molecular_function	glycosyltransferase activity
E	0016763	molecular_function	pentosyltransferase activity
E	0044206	biological_process	UMP salvage
E	0046872	molecular_function	metal ion binding
F	0003824	molecular_function	catalytic activity
F	0004731	molecular_function	purine-nucleoside phosphorylase activity
F	0004850	molecular_function	uridine phosphorylase activity
F	0005737	cellular_component	cytoplasm
F	0005829	cellular_component	cytosol
F	0006152	biological_process	purine nucleoside catabolic process
F	0006218	biological_process	uridine catabolic process
F	0009116	biological_process	nucleoside metabolic process
F	0009164	biological_process	nucleoside catabolic process
F	0009166	biological_process	nucleotide catabolic process
F	0016757	molecular_function	glycosyltransferase activity
F	0016763	molecular_function	pentosyltransferase activity
F	0044206	biological_process	UMP salvage
F	0046872	molecular_function	metal ion binding

Functional Information from PDB Data

site_id	AC1
Number of Residues	15
Details	BINDING SITE FOR RESIDUE THM A 301

Chain	Residue
A	THR93
A	ILE219
A	ILE220
A	HOH467
A	HOH565
B	HIS7
B	ARG47
A	GLY95
A	PHE161
A	GLN165
A	ARG167
A	PHE194
A	GLU195
A	MET196
A	GLU197

site_id	AC2
Number of Residues	2
Details	BINDING SITE FOR RESIDUE CL A 302

Chain	Residue
A	ASN221
A	HOH488

site_id	AC3
Number of Residues	3
Details	BINDING SITE FOR RESIDUE CL A 303

Chain	Residue
A	GLY25
A	ASP26
A	ARG29

site_id	AC4
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG A 304

Chain	Residue
A	HOH573
A	HOH574
A	HOH575
A	HOH576
A	HOH577
A	HOH578

site_id	AC5
Number of Residues	14
Details	BINDING SITE FOR RESIDUE THM B 301

Chain	Residue
A	HIS7
A	ARG47
A	HOH564
B	THR93
B	GLY95
B	PHE161
B	GLN165
B	ARG167
B	GLU195
B	MET196
B	GLU197
B	ILE220
B	HOH406
B	HOH603

site_id	AC6
Number of Residues	3
Details	BINDING SITE FOR RESIDUE CL B 302

Chain	Residue
B	GLY25
B	ASP26
B	ARG29

site_id	AC7
Number of Residues	6
Details	BINDING SITE FOR RESIDUE NA B 303

Chain	Residue
A	GLU48
A	ILE68
A	SER72
B	GLU48
B	ILE68
B	SER72

site_id	AC8
Number of Residues	13
Details	BINDING SITE FOR RESIDUE THM C 301

Chain	Residue
C	THR93
C	GLY95
C	PHE161
C	GLN165
C	ARG167
C	GLU195
C	MET196
C	GLU197
C	ILE220
C	EDO304
C	HOH620
D	HIS7
D	ARG47

site_id	AC9
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO C 302

Chain	Residue
C	TYR162
C	ASP169
C	HOH416
D	PHE6
D	GLN82

site_id	BC1
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO C 303

Chain	Residue
C	ARG178
C	HOH460
C	HOH624
D	LEU120

site_id	BC2
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO C 304

Chain	Residue
C	PHE161
C	THM301
C	HOH657
D	HIS7

site_id	BC3
Number of Residues	4
Details	BINDING SITE FOR RESIDUE CL C 305

Chain	Residue
C	GLY25
C	ASP26
C	ARG29
D	HOH456

site_id	BC4
Number of Residues	6
Details	BINDING SITE FOR RESIDUE NA C 306

Chain	Residue
C	GLU48
C	ILE68
C	SER72
D	GLU48
D	ILE68
D	SER72

site_id	BC5
Number of Residues	16
Details	BINDING SITE FOR RESIDUE THM D 301

Chain	Residue
D	HOH626
D	HOH631
C	HIS7
C	ARG47
C	HOH495
D	ILE68
D	THR93
D	GLY95
D	PHE161
D	GLN165
D	ARG167
D	GLU195
D	MET196
D	GLU197
D	ILE220
D	HOH589

site_id	BC6
Number of Residues	5
Details	BINDING SITE FOR RESIDUE CL D 302

Chain	Residue
C	HOH538
D	GLY25
D	ASP26
D	ARG29
D	HOH511

site_id	BC7
Number of Residues	15
Details	BINDING SITE FOR RESIDUE THM E 301

Chain	Residue
E	ILE68
E	THR93
E	PHE161
E	GLN165
E	ARG167
E	PHE194
E	GLU195
E	MET196
E	GLU197
E	ILE220
E	HOH494
E	HOH568
E	HOH584
F	HIS7
F	ARG47

site_id	BC8
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO E 302

Chain	Residue
E	ARG178
E	HOH538
E	HOH594
F	LEU120
F	HOH447

site_id	BC9
Number of Residues	3
Details	BINDING SITE FOR RESIDUE CL E 303

Chain	Residue
E	GLY25
E	ASP26
E	HOH497

site_id	CC1
Number of Residues	6
Details	BINDING SITE FOR RESIDUE NA E 304

Chain	Residue
E	GLU48
E	ILE68
E	SER72
F	GLU48
F	ILE68
F	SER72

site_id	CC2
Number of Residues	13
Details	BINDING SITE FOR RESIDUE THM F 301

Chain	Residue
E	HIS7
E	ARG47
F	THR93
F	GLY95
F	PHE161
F	GLN165
F	ARG167
F	GLU195
F	MET196
F	GLU197
F	ILE219
F	ILE220
F	HOH529

site_id	CC3
Number of Residues	2
Details	BINDING SITE FOR RESIDUE CL F 302

Chain	Residue
F	ASN221
F	LYS225

site_id	CC4
Number of Residues	2
Details	BINDING SITE FOR RESIDUE CL F 303

Chain	Residue
F	GLY25
F	ASP26

site_id	CC5
Number of Residues	4
Details	BINDING SITE FOR RESIDUE CL F 304

Chain	Residue
F	ARG174
F	VAL175
F	GLN180
F	HOH491

site_id	CC6
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG F 305

Chain	Residue
F	HOH556
F	HOH557
F	HOH558
F	HOH559
F	HOH560
F	HOH561

Functional Information from PROSITE/UniProt

site_id	PS01232
Number of Residues	16
Details	PNP_UDP_1 Purine and other phosphorylases family 1 signature. StGIGgPStSIaveEL

Chain	Residue	Details
A	SER65-LEU80

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)
		EDMap 2fo-fc (MTZ)