4ECE

Crystal structure of purine nucleoside phosphorylase (W16Y, W94Y, W178Y, H257W) mutant from human complexed with guanine

Functional Information from GO Data

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

Functional Information from PDB Data

site_id	AC1
Number of Residues	11
Details	BINDING SITE FOR RESIDUE GUN A 301

Chain	Residue
A	ALA117
A	ASN243
A	HOH417
A	GLY118
A	VAL195
A	PHE200
A	GLU201
A	VAL217
A	GLY218
A	MET219
A	THR242

---

site_id	AC2
Number of Residues	10
Details	BINDING SITE FOR RESIDUE GUN B 301

Chain	Residue
B	ALA117
B	GLY118
B	VAL195
B	PHE200
B	GLU201
B	VAL217
B	MET219
B	THR242
B	ASN243
B	HOH404

---

site_id	AC3
Number of Residues	9
Details	BINDING SITE FOR RESIDUE GUN C 301

Chain	Residue
C	ALA117
C	GLY118
C	PHE200
C	GLU201
C	VAL217
C	MET219
C	THR242
C	ASN243
C	HOH419

---

site_id	AC4
Number of Residues	13
Details	BINDING SITE FOR RESIDUE GUN D 301

Chain	Residue
D	ALA116
D	ALA117
D	GLY118
D	VAL195
D	PHE200
D	GLU201
D	VAL217
D	GLY218
D	MET219
D	THR242
D	ASN243
D	HOH410
D	HOH431

---

site_id	AC5
Number of Residues	9
Details	BINDING SITE FOR RESIDUE GUN E 301

Chain	Residue
E	GLY118
E	VAL195
E	PHE200
E	GLU201
E	VAL217
E	GLY218
E	MET219
E	THR242
E	ASN243

---

site_id	AC6
Number of Residues	9
Details	BINDING SITE FOR RESIDUE GUN F 301

Chain	Residue
F	ALA117
F	GLY118
F	VAL195
F	PHE200
F	GLU201
F	VAL217
F	MET219
F	THR242
F	ASN243

---

Functional Information from PROSITE/UniProt

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

Chain	Residue	Details
A	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
A	SER33	hydrogen bond donor
A	TRP257	electrostatic stabiliser, hydrogen bond acceptor
A	HIS64	electrostatic stabiliser
A	HIS86	electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor
A	TYR88	electrostatic stabiliser, hydrogen bond donor
A	GLU89	activator, electrostatic stabiliser, hydrogen bond acceptor
A	ALA116	electrostatic stabiliser, hydrogen bond donor
A	MET219	electrostatic stabiliser, hydrogen bond donor
A	SER220	electrostatic stabiliser, hydrogen bond donor
A	ASN243	electrostatic stabiliser, hydrogen bond donor, polar interaction

---

site_id	MCSA2
Number of Residues	10
Details	M-CSA 17

Chain	Residue	Details
B	SER33	hydrogen bond donor
B	TRP257	electrostatic stabiliser, hydrogen bond acceptor
B	HIS64	electrostatic stabiliser
B	HIS86	electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor
B	TYR88	electrostatic stabiliser, hydrogen bond donor
B	GLU89	activator, electrostatic stabiliser, hydrogen bond acceptor
B	ALA116	electrostatic stabiliser, hydrogen bond donor
B	MET219	electrostatic stabiliser, hydrogen bond donor
B	SER220	electrostatic stabiliser, hydrogen bond donor
B	ASN243	electrostatic stabiliser, hydrogen bond donor, polar interaction

---

site_id	MCSA3
Number of Residues	10
Details	M-CSA 17

Chain	Residue	Details
C	SER33	hydrogen bond donor
C	TRP257	electrostatic stabiliser, hydrogen bond acceptor
C	HIS64	electrostatic stabiliser
C	HIS86	electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor
C	TYR88	electrostatic stabiliser, hydrogen bond donor
C	GLU89	activator, electrostatic stabiliser, hydrogen bond acceptor
C	ALA116	electrostatic stabiliser, hydrogen bond donor
C	MET219	electrostatic stabiliser, hydrogen bond donor
C	SER220	electrostatic stabiliser, hydrogen bond donor
C	ASN243	electrostatic stabiliser, hydrogen bond donor, polar interaction

---

site_id	MCSA4
Number of Residues	10
Details	M-CSA 17

Chain	Residue	Details
D	SER33	hydrogen bond donor
D	TRP257	electrostatic stabiliser, hydrogen bond acceptor
D	HIS64	electrostatic stabiliser
D	HIS86	electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor
D	TYR88	electrostatic stabiliser, hydrogen bond donor
D	GLU89	activator, electrostatic stabiliser, hydrogen bond acceptor
D	ALA116	electrostatic stabiliser, hydrogen bond donor
D	MET219	electrostatic stabiliser, hydrogen bond donor
D	SER220	electrostatic stabiliser, hydrogen bond donor
D	ASN243	electrostatic stabiliser, hydrogen bond donor, polar interaction

---

site_id	MCSA5
Number of Residues	10
Details	M-CSA 17

Chain	Residue	Details
E	SER33	hydrogen bond donor
E	TRP257	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
F	SER33	hydrogen bond donor
F	TRP257	electrostatic stabiliser, hydrogen bond acceptor
F	HIS64	electrostatic stabiliser
F	HIS86	electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor
F	TYR88	electrostatic stabiliser, hydrogen bond donor
F	GLU89	activator, electrostatic stabiliser, hydrogen bond acceptor
F	ALA116	electrostatic stabiliser, hydrogen bond donor
F	MET219	electrostatic stabiliser, hydrogen bond donor
F	SER220	electrostatic stabiliser, hydrogen bond donor
F	ASN243	electrostatic stabiliser, hydrogen bond donor, polar interaction

---