6VXE
Crystal structure of hydroxyproline dehydratase (HypD) from Clostridioides difficile with substrate trans-4-hydroxy-L-proline bound
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0003824 | molecular_function | catalytic activity |
| A | 0016829 | molecular_function | lyase activity |
| A | 0016835 | molecular_function | carbon-oxygen lyase activity |
| A | 0019471 | biological_process | 4-hydroxyproline metabolic process |
| A | 0019492 | biological_process | proline salvage |
| B | 0003824 | molecular_function | catalytic activity |
| B | 0016829 | molecular_function | lyase activity |
| B | 0016835 | molecular_function | carbon-oxygen lyase activity |
| B | 0019471 | biological_process | 4-hydroxyproline metabolic process |
| B | 0019492 | biological_process | proline salvage |
| C | 0003824 | molecular_function | catalytic activity |
| C | 0016829 | molecular_function | lyase activity |
| C | 0016835 | molecular_function | carbon-oxygen lyase activity |
| C | 0019471 | biological_process | 4-hydroxyproline metabolic process |
| C | 0019492 | biological_process | proline salvage |
| D | 0003824 | molecular_function | catalytic activity |
| D | 0016829 | molecular_function | lyase activity |
| D | 0016835 | molecular_function | carbon-oxygen lyase activity |
| D | 0019471 | biological_process | 4-hydroxyproline metabolic process |
| D | 0019492 | biological_process | proline salvage |
| E | 0003824 | molecular_function | catalytic activity |
| E | 0016829 | molecular_function | lyase activity |
| E | 0016835 | molecular_function | carbon-oxygen lyase activity |
| E | 0019471 | biological_process | 4-hydroxyproline metabolic process |
| E | 0019492 | biological_process | proline salvage |
| F | 0003824 | molecular_function | catalytic activity |
| F | 0016829 | molecular_function | lyase activity |
| F | 0016835 | molecular_function | carbon-oxygen lyase activity |
| F | 0019471 | biological_process | 4-hydroxyproline metabolic process |
| F | 0019492 | biological_process | proline salvage |
| G | 0003824 | molecular_function | catalytic activity |
| G | 0016829 | molecular_function | lyase activity |
| G | 0016835 | molecular_function | carbon-oxygen lyase activity |
| G | 0019471 | biological_process | 4-hydroxyproline metabolic process |
| G | 0019492 | biological_process | proline salvage |
| H | 0003824 | molecular_function | catalytic activity |
| H | 0016829 | molecular_function | lyase activity |
| H | 0016835 | molecular_function | carbon-oxygen lyase activity |
| H | 0019471 | biological_process | 4-hydroxyproline metabolic process |
| H | 0019492 | biological_process | proline salvage |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 12 |
| Details | binding site for residue HYP A 801 |
| Chain | Residue |
| A | PHE152 |
| A | TYR450 |
| A | THR645 |
| A | HOH1009 |
| A | HIS160 |
| A | TRP277 |
| A | ASP278 |
| A | SER334 |
| A | PHE340 |
| A | CYS434 |
| A | GLU436 |
| A | LEU447 |
| site_id | AC2 |
| Number of Residues | 11 |
| Details | binding site for residue HYP B 801 |
| Chain | Residue |
| B | HIS160 |
| B | TRP277 |
| B | ASP278 |
| B | SER334 |
| B | PHE340 |
| B | GLY433 |
| B | CYS434 |
| B | GLU436 |
| B | LEU447 |
| B | TYR450 |
| B | THR645 |
| site_id | AC3 |
| Number of Residues | 12 |
| Details | binding site for residue HYP C 801 |
| Chain | Residue |
| C | PHE152 |
| C | HIS160 |
| C | TRP277 |
| C | ASP278 |
| C | SER334 |
| C | PHE340 |
| C | GLY433 |
| C | CYS434 |
| C | GLU436 |
| C | LEU447 |
| C | TYR450 |
| C | THR645 |
| site_id | AC4 |
| Number of Residues | 10 |
| Details | binding site for residue HYP D 801 |
| Chain | Residue |
| D | PHE152 |
| D | TRP277 |
| D | ASP278 |
| D | SER334 |
| D | PHE340 |
| D | CYS434 |
| D | GLU436 |
| D | LEU447 |
| D | TYR450 |
| D | THR645 |
| site_id | AC5 |
| Number of Residues | 11 |
| Details | binding site for residue HYP E 801 |
| Chain | Residue |
| E | PHE152 |
| E | TRP277 |
| E | ASP278 |
| E | GLU333 |
| E | SER334 |
| E | PHE340 |
| E | CYS434 |
| E | GLU436 |
| E | LEU447 |
| E | TYR450 |
| E | THR645 |
| site_id | AC6 |
| Number of Residues | 11 |
| Details | binding site for residue HYP F 801 |
| Chain | Residue |
| F | PHE152 |
| F | HIS160 |
| F | TRP277 |
| F | ASP278 |
| F | SER334 |
| F | PHE340 |
| F | CYS434 |
| F | GLU436 |
| F | LEU447 |
| F | TYR450 |
| F | THR645 |
| site_id | AC7 |
| Number of Residues | 11 |
| Details | binding site for residue HYP G 801 |
| Chain | Residue |
| G | PHE152 |
| G | HIS160 |
| G | TRP277 |
| G | ASP278 |
| G | GLU333 |
| G | SER334 |
| G | PHE340 |
| G | CYS434 |
| G | GLU436 |
| G | TYR450 |
| G | THR645 |
| site_id | AC8 |
| Number of Residues | 11 |
| Details | binding site for residue HYP H 801 |
| Chain | Residue |
| H | HIS160 |
| H | TRP277 |
| H | ASP278 |
| H | GLU333 |
| H | SER334 |
| H | PHE340 |
| H | CYS434 |
| H | GLU436 |
| H | LEU447 |
| H | TYR450 |
| H | THR645 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 8 |
| Details | ACT_SITE: Cysteine radical intermediate => ECO:0000250|UniProtKB:Q30W70 |
| Chain | Residue | Details |
| A | CYS434 | |
| B | CYS434 | |
| C | CYS434 | |
| D | CYS434 | |
| E | CYS434 | |
| F | CYS434 | |
| G | CYS434 | |
| H | CYS434 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 8 |
| Details | ACT_SITE: Proton acceptor => ECO:0000250|UniProtKB:Q30W70 |
| Chain | Residue | Details |
| A | GLU436 | |
| B | GLU436 | |
| C | GLU436 | |
| D | GLU436 | |
| E | GLU436 | |
| F | GLU436 | |
| G | GLU436 | |
| H | GLU436 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 8 |
| Details | MOD_RES: Glycine radical => ECO:0000255|PROSITE-ProRule:PRU00493, ECO:0000269|PubMed:28183913 |
| Chain | Residue | Details |
| A | GLY765 | |
| B | GLY765 | |
| C | GLY765 | |
| D | GLY765 | |
| E | GLY765 | |
| F | GLY765 | |
| G | GLY765 | |
| H | GLY765 |
