4EB8

Crystal structure of purine nucleoside phosphorylase (W16Y, W94Y, W178Y, H257W) mutant from human complexed with DADMe-ImmG and phosphate

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

Functional Information from PDB Data

site_id	AC1
Number of Residues	11
Details	BINDING SITE FOR RESIDUE PO4 A 301

Chain	Residue
A	GLY32
A	HOH401
A	HOH509
A	SER33
A	HIS64
A	ARG84
A	HIS86
A	ASN115
A	ALA116
A	SER220
A	IM5302

---

site_id	AC2
Number of Residues	17
Details	BINDING SITE FOR RESIDUE IM5 A 302

Chain	Residue
A	TYR88
A	ALA116
A	GLY118
A	VAL195
A	PHE200
A	GLU201
A	VAL217
A	GLY218
A	MET219
A	THR242
A	ASN243
A	TRP257
A	PO4301
A	HOH479
A	HOH509
A	HOH510
C	PHE159

---

site_id	AC3
Number of Residues	10
Details	BINDING SITE FOR RESIDUE PO4 B 301

Chain	Residue
B	GLY32
B	SER33
B	HIS64
B	ARG84
B	HIS86
B	ASN115
B	ALA116
B	SER220
B	IM5302
B	HOH401

---

site_id	AC4
Number of Residues	19
Details	BINDING SITE FOR RESIDUE IM5 B 302

Chain	Residue
A	PHE159
B	SER33
B	HIS86
B	TYR88
B	ALA116
B	ALA117
B	GLY118
B	VAL195
B	PHE200
B	GLU201
B	VAL217
B	GLY218
B	MET219
B	THR242
B	ASN243
B	TRP257
B	PO4301
B	HOH486
B	HOH501

---

site_id	AC5
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO B 303

Chain	Residue
B	TYR10
B	TYR94
B	THR97
B	PHE98
B	ARG101
B	PRO146

---

site_id	AC6
Number of Residues	10
Details	BINDING SITE FOR RESIDUE PO4 C 301

Chain	Residue
C	GLY32
C	SER33
C	HIS64
C	ARG84
C	HIS86
C	ASN115
C	ALA116
C	SER220
C	IM5302
C	HOH401

---

site_id	AC7
Number of Residues	16
Details	BINDING SITE FOR RESIDUE IM5 C 302

Chain	Residue
B	PHE159
C	TYR88
C	ALA116
C	ALA117
C	GLY118
C	PHE200
C	GLU201
C	VAL217
C	GLY218
C	MET219
C	THR242
C	ASN243
C	TRP257
C	PO4301
C	HOH426
C	HOH512

---

site_id	AC8
Number of Residues	1
Details	BINDING SITE FOR RESIDUE EDO C 303

Chain	Residue
C	HOH493

---

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	3
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	3
Details	Binding site: {"evidences":[{"source":"UniProtKB","id":"P55859","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI3
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":"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	3
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	12
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	6
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	3
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	2
Details	Modified residue: {"description":"N-acetylmethionine","evidences":[{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"FEB-2006","submissionDatabase":"UniProtKB","authors":["Bienvenut W.V.","Claeys D."]}},{"source":"PubMed","id":"19413330","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"22223895","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI9
Number of Residues	3
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

---