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 | 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 | 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: 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 | TRP257 | |
| B | MET219 | |
| B | TRP257 | |
| C | MET219 | |
| C | TRP257 |
| 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 | 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 |
