5LHV
X-ray structure of uridine phosphorylase from Vibrio cholerae in complex with uridine and sulfate ion at 1.29 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 | 0005829 | cellular_component | cytosol |
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 |
A | 0047847 | molecular_function | deoxyuridine phosphorylase activity |
B | 0003824 | molecular_function | catalytic activity |
B | 0004850 | molecular_function | uridine phosphorylase activity |
B | 0005737 | cellular_component | cytoplasm |
B | 0005829 | cellular_component | cytosol |
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 |
B | 0047847 | molecular_function | deoxyuridine phosphorylase activity |
C | 0003824 | molecular_function | catalytic activity |
C | 0004850 | molecular_function | uridine phosphorylase activity |
C | 0005737 | cellular_component | cytoplasm |
C | 0005829 | cellular_component | cytosol |
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 |
C | 0047847 | molecular_function | deoxyuridine phosphorylase activity |
D | 0003824 | molecular_function | catalytic activity |
D | 0004850 | molecular_function | uridine phosphorylase activity |
D | 0005737 | cellular_component | cytoplasm |
D | 0005829 | cellular_component | cytosol |
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 |
D | 0047847 | molecular_function | deoxyuridine phosphorylase activity |
E | 0003824 | molecular_function | catalytic activity |
E | 0004850 | molecular_function | uridine phosphorylase activity |
E | 0005737 | cellular_component | cytoplasm |
E | 0005829 | cellular_component | cytosol |
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 |
E | 0047847 | molecular_function | deoxyuridine phosphorylase activity |
F | 0003824 | molecular_function | catalytic activity |
F | 0004850 | molecular_function | uridine phosphorylase activity |
F | 0005737 | cellular_component | cytoplasm |
F | 0005829 | cellular_component | cytosol |
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 |
F | 0047847 | molecular_function | deoxyuridine phosphorylase activity |
Functional Information from PDB Data
site_id | AC1 |
Number of Residues | 10 |
Details | binding site for residue SO4 A 301 |
Chain | Residue |
A | GLY25 |
B | ARG47 |
A | ARG29 |
A | ARG90 |
A | VAL91 |
A | GLY92 |
A | THR93 |
A | URI303 |
A | HOH403 |
A | HOH404 |
site_id | AC2 |
Number of Residues | 6 |
Details | binding site for residue SO4 A 302 |
Chain | Residue |
A | ARG177 |
A | HOH407 |
A | HOH468 |
A | HOH518 |
C | ARG177 |
E | ARG177 |
site_id | AC3 |
Number of Residues | 19 |
Details | binding site for residue URI A 303 |
Chain | Residue |
A | ARG90 |
A | THR93 |
A | THR94 |
A | GLY95 |
A | PHE161 |
A | GLN165 |
A | ARG167 |
A | GLU195 |
A | MET196 |
A | GLU197 |
A | SO4301 |
A | URA304 |
A | HOH401 |
A | HOH402 |
A | HOH403 |
A | HOH404 |
A | HOH436 |
A | HOH444 |
B | HIS7 |
site_id | AC4 |
Number of Residues | 11 |
Details | binding site for residue URA A 304 |
Chain | Residue |
A | THR94 |
A | GLY95 |
A | GLN165 |
A | ARG167 |
A | PHE194 |
A | GLU195 |
A | MET196 |
A | ILE220 |
A | URI303 |
A | HOH404 |
A | HOH436 |
site_id | AC5 |
Number of Residues | 5 |
Details | binding site for residue MG A 305 |
Chain | Residue |
A | HOH412 |
A | HOH518 |
A | HOH646 |
C | HOH465 |
C | HOH658 |
site_id | AC6 |
Number of Residues | 2 |
Details | binding site for residue CL A 306 |
Chain | Residue |
A | PHE133 |
F | HOH524 |
site_id | AC7 |
Number of Residues | 6 |
Details | binding site for residue NA A 307 |
Chain | Residue |
A | GLU48 |
A | ILE68 |
A | SER72 |
B | GLU48 |
B | ILE68 |
B | SER72 |
site_id | AC8 |
Number of Residues | 7 |
Details | binding site for residue GOL A 308 |
Chain | Residue |
A | ARG178 |
A | GLU185 |
A | HOH415 |
A | HOH423 |
E | ARG177 |
F | PRO124 |
F | GLU126 |
site_id | AC9 |
Number of Residues | 10 |
Details | binding site for residue SO4 B 301 |
Chain | Residue |
A | ARG47 |
B | GLY25 |
B | ARG29 |
B | ARG90 |
B | VAL91 |
B | GLY92 |
B | THR93 |
B | URI303 |
B | HOH401 |
B | HOH421 |
site_id | AD1 |
Number of Residues | 7 |
Details | binding site for residue SO4 B 302 |
Chain | Residue |
B | ARG177 |
B | HOH404 |
B | HOH469 |
B | HOH513 |
B | HOH542 |
D | ARG177 |
F | ARG177 |
site_id | AD2 |
Number of Residues | 20 |
Details | binding site for residue URI B 303 |
Chain | Residue |
B | HOH420 |
B | HOH421 |
B | HOH431 |
B | HOH466 |
A | HIS7 |
B | ARG90 |
B | THR93 |
B | THR94 |
B | GLY95 |
B | PHE161 |
B | GLN165 |
B | ARG167 |
B | GLU195 |
B | MET196 |
B | GLU197 |
B | ILE220 |
B | SO4301 |
B | URA304 |
B | HOH401 |
B | HOH410 |
site_id | AD3 |
Number of Residues | 11 |
Details | binding site for residue URA B 304 |
Chain | Residue |
B | THR93 |
B | THR94 |
B | GLY95 |
B | GLN165 |
B | ARG167 |
B | GLU195 |
B | MET196 |
B | ILE220 |
B | URI303 |
B | HOH401 |
B | HOH431 |
site_id | AD4 |
Number of Residues | 6 |
Details | binding site for residue MG B 305 |
Chain | Residue |
B | HOH419 |
B | HOH542 |
B | HOH648 |
F | HOH558 |
F | HOH643 |
F | HOH660 |
site_id | AD5 |
Number of Residues | 2 |
Details | binding site for residue CL B 306 |
Chain | Residue |
B | PHE133 |
B | HOH507 |
site_id | AD6 |
Number of Residues | 7 |
Details | binding site for residue GOL B 307 |
Chain | Residue |
B | ARG178 |
B | GLU185 |
B | HOH418 |
B | HOH437 |
C | PRO124 |
C | GLU126 |
D | ARG177 |
site_id | AD7 |
Number of Residues | 10 |
Details | binding site for residue SO4 C 301 |
Chain | Residue |
C | GLY25 |
C | ARG29 |
C | ARG90 |
C | VAL91 |
C | GLY92 |
C | THR93 |
C | URI302 |
C | HOH401 |
C | HOH402 |
D | ARG47 |
site_id | AD8 |
Number of Residues | 19 |
Details | binding site for residue URI C 302 |
Chain | Residue |
C | ARG90 |
C | THR93 |
C | THR94 |
C | GLY95 |
C | PHE161 |
C | GLN165 |
C | ARG167 |
C | GLU195 |
C | MET196 |
C | GLU197 |
C | SO4301 |
C | URA303 |
C | HOH401 |
C | HOH402 |
C | HOH408 |
C | HOH410 |
C | HOH419 |
C | HOH428 |
D | HIS7 |
site_id | AD9 |
Number of Residues | 12 |
Details | binding site for residue URA C 303 |
Chain | Residue |
C | THR94 |
C | GLY95 |
C | PHE161 |
C | GLN165 |
C | ARG167 |
C | PHE194 |
C | GLU195 |
C | MET196 |
C | ILE220 |
C | URI302 |
C | HOH402 |
C | HOH428 |
site_id | AE1 |
Number of Residues | 5 |
Details | binding site for residue MG C 304 |
Chain | Residue |
C | HOH546 |
C | HOH555 |
C | HOH584 |
C | HOH631 |
C | HOH643 |
site_id | AE2 |
Number of Residues | 2 |
Details | binding site for residue CL C 305 |
Chain | Residue |
C | PHE133 |
C | HOH519 |
site_id | AE3 |
Number of Residues | 6 |
Details | binding site for residue NA C 306 |
Chain | Residue |
C | GLU48 |
C | ILE68 |
C | SER72 |
D | GLU48 |
D | ILE68 |
D | SER72 |
site_id | AE4 |
Number of Residues | 7 |
Details | binding site for residue GOL C 307 |
Chain | Residue |
A | ARG177 |
B | PRO124 |
B | GLU126 |
C | ARG178 |
C | GLU185 |
C | HOH409 |
C | HOH412 |
site_id | AE5 |
Number of Residues | 10 |
Details | binding site for residue SO4 D 301 |
Chain | Residue |
C | ARG47 |
D | GLY25 |
D | ARG29 |
D | ARG90 |
D | VAL91 |
D | GLY92 |
D | THR93 |
D | URI302 |
D | HOH401 |
D | HOH415 |
site_id | AE6 |
Number of Residues | 21 |
Details | binding site for residue URI D 302 |
Chain | Residue |
C | HIS7 |
D | ARG90 |
D | THR93 |
D | THR94 |
D | GLY95 |
D | PHE161 |
D | GLN165 |
D | ARG167 |
D | PHE194 |
D | GLU195 |
D | MET196 |
D | GLU197 |
D | ILE220 |
D | SO4301 |
D | URA303 |
D | HOH401 |
D | HOH405 |
D | HOH415 |
D | HOH416 |
D | HOH418 |
D | HOH447 |
site_id | AE7 |
Number of Residues | 13 |
Details | binding site for residue URA D 303 |
Chain | Residue |
D | THR93 |
D | THR94 |
D | GLY95 |
D | PHE161 |
D | GLN165 |
D | ARG167 |
D | PHE194 |
D | GLU195 |
D | MET196 |
D | ILE220 |
D | URI302 |
D | HOH401 |
D | HOH418 |
site_id | AE8 |
Number of Residues | 5 |
Details | binding site for residue MG D 304 |
Chain | Residue |
B | HOH513 |
B | HOH553 |
B | HOH632 |
B | HOH655 |
D | HOH402 |
site_id | AE9 |
Number of Residues | 2 |
Details | binding site for residue CL D 305 |
Chain | Residue |
D | PHE133 |
D | HOH500 |
site_id | AF1 |
Number of Residues | 8 |
Details | binding site for residue GOL D 306 |
Chain | Residue |
D | ARG178 |
D | GLU185 |
D | HOH408 |
D | HOH410 |
D | HOH555 |
E | PRO124 |
E | GLU126 |
F | ARG177 |
site_id | AF2 |
Number of Residues | 11 |
Details | binding site for residue SO4 E 301 |
Chain | Residue |
E | GLY25 |
E | ARG29 |
E | ARG90 |
E | VAL91 |
E | GLY92 |
E | THR93 |
E | URI302 |
E | HOH401 |
E | HOH414 |
E | HOH468 |
F | ARG47 |
site_id | AF3 |
Number of Residues | 20 |
Details | binding site for residue URI E 302 |
Chain | Residue |
E | ARG90 |
E | THR93 |
E | THR94 |
E | GLY95 |
E | PHE161 |
E | GLN165 |
E | ARG167 |
E | PHE194 |
E | GLU195 |
E | MET196 |
E | GLU197 |
E | SO4301 |
E | URA303 |
E | HOH401 |
E | HOH414 |
E | HOH424 |
E | HOH443 |
E | HOH463 |
E | HOH468 |
F | HIS7 |
site_id | AF4 |
Number of Residues | 13 |
Details | binding site for residue URA E 303 |
Chain | Residue |
E | THR93 |
E | THR94 |
E | GLY95 |
E | PHE161 |
E | GLN165 |
E | ARG167 |
E | PHE194 |
E | GLU195 |
E | MET196 |
E | ILE220 |
E | URI302 |
E | HOH401 |
E | HOH463 |
site_id | AF5 |
Number of Residues | 5 |
Details | binding site for residue MG E 304 |
Chain | Residue |
A | HOH468 |
A | HOH483 |
A | HOH635 |
A | HOH639 |
E | HOH412 |
site_id | AF6 |
Number of Residues | 3 |
Details | binding site for residue CL E 305 |
Chain | Residue |
D | HOH501 |
E | PHE133 |
E | HOH632 |
site_id | AF7 |
Number of Residues | 6 |
Details | binding site for residue NA E 306 |
Chain | Residue |
E | GLU48 |
E | ILE68 |
E | SER72 |
F | GLU48 |
F | ILE68 |
F | SER72 |
site_id | AF8 |
Number of Residues | 7 |
Details | binding site for residue GOL E 307 |
Chain | Residue |
C | ARG177 |
D | PRO124 |
D | GLU126 |
E | ARG178 |
E | GLU185 |
E | HOH418 |
E | HOH460 |
site_id | AF9 |
Number of Residues | 4 |
Details | binding site for residue MG E 308 |
Chain | Residue |
E | HOH572 |
E | HOH598 |
E | HOH599 |
E | HOH654 |
site_id | AG1 |
Number of Residues | 10 |
Details | binding site for residue SO4 F 301 |
Chain | Residue |
E | ARG47 |
F | GLY25 |
F | ARG29 |
F | ARG90 |
F | VAL91 |
F | GLY92 |
F | THR93 |
F | URI302 |
F | HOH402 |
F | HOH403 |
site_id | AG2 |
Number of Residues | 20 |
Details | binding site for residue URI F 302 |
Chain | Residue |
E | HIS7 |
F | ARG90 |
F | THR93 |
F | THR94 |
F | GLY95 |
F | PHE161 |
F | GLN165 |
F | ARG167 |
F | GLU195 |
F | MET196 |
F | GLU197 |
F | ILE220 |
F | SO4301 |
F | URA303 |
F | HOH401 |
F | HOH402 |
F | HOH403 |
F | HOH410 |
F | HOH430 |
F | HOH452 |
site_id | AG3 |
Number of Residues | 12 |
Details | binding site for residue URA F 303 |
Chain | Residue |
F | THR93 |
F | THR94 |
F | GLY95 |
F | PHE161 |
F | GLN165 |
F | ARG167 |
F | GLU195 |
F | MET196 |
F | ILE220 |
F | URI302 |
F | HOH403 |
F | HOH452 |
site_id | AG4 |
Number of Residues | 4 |
Details | binding site for residue MG F 304 |
Chain | Residue |
B | HOH469 |
D | HOH492 |
D | HOH612 |
F | HOH425 |
site_id | AG5 |
Number of Residues | 2 |
Details | binding site for residue CL F 305 |
Chain | Residue |
A | HOH526 |
F | PHE133 |
site_id | AG6 |
Number of Residues | 7 |
Details | binding site for residue GOL F 306 |
Chain | Residue |
A | PRO124 |
A | GLU126 |
B | ARG177 |
F | ARG178 |
F | GLU185 |
F | HOH423 |
F | HOH512 |
site_id | AG7 |
Number of Residues | 10 |
Details | binding site for residue GOL F 307 |
Chain | Residue |
F | ASP132 |
F | CYS205 |
F | ALA206 |
F | GLY209 |
F | LEU210 |
F | LYS211 |
F | HOH407 |
F | HOH421 |
F | HOH515 |
F | HOH625 |
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 |