Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

4EAR

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	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	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	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	19
Details	BINDING SITE FOR RESIDUE IM5 A 301

Chain	Residue
A	SER33
A	GLY218
A	MET219
A	THR242
A	ASN243
A	FT6257
A	PO4302
A	HOH409
A	HOH412
A	HOH538
C	PHE159
A	HIS86
A	TYR88
A	ALA116
A	GLY118
A	VAL195
A	PHE200
A	GLU201
A	VAL217

site_id	AC2
Number of Residues	11
Details	BINDING SITE FOR RESIDUE PO4 A 302

Chain	Residue
A	GLY32
A	SER33
A	HIS64
A	ARG84
A	HIS86
A	ASN115
A	ALA116
A	SER220
A	IM5301
A	HOH401
A	HOH409

site_id	AC3
Number of Residues	17
Details	BINDING SITE FOR RESIDUE IM5 B 301

Chain	Residue
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	FT6257
B	VAL260
B	PO4302
B	HOH410
B	HOH555

site_id	AC4
Number of Residues	11
Details	BINDING SITE FOR RESIDUE PO4 B 302

Chain	Residue
B	GLY32
B	SER33
B	HIS64
B	ARG84
B	HIS86
B	ASN115
B	ALA116
B	SER220
B	IM5301
B	HOH405
B	HOH423

site_id	AC5
Number of Residues	20
Details	BINDING SITE FOR RESIDUE IM5 C 301

Chain	Residue
B	PHE159
C	SER33
C	HIS86
C	TYR88
C	ALA116
C	GLY118
C	VAL195
C	PHE200
C	GLU201
C	VAL217
C	GLY218
C	MET219
C	THR242
C	ASN243
C	FT6257
C	VAL260
C	PO4302
C	HOH412
C	HOH421
C	HOH551

site_id	AC6
Number of Residues	11
Details	BINDING SITE FOR RESIDUE PO4 C 302

Chain	Residue
C	GLY32
C	SER33
C	HIS64
C	ARG84
C	HIS86
C	ASN115
C	ALA116
C	SER220
C	IM5301
C	HOH405
C	HOH421

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: BINDING => ECO:0000269\|PubMed:23438750, ECO:0000305\|PubMed:14706628, ECO:0000305\|PubMed:1763067, ECO:0007744\|PDB:1RCT, ECO:0007744\|PDB:1ULA, ECO:0007744\|PDB:1ULB, ECO:0007744\|PDB:4EAR, ECO:0007744\|PDB:4EB8, ECO:0007744\|PDB:4GKA

Chain	Residue	Details
A	SER33
B	SER33
C	SER33

site_id	SWS_FT_FI2
Number of Residues	3
Details	BINDING: BINDING => ECO:0000250\|UniProtKB:P55859

Chain	Residue	Details
A	HIS64
B	HIS64
C	HIS64

site_id	SWS_FT_FI3
Number of Residues	3
Details	BINDING: BINDING => ECO:0000269\|PubMed:23438750, ECO:0000305\|PubMed:14706628, ECO:0000305\|PubMed:1763067, ECO:0007744\|PDB:1RCT, ECO:0007744\|PDB:1ULA, ECO:0007744\|PDB:1ULB, ECO:0007744\|PDB:1V3Q, ECO:0007744\|PDB:4EAR, ECO:0007744\|PDB:4EB8, ECO:0007744\|PDB:4GKA

Chain	Residue	Details
A	ARG84
B	ARG84
C	ARG84

site_id	SWS_FT_FI4
Number of Residues	3
Details	BINDING: BINDING => ECO:0000269\|PubMed:14706628, ECO:0000269\|PubMed:23438750, ECO:0007744\|PDB:1RCT, ECO:0007744\|PDB:4EAR, ECO:0007744\|PDB:4EB8

Chain	Residue	Details
A	TYR88
B	TYR88
C	TYR88

site_id	SWS_FT_FI5
Number of Residues	12
Details	BINDING: BINDING => ECO:0000269\|PubMed:14706628, ECO:0000269\|PubMed:23438750, ECO:0000305\|PubMed:1763067, ECO:0007744\|PDB:1RCT, ECO:0007744\|PDB:1ULB, ECO:0007744\|PDB:4EAR, ECO:0007744\|PDB:4EB8, ECO:0007744\|PDB:4GKA

Chain	Residue	Details
A	ALA116
C	GLU201
C	SER220
C	ASN243
A	GLU201
A	SER220
A	ASN243
B	ALA116
B	GLU201
B	SER220
B	ASN243
C	ALA116

site_id	SWS_FT_FI6
Number of Residues	6
Details	BINDING: BINDING => ECO:0000269\|PubMed:14706628, ECO:0007744\|PDB:1RCT

Chain	Residue	Details
A	MET219
A	FT6257
B	MET219
B	FT6257
C	MET219
C	FT6257

site_id	SWS_FT_FI7
Number of Residues	3
Details	SITE: Important for substrate specificity => ECO:0000269\|PubMed:9305964

Chain	Residue	Details
A	ASN243
B	ASN243
C	ASN243

site_id	SWS_FT_FI8
Number of Residues	3
Details	MOD_RES: N-acetylmethionine => ECO:0000269\|Ref.8, ECO:0007744\|PubMed:19413330, ECO:0007744\|PubMed:22223895

Chain	Residue	Details
A	MET1
B	MET1
C	MET1

site_id	SWS_FT_FI9
Number of Residues	3
Details	MOD_RES: Phosphoserine => ECO:0007744\|PubMed:23186163

Chain	Residue	Details
A	SER251
B	SER251
C	SER251

Catalytic Information from CSA

site_id	MCSA1
Number of Residues	10
Details	M-CSA 17

Chain	Residue	Details
A	SER33	hydrogen bond donor
A	FT6257	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	FT6257	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	FT6257	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

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