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 |