Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

5M2T

X-ray structure of uridine phosphorylase from Vibrio cholerae in complex with uridine at 1.03 A resolution

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0003824	molecular_function	catalytic activity
A	0004850	molecular_function	uridine phosphorylase activity
A	0005737	cellular_component	cytoplasm
A	0005829	cellular_component	cytosol
A	0009116	biological_process	nucleoside metabolic process
A	0009164	biological_process	nucleoside catabolic process
A	0009166	biological_process	nucleotide catabolic process
A	0016740	molecular_function	transferase activity
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	0004850	molecular_function	uridine phosphorylase activity
B	0005737	cellular_component	cytoplasm
B	0005829	cellular_component	cytosol
B	0009116	biological_process	nucleoside metabolic process
B	0009164	biological_process	nucleoside catabolic process
B	0009166	biological_process	nucleotide catabolic process
B	0016740	molecular_function	transferase activity
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	0004850	molecular_function	uridine phosphorylase activity
C	0005737	cellular_component	cytoplasm
C	0005829	cellular_component	cytosol
C	0009116	biological_process	nucleoside metabolic process
C	0009164	biological_process	nucleoside catabolic process
C	0009166	biological_process	nucleotide catabolic process
C	0016740	molecular_function	transferase activity
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	0004850	molecular_function	uridine phosphorylase activity
D	0005737	cellular_component	cytoplasm
D	0005829	cellular_component	cytosol
D	0009116	biological_process	nucleoside metabolic process
D	0009164	biological_process	nucleoside catabolic process
D	0009166	biological_process	nucleotide catabolic process
D	0016740	molecular_function	transferase activity
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	0004850	molecular_function	uridine phosphorylase activity
E	0005737	cellular_component	cytoplasm
E	0005829	cellular_component	cytosol
E	0009116	biological_process	nucleoside metabolic process
E	0009164	biological_process	nucleoside catabolic process
E	0009166	biological_process	nucleotide catabolic process
E	0016740	molecular_function	transferase activity
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	0004850	molecular_function	uridine phosphorylase activity
F	0005737	cellular_component	cytoplasm
F	0005829	cellular_component	cytosol
F	0009116	biological_process	nucleoside metabolic process
F	0009164	biological_process	nucleoside catabolic process
F	0009166	biological_process	nucleotide catabolic process
F	0016740	molecular_function	transferase activity
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 URI A 301

Chain	Residue
A	THR93
A	ILE220
A	HOH422
A	HOH429
A	HOH491
A	HOH514
B	HIS7
A	THR94
A	GLY95
A	PHE161
A	GLN165
A	ARG167
A	GLU195
A	MET196
A	GLU197

site_id	AC2
Number of Residues	6
Details	binding site for residue NA A 302

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

site_id	AC3
Number of Residues	18
Details	binding site for residue URI B 301

Chain	Residue
A	HIS7
A	ARG47
B	ILE68
B	ARG90
B	THR93
B	THR94
B	GLY95
B	PHE161
B	GLN165
B	ARG167
B	GLU195
B	MET196
B	GLU197
B	ILE220
B	HOH422
B	HOH513
B	HOH521
B	HOH606

site_id	AC4
Number of Residues	4
Details	binding site for residue CL B 302

Chain	Residue
A	HOH601
B	GLY25
B	ASP26
B	ARG29

site_id	AC5
Number of Residues	14
Details	binding site for residue URI C 301

Chain	Residue
C	THR93
C	THR94
C	GLY95
C	PHE161
C	GLN165
C	ARG167
C	GLU195
C	MET196
C	GLU197
C	HOH434
C	HOH463
C	HOH530
C	HOH573
D	HIS7

site_id	AC6
Number of Residues	5
Details	binding site for residue CL C 302

Chain	Residue
C	GLY25
C	ASP26
C	HOH471
C	HOH581
C	HOH617

site_id	AC7
Number of Residues	3
Details	binding site for residue CL C 303

Chain	Residue
B	HOH540
C	PHE133
C	HOH532

site_id	AC8
Number of Residues	6
Details	binding site for residue NA C 304

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

site_id	AC9
Number of Residues	14
Details	binding site for residue URI D 301

Chain	Residue
C	HIS7
D	THR93
D	THR94
D	GLY95
D	PHE161
D	GLN165
D	ARG167
D	GLU195
D	MET196
D	GLU197
D	HOH529
D	HOH559
D	HOH571
D	HOH610

site_id	AD1
Number of Residues	2
Details	binding site for residue CL D 302

Chain	Residue
D	PHE133
E	HOH544

site_id	AD2
Number of Residues	5
Details	binding site for residue CL D 303

Chain	Residue
C	HOH591
D	GLY25
D	ASP26
D	ARG29
D	HOH509

site_id	AD3
Number of Residues	4
Details	binding site for residue MG D 304

Chain	Residue
D	HOH453
D	HOH543
D	HOH606
D	HOH656

site_id	AD4
Number of Residues	15
Details	binding site for residue URI E 301

Chain	Residue
E	PHE161
E	GLN165
E	ARG167
E	GLU195
E	MET196
E	GLU197
E	ILE220
E	EDO303
E	HOH532
E	HOH569
F	HIS7
F	HOH418
E	THR93
E	THR94
E	GLY95

site_id	AD5
Number of Residues	6
Details	binding site for residue NA E 302

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

site_id	AD6
Number of Residues	8
Details	binding site for residue EDO E 303

Chain	Residue
E	ARG90
E	GLY92
E	THR93
E	GLU197
E	URI301
E	HOH410
E	HOH423
F	ARG47

site_id	AD7
Number of Residues	14
Details	binding site for residue URI F 301

Chain	Residue
E	HIS7
F	THR93
F	THR94
F	GLY95
F	PHE161
F	GLN165
F	ARG167
F	GLU195
F	MET196
F	GLU197
F	HOH443
F	HOH490
F	HOH554
F	HOH604

site_id	AD8
Number of Residues	4
Details	binding site for residue CL F 302

Chain	Residue
F	GLY25
F	ASP26
F	ARG29
F	HOH644

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)