Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

4D8Y

Crystal structure of the hexameric purine nucleoside phosphorylase from Bacillus subtilis in space group P212121 at pH 5.6

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0003824	molecular_function	catalytic activity
A	0004731	molecular_function	purine-nucleoside phosphorylase activity
A	0005829	cellular_component	cytosol
A	0006139	biological_process	nucleobase-containing compound metabolic process
A	0006152	biological_process	purine nucleoside catabolic process
A	0009116	biological_process	nucleoside metabolic process
A	0009164	biological_process	nucleoside catabolic process
A	0016740	molecular_function	transferase activity
A	0016757	molecular_function	glycosyltransferase activity
A	0016763	molecular_function	pentosyltransferase activity
A	0042278	biological_process	purine nucleoside metabolic process
B	0003824	molecular_function	catalytic activity
B	0004731	molecular_function	purine-nucleoside phosphorylase activity
B	0005829	cellular_component	cytosol
B	0006139	biological_process	nucleobase-containing compound metabolic process
B	0006152	biological_process	purine nucleoside catabolic process
B	0009116	biological_process	nucleoside metabolic process
B	0009164	biological_process	nucleoside catabolic process
B	0016740	molecular_function	transferase activity
B	0016757	molecular_function	glycosyltransferase activity
B	0016763	molecular_function	pentosyltransferase activity
B	0042278	biological_process	purine nucleoside metabolic process
C	0003824	molecular_function	catalytic activity
C	0004731	molecular_function	purine-nucleoside phosphorylase activity
C	0005829	cellular_component	cytosol
C	0006139	biological_process	nucleobase-containing compound metabolic process
C	0006152	biological_process	purine nucleoside catabolic process
C	0009116	biological_process	nucleoside metabolic process
C	0009164	biological_process	nucleoside catabolic process
C	0016740	molecular_function	transferase activity
C	0016757	molecular_function	glycosyltransferase activity
C	0016763	molecular_function	pentosyltransferase activity
C	0042278	biological_process	purine nucleoside metabolic process
D	0003824	molecular_function	catalytic activity
D	0004731	molecular_function	purine-nucleoside phosphorylase activity
D	0005829	cellular_component	cytosol
D	0006139	biological_process	nucleobase-containing compound metabolic process
D	0006152	biological_process	purine nucleoside catabolic process
D	0009116	biological_process	nucleoside metabolic process
D	0009164	biological_process	nucleoside catabolic process
D	0016740	molecular_function	transferase activity
D	0016757	molecular_function	glycosyltransferase activity
D	0016763	molecular_function	pentosyltransferase activity
D	0042278	biological_process	purine nucleoside metabolic process
E	0003824	molecular_function	catalytic activity
E	0004731	molecular_function	purine-nucleoside phosphorylase activity
E	0005829	cellular_component	cytosol
E	0006139	biological_process	nucleobase-containing compound metabolic process
E	0006152	biological_process	purine nucleoside catabolic process
E	0009116	biological_process	nucleoside metabolic process
E	0009164	biological_process	nucleoside catabolic process
E	0016740	molecular_function	transferase activity
E	0016757	molecular_function	glycosyltransferase activity
E	0016763	molecular_function	pentosyltransferase activity
E	0042278	biological_process	purine nucleoside metabolic process
F	0003824	molecular_function	catalytic activity
F	0004731	molecular_function	purine-nucleoside phosphorylase activity
F	0005829	cellular_component	cytosol
F	0006139	biological_process	nucleobase-containing compound metabolic process
F	0006152	biological_process	purine nucleoside catabolic process
F	0009116	biological_process	nucleoside metabolic process
F	0009164	biological_process	nucleoside catabolic process
F	0016740	molecular_function	transferase activity
F	0016757	molecular_function	glycosyltransferase activity
F	0016763	molecular_function	pentosyltransferase activity
F	0042278	biological_process	purine nucleoside metabolic process

Functional Information from PDB Data

site_id	AC1
Number of Residues	8
Details	BINDING SITE FOR RESIDUE SO4 A 301

Chain	Residue
A	GLY20
A	ARG87
A	GLY89
A	SER90
A	HOH425
A	HOH426
A	HOH510
D	ARG43

site_id	AC2
Number of Residues	8
Details	BINDING SITE FOR RESIDUE SO4 A 302

Chain	Residue
A	ARG216
A	GLN217
A	HOH459
D	GLY-7
D	LEU-6
D	ARG-3
D	HOH492
A	ARG24

site_id	AC3
Number of Residues	8
Details	BINDING SITE FOR RESIDUE GOL A 303

Chain	Residue
A	TYR160
A	ASP162
A	HOH447
A	HOH517
D	ASN74
D	LEU187
D	LYS190
D	HIS191

site_id	AC4
Number of Residues	7
Details	BINDING SITE FOR RESIDUE GOL A 304

Chain	Residue
A	ASN74
A	LEU187
A	LYS190
A	HIS191
A	HOH484
D	TYR160
D	ASP162

site_id	AC5
Number of Residues	8
Details	BINDING SITE FOR RESIDUE SO4 B 301

Chain	Residue
B	GLY20
B	ARG87
B	GLY89
B	SER90
B	HOH428
B	HOH437
B	HOH485
C	ARG43

site_id	AC6
Number of Residues	9
Details	BINDING SITE FOR RESIDUE SO4 B 302

Chain	Residue
B	ARG24
B	ALA213
B	ARG216
B	GLN217
B	HOH467
B	HOH532
C	LEU-6
C	ARG-3
C	GLY-7

site_id	AC7
Number of Residues	11
Details	BINDING SITE FOR RESIDUE GOL B 303

Chain	Residue
A	GLY173
B	CYS128
B	ALA129
B	ALA189
B	HOH405
B	HOH411
B	HOH413
B	HOH430
B	HOH466
B	HOH474
B	HOH543

site_id	AC8
Number of Residues	8
Details	BINDING SITE FOR RESIDUE SO4 C 301

Chain	Residue
B	ARG43
C	GLY20
C	ARG87
C	GLY89
C	SER90
C	HOH424
C	HOH443
C	HOH454

site_id	AC9
Number of Residues	9
Details	BINDING SITE FOR RESIDUE SO4 C 302

Chain	Residue
B	GLY-7
B	LEU-6
B	ARG-3
C	ARG24
C	ARG216
C	GLN217
C	HOH453
C	HOH462
C	HOH497

site_id	BC1
Number of Residues	10
Details	BINDING SITE FOR RESIDUE GOL C 303

Chain	Residue
C	CYS128
C	ALA129
C	ALA189
C	HOH417
C	HOH420
C	HOH421
C	HOH429
C	HOH459
C	HOH467
E	GLY173

site_id	BC2
Number of Residues	7
Details	BINDING SITE FOR RESIDUE GOL C 304

Chain	Residue
B	TYR160
B	ASP162
C	ASN74
C	LEU187
C	LYS190
C	HIS191
C	HOH552

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

Chain	Residue
C	THR212
C	ALA213
C	GLU214
C	ARG216

site_id	BC4
Number of Residues	7
Details	BINDING SITE FOR RESIDUE GOL C 306

Chain	Residue
B	LYS190
B	HIS191
C	TYR160
C	ASP162
C	HOH565
B	ASN74
B	LEU187

site_id	BC5
Number of Residues	8
Details	BINDING SITE FOR RESIDUE SO4 D 301

Chain	Residue
A	ARG43
D	GLY20
D	ARG87
D	GLY89
D	SER90
D	HOH428
D	HOH434
D	HOH458

site_id	BC6
Number of Residues	10
Details	BINDING SITE FOR RESIDUE SO4 D 302

Chain	Residue
A	ARG-3
A	LEU-6
A	GLY-7
D	ARG24
D	ALA213
D	ARG216
D	GLN217
D	HOH451
D	HOH482
D	HOH498

site_id	BC7
Number of Residues	9
Details	BINDING SITE FOR RESIDUE GOL D 303

Chain	Residue
D	CYS128
D	ALA129
D	ALA189
D	HOH406
D	HOH419
D	HOH425
D	HOH439
D	HOH469
D	HOH569

site_id	BC8
Number of Residues	10
Details	BINDING SITE FOR RESIDUE SO4 E 301

Chain	Residue
E	ARG24
E	ALA213
E	ARG216
E	GLN217
E	HOH456
E	HOH505
F	GLY-7
F	LEU-6
F	ARG-3
F	HOH460

site_id	BC9
Number of Residues	8
Details	BINDING SITE FOR RESIDUE SO4 E 302

Chain	Residue
E	GLY20
E	ARG87
E	GLY89
E	SER90
E	HOH410
E	HOH422
E	HOH443
F	ARG43

site_id	CC1
Number of Residues	10
Details	BINDING SITE FOR RESIDUE GOL E 303

Chain	Residue
C	HOH409
E	CYS128
E	ALA129
E	ALA189
E	HOH409
E	HOH416
E	HOH428
E	HOH451
E	HOH452
E	HOH492

site_id	CC2
Number of Residues	7
Details	BINDING SITE FOR RESIDUE GOL E 304

Chain	Residue
E	TYR160
E	ASP162
E	HOH534
F	ASN74
F	LEU187
F	LYS190
F	HIS191

site_id	CC3
Number of Residues	8
Details	BINDING SITE FOR RESIDUE SO4 F 301

Chain	Residue
E	ARG43
F	GLY20
F	ARG87
F	GLY89
F	SER90
F	HOH419
F	HOH507
F	HOH537

site_id	CC4
Number of Residues	8
Details	BINDING SITE FOR RESIDUE SO4 F 302

Chain	Residue
E	GLY-7
E	LEU-6
E	ARG-3
E	HOH494
F	ARG24
F	ARG216
F	GLN217
F	HOH491

site_id	CC5
Number of Residues	9
Details	BINDING SITE FOR RESIDUE GOL F 303

Chain	Residue
D	HOH423
F	CYS128
F	ALA129
F	ALA189
F	HOH414
F	HOH420
F	HOH423
F	HOH461
F	HOH530

site_id	CC6
Number of Residues	7
Details	BINDING SITE FOR RESIDUE GOL F 304

Chain	Residue
E	ASN74
E	LEU187
E	LYS190
E	HIS191
F	TYR160
F	ASP162
F	HOH463

site_id	CC7
Number of Residues	5
Details	BINDING SITE FOR RESIDUE GOL F 305

Chain	Residue
F	SER164
F	GLN165
F	ILE166
F	GLU167
F	HOH437

Functional Information from PROSITE/UniProt

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

Chain	Residue	Details
A	GLY61-LEU76

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	6
Details	Active site: {"description":"Proton donor","evidences":[{"source":"HAMAP-Rule","id":"MF_01627","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	12
Details	Binding site: {"evidences":[{"source":"UniProtKB","id":"P50389","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	48
Details	Binding site: {"description":"in other chain","evidences":[{"source":"UniProtKB","id":"P50389","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	6
Details	Site: {"description":"Important for catalytic activity","evidences":[{"source":"HAMAP-Rule","id":"MF_01627","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

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