3K8O

Crystal structure of human purine nucleoside phosphorylase in complex with DATMe-ImmH

Functional Information from GO Data

Chain	GOid	namespace	contents
E	0000255	biological_process	allantoin metabolic process
E	0001882	molecular_function	nucleoside binding
E	0002060	molecular_function	purine nucleobase binding
E	0003824	molecular_function	catalytic activity
E	0004731	molecular_function	purine-nucleoside phosphorylase activity
E	0005515	molecular_function	protein binding
E	0005576	cellular_component	extracellular region
E	0005737	cellular_component	cytoplasm
E	0005829	cellular_component	cytosol
E	0006139	biological_process	nucleobase-containing compound metabolic process
E	0006148	biological_process	inosine catabolic process
E	0006149	biological_process	deoxyinosine catabolic process
E	0006157	biological_process	deoxyadenosine catabolic process
E	0006166	biological_process	purine ribonucleoside salvage
E	0006204	biological_process	IMP catabolic process
E	0006738	biological_process	nicotinamide riboside catabolic process
E	0006955	biological_process	immune response
E	0009116	biological_process	nucleoside metabolic process
E	0009165	biological_process	nucleotide biosynthetic process
E	0009410	biological_process	response to xenobiotic stimulus
E	0016740	molecular_function	transferase activity
E	0016757	molecular_function	glycosyltransferase activity
E	0016763	molecular_function	pentosyltransferase activity
E	0032743	biological_process	positive regulation of interleukin-2 production
E	0034418	biological_process	urate biosynthetic process
E	0034774	cellular_component	secretory granule lumen
E	0042102	biological_process	positive regulation of T cell proliferation
E	0042301	molecular_function	phosphate ion binding
E	0042802	molecular_function	identical protein binding
E	0043101	biological_process	purine-containing compound salvage
E	0046059	biological_process	dAMP catabolic process
E	0046638	biological_process	positive regulation of alpha-beta T cell differentiation
E	0047975	molecular_function	guanosine phosphorylase activity
E	0070062	cellular_component	extracellular exosome
E	1904813	cellular_component	ficolin-1-rich granule lumen
Q	0000255	biological_process	allantoin metabolic process
Q	0001882	molecular_function	nucleoside binding
Q	0002060	molecular_function	purine nucleobase binding
Q	0003824	molecular_function	catalytic activity
Q	0004731	molecular_function	purine-nucleoside phosphorylase activity
Q	0005515	molecular_function	protein binding
Q	0005576	cellular_component	extracellular region
Q	0005737	cellular_component	cytoplasm
Q	0005829	cellular_component	cytosol
Q	0006139	biological_process	nucleobase-containing compound metabolic process
Q	0006148	biological_process	inosine catabolic process
Q	0006149	biological_process	deoxyinosine catabolic process
Q	0006157	biological_process	deoxyadenosine catabolic process
Q	0006166	biological_process	purine ribonucleoside salvage
Q	0006204	biological_process	IMP catabolic process
Q	0006738	biological_process	nicotinamide riboside catabolic process
Q	0006955	biological_process	immune response
Q	0009116	biological_process	nucleoside metabolic process
Q	0009165	biological_process	nucleotide biosynthetic process
Q	0009410	biological_process	response to xenobiotic stimulus
Q	0016740	molecular_function	transferase activity
Q	0016757	molecular_function	glycosyltransferase activity
Q	0016763	molecular_function	pentosyltransferase activity
Q	0032743	biological_process	positive regulation of interleukin-2 production
Q	0034418	biological_process	urate biosynthetic process
Q	0034774	cellular_component	secretory granule lumen
Q	0042102	biological_process	positive regulation of T cell proliferation
Q	0042301	molecular_function	phosphate ion binding
Q	0042802	molecular_function	identical protein binding
Q	0043101	biological_process	purine-containing compound salvage
Q	0046059	biological_process	dAMP catabolic process
Q	0046638	biological_process	positive regulation of alpha-beta T cell differentiation
Q	0047975	molecular_function	guanosine phosphorylase activity
Q	0070062	cellular_component	extracellular exosome
Q	1904813	cellular_component	ficolin-1-rich granule lumen
S	0000255	biological_process	allantoin metabolic process
S	0001882	molecular_function	nucleoside binding
S	0002060	molecular_function	purine nucleobase binding
S	0003824	molecular_function	catalytic activity
S	0004731	molecular_function	purine-nucleoside phosphorylase activity
S	0005515	molecular_function	protein binding
S	0005576	cellular_component	extracellular region
S	0005737	cellular_component	cytoplasm
S	0005829	cellular_component	cytosol
S	0006139	biological_process	nucleobase-containing compound metabolic process
S	0006148	biological_process	inosine catabolic process
S	0006149	biological_process	deoxyinosine catabolic process
S	0006157	biological_process	deoxyadenosine catabolic process
S	0006166	biological_process	purine ribonucleoside salvage
S	0006204	biological_process	IMP catabolic process
S	0006738	biological_process	nicotinamide riboside catabolic process
S	0006955	biological_process	immune response
S	0009116	biological_process	nucleoside metabolic process
S	0009165	biological_process	nucleotide biosynthetic process
S	0009410	biological_process	response to xenobiotic stimulus
S	0016740	molecular_function	transferase activity
S	0016757	molecular_function	glycosyltransferase activity
S	0016763	molecular_function	pentosyltransferase activity
S	0032743	biological_process	positive regulation of interleukin-2 production
S	0034418	biological_process	urate biosynthetic process
S	0034774	cellular_component	secretory granule lumen
S	0042102	biological_process	positive regulation of T cell proliferation
S	0042301	molecular_function	phosphate ion binding
S	0042802	molecular_function	identical protein binding
S	0043101	biological_process	purine-containing compound salvage
S	0046059	biological_process	dAMP catabolic process
S	0046638	biological_process	positive regulation of alpha-beta T cell differentiation
S	0047975	molecular_function	guanosine phosphorylase activity
S	0070062	cellular_component	extracellular exosome
S	1904813	cellular_component	ficolin-1-rich granule lumen
T	0000255	biological_process	allantoin metabolic process
T	0001882	molecular_function	nucleoside binding
T	0002060	molecular_function	purine nucleobase binding
T	0003824	molecular_function	catalytic activity
T	0004731	molecular_function	purine-nucleoside phosphorylase activity
T	0005515	molecular_function	protein binding
T	0005576	cellular_component	extracellular region
T	0005737	cellular_component	cytoplasm
T	0005829	cellular_component	cytosol
T	0006139	biological_process	nucleobase-containing compound metabolic process
T	0006148	biological_process	inosine catabolic process
T	0006149	biological_process	deoxyinosine catabolic process
T	0006157	biological_process	deoxyadenosine catabolic process
T	0006166	biological_process	purine ribonucleoside salvage
T	0006204	biological_process	IMP catabolic process
T	0006738	biological_process	nicotinamide riboside catabolic process
T	0006955	biological_process	immune response
T	0009116	biological_process	nucleoside metabolic process
T	0009165	biological_process	nucleotide biosynthetic process
T	0009410	biological_process	response to xenobiotic stimulus
T	0016740	molecular_function	transferase activity
T	0016757	molecular_function	glycosyltransferase activity
T	0016763	molecular_function	pentosyltransferase activity
T	0032743	biological_process	positive regulation of interleukin-2 production
T	0034418	biological_process	urate biosynthetic process
T	0034774	cellular_component	secretory granule lumen
T	0042102	biological_process	positive regulation of T cell proliferation
T	0042301	molecular_function	phosphate ion binding
T	0042802	molecular_function	identical protein binding
T	0043101	biological_process	purine-containing compound salvage
T	0046059	biological_process	dAMP catabolic process
T	0046638	biological_process	positive regulation of alpha-beta T cell differentiation
T	0047975	molecular_function	guanosine phosphorylase activity
T	0070062	cellular_component	extracellular exosome
T	1904813	cellular_component	ficolin-1-rich granule lumen
U	0000255	biological_process	allantoin metabolic process
U	0001882	molecular_function	nucleoside binding
U	0002060	molecular_function	purine nucleobase binding
U	0003824	molecular_function	catalytic activity
U	0004731	molecular_function	purine-nucleoside phosphorylase activity
U	0005515	molecular_function	protein binding
U	0005576	cellular_component	extracellular region
U	0005737	cellular_component	cytoplasm
U	0005829	cellular_component	cytosol
U	0006139	biological_process	nucleobase-containing compound metabolic process
U	0006148	biological_process	inosine catabolic process
U	0006149	biological_process	deoxyinosine catabolic process
U	0006157	biological_process	deoxyadenosine catabolic process
U	0006166	biological_process	purine ribonucleoside salvage
U	0006204	biological_process	IMP catabolic process
U	0006738	biological_process	nicotinamide riboside catabolic process
U	0006955	biological_process	immune response
U	0009116	biological_process	nucleoside metabolic process
U	0009165	biological_process	nucleotide biosynthetic process
U	0009410	biological_process	response to xenobiotic stimulus
U	0016740	molecular_function	transferase activity
U	0016757	molecular_function	glycosyltransferase activity
U	0016763	molecular_function	pentosyltransferase activity
U	0032743	biological_process	positive regulation of interleukin-2 production
U	0034418	biological_process	urate biosynthetic process
U	0034774	cellular_component	secretory granule lumen
U	0042102	biological_process	positive regulation of T cell proliferation
U	0042301	molecular_function	phosphate ion binding
U	0042802	molecular_function	identical protein binding
U	0043101	biological_process	purine-containing compound salvage
U	0046059	biological_process	dAMP catabolic process
U	0046638	biological_process	positive regulation of alpha-beta T cell differentiation
U	0047975	molecular_function	guanosine phosphorylase activity
U	0070062	cellular_component	extracellular exosome
U	1904813	cellular_component	ficolin-1-rich granule lumen
Y	0000255	biological_process	allantoin metabolic process
Y	0001882	molecular_function	nucleoside binding
Y	0002060	molecular_function	purine nucleobase binding
Y	0003824	molecular_function	catalytic activity
Y	0004731	molecular_function	purine-nucleoside phosphorylase activity
Y	0005515	molecular_function	protein binding
Y	0005576	cellular_component	extracellular region
Y	0005737	cellular_component	cytoplasm
Y	0005829	cellular_component	cytosol
Y	0006139	biological_process	nucleobase-containing compound metabolic process
Y	0006148	biological_process	inosine catabolic process
Y	0006149	biological_process	deoxyinosine catabolic process
Y	0006157	biological_process	deoxyadenosine catabolic process
Y	0006166	biological_process	purine ribonucleoside salvage
Y	0006204	biological_process	IMP catabolic process
Y	0006738	biological_process	nicotinamide riboside catabolic process
Y	0006955	biological_process	immune response
Y	0009116	biological_process	nucleoside metabolic process
Y	0009165	biological_process	nucleotide biosynthetic process
Y	0009410	biological_process	response to xenobiotic stimulus
Y	0016740	molecular_function	transferase activity
Y	0016757	molecular_function	glycosyltransferase activity
Y	0016763	molecular_function	pentosyltransferase activity
Y	0032743	biological_process	positive regulation of interleukin-2 production
Y	0034418	biological_process	urate biosynthetic process
Y	0034774	cellular_component	secretory granule lumen
Y	0042102	biological_process	positive regulation of T cell proliferation
Y	0042301	molecular_function	phosphate ion binding
Y	0042802	molecular_function	identical protein binding
Y	0043101	biological_process	purine-containing compound salvage
Y	0046059	biological_process	dAMP catabolic process
Y	0046638	biological_process	positive regulation of alpha-beta T cell differentiation
Y	0047975	molecular_function	guanosine phosphorylase activity
Y	0070062	cellular_component	extracellular exosome
Y	1904813	cellular_component	ficolin-1-rich granule lumen

Functional Information from PDB Data

site_id	AC1
Number of Residues	3
Details	BINDING SITE FOR RESIDUE SO4 E 1002

Chain	Residue
E	ARG207
E	TYR249
Y	ARG133

---

site_id	AC2
Number of Residues	10
Details	BINDING SITE FOR RESIDUE SO4 E 1003

Chain	Residue
E	ALA116
E	SER220
E	HOH290
E	2299006
E	GLY32
E	SER33
E	HIS64
E	ARG84
E	HIS86
E	ASN115

---

site_id	AC3
Number of Residues	3
Details	BINDING SITE FOR RESIDUE SO4 E 1006

Chain	Residue
E	ARG148
Q	PRO92
Q	GLN144

---

site_id	AC4
Number of Residues	16
Details	BINDING SITE FOR RESIDUE 229 E 9006

Chain	Residue
E	TYR88
E	ALA116
E	GLY118
E	PHE200
E	GLU201
E	VAL217
E	GLY218
E	MET219
E	THR242
E	ASN243
E	VAL245
E	HIS257
E	VAL260
E	HOH299
E	SO41003
Y	PHE159

---

site_id	AC5
Number of Residues	3
Details	BINDING SITE FOR RESIDUE SO4 Q 1005

Chain	Residue
Q	ARG148
Y	PRO92
Y	GLN144

---

site_id	AC6
Number of Residues	3
Details	BINDING SITE FOR RESIDUE SO4 Q 1012

Chain	Residue
Q	ARG133
Y	ARG207
Y	TYR249

---

site_id	AC7
Number of Residues	10
Details	BINDING SITE FOR RESIDUE SO4 Q 2001

Chain	Residue
Q	GLY32
Q	SER33
Q	HIS64
Q	ARG84
Q	HIS86
Q	ASN115
Q	ALA116
Q	SER220
Q	HOH297
Q	2299002

---

site_id	AC8
Number of Residues	17
Details	BINDING SITE FOR RESIDUE 229 Q 9002

Chain	Residue
E	PHE159
Q	TYR88
Q	ALA116
Q	ALA117
Q	GLY118
Q	PHE200
Q	GLU201
Q	VAL217
Q	GLY218
Q	MET219
Q	THR242
Q	ASN243
Q	VAL245
Q	HIS257
Q	VAL260
Q	HOH308
Q	SO42001

---

site_id	AC9
Number of Residues	3
Details	BINDING SITE FOR RESIDUE SO4 S 1010

Chain	Residue
S	ARG148
T	PRO92
T	GLN144

---

site_id	BC1
Number of Residues	3
Details	BINDING SITE FOR RESIDUE SO4 S 1013

Chain	Residue
S	ARG133
T	ARG207
T	TYR249

---

site_id	BC2
Number of Residues	10
Details	BINDING SITE FOR RESIDUE SO4 S 3001

Chain	Residue
S	GLY32
S	SER33
S	HIS64
S	ARG84
S	HIS86
S	ASN115
S	ALA116
S	SER220
S	HOH317
S	2299005

---

site_id	BC3
Number of Residues	16
Details	BINDING SITE FOR RESIDUE 229 S 9005

Chain	Residue
S	TYR88
S	ALA116
S	ALA117
S	GLY118
S	PHE200
S	GLU201
S	VAL217
S	GLY218
S	MET219
S	THR242
S	ASN243
S	VAL245
S	HIS257
S	HOH310
S	SO43001
U	PHE159

---

site_id	BC4
Number of Residues	3
Details	BINDING SITE FOR RESIDUE SO4 T 1007

Chain	Residue
U	TYR249
T	ARG133
U	ARG207

---

site_id	BC5
Number of Residues	10
Details	BINDING SITE FOR RESIDUE SO4 T 5001

Chain	Residue
T	GLY32
T	SER33
T	HIS64
T	ARG84
T	HIS86
T	ASN115
T	ALA116
T	SER220
T	HOH290
T	2299004

---

site_id	BC6
Number of Residues	16
Details	BINDING SITE FOR RESIDUE 229 T 9004

Chain	Residue
S	PHE159
T	TYR88
T	ALA116
T	ALA117
T	GLY118
T	PHE200
T	GLU201
T	VAL217
T	GLY218
T	MET219
T	THR242
T	ASN243
T	VAL245
T	HIS257
T	HOH299
T	SO45001

---

site_id	BC7
Number of Residues	3
Details	BINDING SITE FOR RESIDUE SO4 U 1008

Chain	Residue
T	ARG148
U	PRO92
U	GLN144

---

site_id	BC8
Number of Residues	3
Details	BINDING SITE FOR RESIDUE SO4 U 1009

Chain	Residue
S	PRO92
S	GLN144
U	ARG148

---

site_id	BC9
Number of Residues	10
Details	BINDING SITE FOR RESIDUE SO4 U 4001

Chain	Residue
U	GLY32
U	SER33
U	HIS64
U	ARG84
U	HIS86
U	ASN115
U	ALA116
U	SER220
U	HOH290
U	2299003

---

site_id	CC1
Number of Residues	17
Details	BINDING SITE FOR RESIDUE 229 U 9003

Chain	Residue
T	PHE159
U	SER33
U	TYR88
U	ALA116
U	ALA117
U	GLY118
U	PHE200
U	GLU201
U	VAL217
U	GLY218
U	MET219
U	THR242
U	ASN243
U	VAL245
U	HIS257
U	HOH305
U	SO44001

---

site_id	CC2
Number of Residues	10
Details	BINDING SITE FOR RESIDUE SO4 Y 1001

Chain	Residue
Y	GLY32
Y	SER33
Y	HIS64
Y	ARG84
Y	HIS86
Y	ASN115
Y	ALA116
Y	SER220
Y	HOH292
Y	2299001

---

site_id	CC3
Number of Residues	3
Details	BINDING SITE FOR RESIDUE SO4 Y 1004

Chain	Residue
E	PRO92
E	GLN144
Y	ARG148

---

site_id	CC4
Number of Residues	14
Details	BINDING SITE FOR RESIDUE 229 Y 9001

Chain	Residue
Q	PHE159
Y	TYR88
Y	ALA116
Y	ALA117
Y	GLY118
Y	PHE200
Y	GLU201
Y	GLY218
Y	MET219
Y	THR242
Y	ASN243
Y	HIS257
Y	VAL260
Y	SO41001

---

Functional Information from PROSITE/UniProt

site_id	PS01240
Number of Residues	42
Details	PNP_MTAP_2 Purine and other phosphorylases family 2 signature. VmmqGrfHmYegypLwkvTfpVrVfhllGvdt.LVvtNAaGGL

Chain	Residue	Details
E	VAL79-LEU120

---

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	6
Details	Binding site: {"evidences":[{"source":"PubMed","id":"23438750","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"14706628","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"1763067","evidenceCode":"ECO:0000305"},{"source":"PDB","id":"1RCT","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1ULA","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1ULB","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4EAR","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4EB8","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4GKA","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI2
Number of Residues	6
Details	Binding site: {"evidences":[{"source":"UniProtKB","id":"P55859","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI3
Number of Residues	12
Details	Binding site: {"evidences":[{"source":"PubMed","id":"23438750","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"14706628","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"1763067","evidenceCode":"ECO:0000305"},{"source":"PDB","id":"1RCT","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1ULA","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1ULB","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1V3Q","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4EAR","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4EB8","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4GKA","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI4
Number of Residues	6
Details	Binding site: {"evidences":[{"source":"PubMed","id":"14706628","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"23438750","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1RCT","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4EAR","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4EB8","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI5
Number of Residues	24
Details	Binding site: {"evidences":[{"source":"PubMed","id":"14706628","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"23438750","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"1763067","evidenceCode":"ECO:0000305"},{"source":"PDB","id":"1RCT","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1ULB","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4EAR","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4EB8","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4GKA","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI6
Number of Residues	12
Details	Binding site: {"evidences":[{"source":"PubMed","id":"14706628","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1RCT","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI7
Number of Residues	6
Details	Site: {"description":"Important for substrate specificity","evidences":[{"source":"PubMed","id":"9305964","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI8
Number of Residues	6
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"23186163","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

Catalytic Information from CSA

site_id	MCSA1
Number of Residues	10
Details	M-CSA 17

Chain

Residue

Details

---

site_id	MCSA2
Number of Residues	10
Details	M-CSA 17

Chain

Residue

Details

---

site_id	MCSA3
Number of Residues	10
Details	M-CSA 17

Chain

Residue

Details

---

site_id	MCSA4
Number of Residues	10
Details	M-CSA 17

Chain

Residue

Details

---

site_id	MCSA5
Number of Residues	10
Details	M-CSA 17

Chain	Residue	Details
E	SER33	hydrogen bond donor
E	HIS257	electrostatic stabiliser, hydrogen bond acceptor
E	HIS64	electrostatic stabiliser
E	HIS86	electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor
E	TYR88	electrostatic stabiliser, hydrogen bond donor
E	GLU89	activator, electrostatic stabiliser, hydrogen bond acceptor
E	ALA116	electrostatic stabiliser, hydrogen bond donor
E	MET219	electrostatic stabiliser, hydrogen bond donor
E	SER220	electrostatic stabiliser, hydrogen bond donor
E	ASN243	electrostatic stabiliser, hydrogen bond donor, polar interaction

---

site_id	MCSA6
Number of Residues	10
Details	M-CSA 17

Chain

Residue

Details

---