4K6O
X-ray structure uridine phosphorylase from Vibrio cholerae in complex with 6-methyluracil at 1.17 A resolution
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0003824 | molecular_function | catalytic activity |
| A | 0004850 | molecular_function | uridine phosphorylase activity |
| A | 0005737 | cellular_component | cytoplasm |
| A | 0009116 | biological_process | nucleoside metabolic process |
| A | 0009164 | biological_process | nucleoside catabolic process |
| A | 0009166 | biological_process | nucleotide catabolic process |
| A | 0016757 | molecular_function | glycosyltransferase activity |
| A | 0016763 | molecular_function | pentosyltransferase activity |
| A | 0044206 | biological_process | UMP salvage |
| A | 0046872 | molecular_function | metal ion binding |
| B | 0003824 | molecular_function | catalytic activity |
| B | 0004850 | molecular_function | uridine phosphorylase activity |
| B | 0005737 | cellular_component | cytoplasm |
| B | 0009116 | biological_process | nucleoside metabolic process |
| B | 0009164 | biological_process | nucleoside catabolic process |
| B | 0009166 | biological_process | nucleotide catabolic process |
| B | 0016757 | molecular_function | glycosyltransferase activity |
| B | 0016763 | molecular_function | pentosyltransferase activity |
| B | 0044206 | biological_process | UMP salvage |
| B | 0046872 | molecular_function | metal ion binding |
| C | 0003824 | molecular_function | catalytic activity |
| C | 0004850 | molecular_function | uridine phosphorylase activity |
| C | 0005737 | cellular_component | cytoplasm |
| C | 0009116 | biological_process | nucleoside metabolic process |
| C | 0009164 | biological_process | nucleoside catabolic process |
| C | 0009166 | biological_process | nucleotide catabolic process |
| C | 0016757 | molecular_function | glycosyltransferase activity |
| C | 0016763 | molecular_function | pentosyltransferase activity |
| C | 0044206 | biological_process | UMP salvage |
| C | 0046872 | molecular_function | metal ion binding |
| D | 0003824 | molecular_function | catalytic activity |
| D | 0004850 | molecular_function | uridine phosphorylase activity |
| D | 0005737 | cellular_component | cytoplasm |
| D | 0009116 | biological_process | nucleoside metabolic process |
| D | 0009164 | biological_process | nucleoside catabolic process |
| D | 0009166 | biological_process | nucleotide catabolic process |
| D | 0016757 | molecular_function | glycosyltransferase activity |
| D | 0016763 | molecular_function | pentosyltransferase activity |
| D | 0044206 | biological_process | UMP salvage |
| D | 0046872 | molecular_function | metal ion binding |
| E | 0003824 | molecular_function | catalytic activity |
| E | 0004850 | molecular_function | uridine phosphorylase activity |
| E | 0005737 | cellular_component | cytoplasm |
| E | 0009116 | biological_process | nucleoside metabolic process |
| E | 0009164 | biological_process | nucleoside catabolic process |
| E | 0009166 | biological_process | nucleotide catabolic process |
| E | 0016757 | molecular_function | glycosyltransferase activity |
| E | 0016763 | molecular_function | pentosyltransferase activity |
| E | 0044206 | biological_process | UMP salvage |
| E | 0046872 | molecular_function | metal ion binding |
| F | 0003824 | molecular_function | catalytic activity |
| F | 0004850 | molecular_function | uridine phosphorylase activity |
| F | 0005737 | cellular_component | cytoplasm |
| F | 0009116 | biological_process | nucleoside metabolic process |
| F | 0009164 | biological_process | nucleoside catabolic process |
| F | 0009166 | biological_process | nucleotide catabolic process |
| F | 0016757 | molecular_function | glycosyltransferase activity |
| F | 0016763 | molecular_function | pentosyltransferase activity |
| F | 0044206 | biological_process | UMP salvage |
| F | 0046872 | molecular_function | metal ion binding |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE CL A 301 |
| Chain | Residue |
| A | ALA44 |
| A | SER45 |
| A | HOH572 |
| A | HOH665 |
| site_id | AC2 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE CL A 302 |
| Chain | Residue |
| A | GLY25 |
| A | ASP26 |
| A | HOH478 |
| A | HOH491 |
| B | HOH531 |
| site_id | AC3 |
| Number of Residues | 12 |
| Details | BINDING SITE FOR RESIDUE 6MU A 303 |
| Chain | Residue |
| A | THR93 |
| A | GLY95 |
| A | PHE161 |
| A | GLN165 |
| A | ARG167 |
| A | GLU195 |
| A | MET196 |
| A | ILE219 |
| A | HOH463 |
| A | HOH512 |
| A | HOH530 |
| A | HOH562 |
| site_id | AC4 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE MG A 304 |
| Chain | Residue |
| A | GLN180 |
| A | HOH496 |
| A | HOH499 |
| A | HOH535 |
| A | HOH543 |
| A | HOH600 |
| site_id | AC5 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE MG A 305 |
| Chain | Residue |
| A | HOH457 |
| A | HOH461 |
| A | HOH474 |
| A | HOH493 |
| A | HOH519 |
| A | HOH546 |
| site_id | AC6 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE NA A 306 |
| Chain | Residue |
| A | GLU48 |
| A | ILE68 |
| A | SER72 |
| B | GLU48 |
| B | ILE68 |
| B | SER72 |
| site_id | AC7 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE EDO A 307 |
| Chain | Residue |
| A | MET125 |
| A | GLU126 |
| A | HOH487 |
| F | MET125 |
| site_id | AC8 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE EOH A 308 |
| Chain | Residue |
| A | ARG178 |
| A | HOH584 |
| A | HOH611 |
| B | LEU120 |
| B | HOH431 |
| B | HOH435 |
| site_id | AC9 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE CL A 309 |
| Chain | Residue |
| A | PHE133 |
| A | HOH519 |
| A | HOH602 |
| F | THR110 |
| F | HOH440 |
| site_id | BC1 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE CL B 301 |
| Chain | Residue |
| B | GLY25 |
| B | ASP26 |
| B | HOH543 |
| B | HOH646 |
| B | HOH733 |
| site_id | BC2 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE CL B 302 |
| Chain | Residue |
| B | ASN221 |
| B | HOH593 |
| site_id | BC3 |
| Number of Residues | 11 |
| Details | BINDING SITE FOR RESIDUE 6MU B 303 |
| Chain | Residue |
| B | THR93 |
| B | GLY95 |
| B | PHE161 |
| B | GLN165 |
| B | ARG167 |
| B | GLU195 |
| B | MET196 |
| B | ILE219 |
| B | ILE220 |
| B | TRS308 |
| B | HOH417 |
| site_id | BC4 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE MG B 304 |
| Chain | Residue |
| B | GLN180 |
| B | HOH471 |
| B | HOH500 |
| B | HOH510 |
| B | HOH563 |
| B | HOH598 |
| site_id | BC5 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE MG B 305 |
| Chain | Residue |
| B | HOH444 |
| B | HOH446 |
| B | HOH506 |
| B | HOH518 |
| B | HOH727 |
| site_id | BC6 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE MG B 306 |
| Chain | Residue |
| B | HOH456 |
| B | HOH463 |
| site_id | BC7 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE NA B 307 |
| Chain | Residue |
| B | ARG167 |
| B | THR170 |
| B | ARG174 |
| B | HOH404 |
| site_id | BC8 |
| Number of Residues | 12 |
| Details | BINDING SITE FOR RESIDUE TRS B 308 |
| Chain | Residue |
| B | HOH576 |
| B | HOH698 |
| A | HIS7 |
| A | ARG47 |
| B | ILE68 |
| B | THR93 |
| B | GLU195 |
| B | MET196 |
| B | GLU197 |
| B | 6MU303 |
| B | HOH402 |
| B | HOH521 |
| site_id | BC9 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE EDO B 309 |
| Chain | Residue |
| B | PRO99 |
| B | VAL101 |
| B | ASN102 |
| B | VAL103 |
| B | ASN221 |
| B | HOH593 |
| B | HOH622 |
| B | HOH629 |
| site_id | CC1 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE EOH B 310 |
| Chain | Residue |
| A | LEU120 |
| A | HOH431 |
| B | ARG178 |
| B | HOH428 |
| B | HOH618 |
| C | HOH647 |
| site_id | CC2 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE CL C 301 |
| Chain | Residue |
| C | GLY25 |
| C | ASP26 |
| C | HOH786 |
| site_id | CC3 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE CL C 302 |
| Chain | Residue |
| C | ASN221 |
| C | HOH594 |
| site_id | CC4 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE CL C 303 |
| Chain | Residue |
| B | THR110 |
| B | HOH493 |
| C | PHE133 |
| C | HOH446 |
| C | HOH682 |
| site_id | CC5 |
| Number of Residues | 10 |
| Details | BINDING SITE FOR RESIDUE 6MU C 304 |
| Chain | Residue |
| C | THR93 |
| C | GLY95 |
| C | PHE161 |
| C | GLN165 |
| C | ARG167 |
| C | GLU195 |
| C | MET196 |
| C | ILE220 |
| C | TRS309 |
| C | HOH403 |
| site_id | CC6 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE MG C 305 |
| Chain | Residue |
| C | GLN180 |
| C | HOH525 |
| C | HOH579 |
| C | HOH591 |
| C | HOH601 |
| E | HOH543 |
| site_id | CC7 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE MG C 306 |
| Chain | Residue |
| C | HOH603 |
| C | HOH624 |
| C | HOH692 |
| C | HOH754 |
| C | HOH758 |
| C | HOH789 |
| site_id | CC8 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE MG C 307 |
| Chain | Residue |
| B | HOH493 |
| B | HOH527 |
| C | HOH439 |
| C | HOH444 |
| C | HOH450 |
| C | HOH533 |
| site_id | CC9 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE NA C 308 |
| Chain | Residue |
| C | GLU48 |
| C | ILE68 |
| C | SER72 |
| D | GLU48 |
| D | ILE68 |
| D | SER72 |
| site_id | DC1 |
| Number of Residues | 11 |
| Details | BINDING SITE FOR RESIDUE TRS C 309 |
| Chain | Residue |
| C | ILE68 |
| C | THR93 |
| C | GLU195 |
| C | MET196 |
| C | GLU197 |
| C | 6MU304 |
| C | HOH472 |
| C | HOH520 |
| C | HOH731 |
| D | HIS7 |
| D | ARG47 |
| site_id | DC2 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE EOH C 310 |
| Chain | Residue |
| C | VAL101 |
| C | ASN102 |
| C | VAL103 |
| C | ASN221 |
| C | HOH594 |
| C | HOH649 |
| C | HOH705 |
| site_id | DC3 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE EOH C 311 |
| Chain | Residue |
| B | HOH631 |
| C | ARG178 |
| C | HOH630 |
| C | HOH635 |
| D | LEU120 |
| D | HOH418 |
| D | HOH427 |
| site_id | DC4 |
| Number of Residues | 10 |
| Details | BINDING SITE FOR RESIDUE GOL C 312 |
| Chain | Residue |
| C | ARG47 |
| C | HOH477 |
| C | HOH704 |
| D | GLY25 |
| D | ILE68 |
| D | ARG90 |
| D | MET196 |
| D | GLU197 |
| D | HOH670 |
| D | HOH821 |
| site_id | DC5 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE CL D 301 |
| Chain | Residue |
| C | HOH523 |
| D | GLY25 |
| D | ASP26 |
| D | HOH559 |
| site_id | DC6 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE 6MU D 302 |
| Chain | Residue |
| D | THR93 |
| D | GLY95 |
| D | GLN165 |
| D | ARG167 |
| D | GLU195 |
| D | MET196 |
| D | HOH445 |
| D | HOH810 |
| site_id | DC7 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE MG D 303 |
| Chain | Residue |
| D | GLN180 |
| D | HOH464 |
| D | HOH498 |
| D | HOH499 |
| D | HOH544 |
| D | HOH631 |
| site_id | DC8 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE MG D 304 |
| Chain | Residue |
| D | HIS46 |
| D | HOH518 |
| D | HOH652 |
| D | HOH797 |
| D | HOH814 |
| site_id | DC9 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE MG D 305 |
| Chain | Residue |
| D | HOH439 |
| D | HOH442 |
| D | HOH480 |
| D | HOH755 |
| D | HOH757 |
| site_id | EC1 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE EDO D 306 |
| Chain | Residue |
| D | MET125 |
| D | GLU126 |
| D | HOH534 |
| E | MET125 |
| E | GLU126 |
| site_id | EC2 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE EOH D 307 |
| Chain | Residue |
| C | LEU120 |
| C | HOH427 |
| C | HOH428 |
| D | ARG178 |
| D | HOH560 |
| D | HOH562 |
| D | HOH778 |
| site_id | EC3 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE CL E 301 |
| Chain | Residue |
| E | GLY25 |
| E | ASP26 |
| E | ARG29 |
| F | HOH601 |
| site_id | EC4 |
| Number of Residues | 11 |
| Details | BINDING SITE FOR RESIDUE 6MU E 302 |
| Chain | Residue |
| E | THR93 |
| E | GLY95 |
| E | PHE161 |
| E | GLN165 |
| E | ARG167 |
| E | PHE194 |
| E | GLU195 |
| E | MET196 |
| E | ILE220 |
| E | TRS306 |
| E | HOH420 |
| site_id | EC5 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE MG E 303 |
| Chain | Residue |
| A | HOH795 |
| E | GLN180 |
| E | HOH654 |
| E | HOH681 |
| E | HOH728 |
| site_id | EC6 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE NA E 304 |
| Chain | Residue |
| E | GLU48 |
| E | ILE68 |
| E | SER72 |
| F | GLU48 |
| F | ILE68 |
| F | SER72 |
| site_id | EC7 |
| Number of Residues | 10 |
| Details | BINDING SITE FOR RESIDUE TRS E 305 |
| Chain | Residue |
| E | HIS7 |
| E | ARG47 |
| E | HOH486 |
| E | HOH526 |
| E | HOH799 |
| F | ILE68 |
| F | THR93 |
| F | GLU197 |
| F | 6MU303 |
| F | HOH831 |
| site_id | EC8 |
| Number of Residues | 12 |
| Details | BINDING SITE FOR RESIDUE TRS E 306 |
| Chain | Residue |
| E | ILE68 |
| E | THR93 |
| E | GLU195 |
| E | MET196 |
| E | GLU197 |
| E | 6MU302 |
| E | HOH457 |
| E | HOH520 |
| E | HOH702 |
| E | HOH724 |
| F | HIS7 |
| F | ARG47 |
| site_id | EC9 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE EOH E 307 |
| Chain | Residue |
| D | HOH595 |
| E | ARG178 |
| E | HOH602 |
| F | LEU120 |
| F | HOH423 |
| F | HOH430 |
| site_id | FC1 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE MG E 308 |
| Chain | Residue |
| E | HOH461 |
| E | HOH491 |
| E | HOH518 |
| E | HOH788 |
| E | HOH821 |
| site_id | FC2 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE CL F 301 |
| Chain | Residue |
| F | GLY25 |
| F | ASP26 |
| F | ARG29 |
| F | HOH805 |
| site_id | FC3 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE CL F 302 |
| Chain | Residue |
| F | ARG29 |
| F | ALA238 |
| F | ILE241 |
| F | HOH447 |
| F | HOH728 |
| site_id | FC4 |
| Number of Residues | 11 |
| Details | BINDING SITE FOR RESIDUE 6MU F 303 |
| Chain | Residue |
| E | TRS305 |
| F | THR93 |
| F | GLY95 |
| F | PHE161 |
| F | GLN165 |
| F | ARG167 |
| F | PHE194 |
| F | GLU195 |
| F | MET196 |
| F | ILE220 |
| F | HOH416 |
| site_id | FC5 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE MG F 304 |
| Chain | Residue |
| F | GLN180 |
| F | HOH594 |
| F | HOH605 |
| F | HOH607 |
| F | HOH676 |
| F | HOH827 |
| site_id | FC6 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE MG F 305 |
| Chain | Residue |
| F | ASN102 |
| F | MG306 |
| F | HOH468 |
| F | HOH501 |
| site_id | FC7 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE MG F 306 |
| Chain | Residue |
| F | MG305 |
| F | HOH468 |
| F | HOH501 |
| F | HOH558 |
| site_id | FC8 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE EDO F 307 |
| Chain | Residue |
| E | LYS3 |
| E | GLN82 |
| F | ASP169 |
| F | THR170 |
| F | PHE171 |
| F | HOH523 |
| site_id | FC9 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE EOH F 308 |
| Chain | Residue |
| E | LEU120 |
| E | HOH428 |
| E | HOH437 |
| F | ARG178 |
| F | HOH571 |
| F | HOH622 |
Functional Information from PROSITE/UniProt
| site_id | PS01232 |
| Number of Residues | 16 |
| Details | PNP_UDP_1 Purine and other phosphorylases family 1 signature. StGIGgPStSIaveEL |
| Chain | Residue | Details |
| A | SER65-LEU80 |
