4ZDQ
Crystal Structure of 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase (IspD) from Burkholderia thailandensis complexed with CTP
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0003824 | molecular_function | catalytic activity |
| A | 0008299 | biological_process | isoprenoid biosynthetic process |
| A | 0016779 | molecular_function | nucleotidyltransferase activity |
| A | 0019288 | biological_process | isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway |
| A | 0050518 | molecular_function | 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase activity |
| A | 0070567 | molecular_function | cytidylyltransferase activity |
| B | 0003824 | molecular_function | catalytic activity |
| B | 0008299 | biological_process | isoprenoid biosynthetic process |
| B | 0016779 | molecular_function | nucleotidyltransferase activity |
| B | 0019288 | biological_process | isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway |
| B | 0050518 | molecular_function | 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase activity |
| B | 0070567 | molecular_function | cytidylyltransferase activity |
| C | 0003824 | molecular_function | catalytic activity |
| C | 0008299 | biological_process | isoprenoid biosynthetic process |
| C | 0016779 | molecular_function | nucleotidyltransferase activity |
| C | 0019288 | biological_process | isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway |
| C | 0050518 | molecular_function | 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase activity |
| C | 0070567 | molecular_function | cytidylyltransferase activity |
| D | 0003824 | molecular_function | catalytic activity |
| D | 0008299 | biological_process | isoprenoid biosynthetic process |
| D | 0016779 | molecular_function | nucleotidyltransferase activity |
| D | 0019288 | biological_process | isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway |
| D | 0050518 | molecular_function | 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase activity |
| D | 0070567 | molecular_function | cytidylyltransferase activity |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 21 |
| Details | binding site for residue CTP A 301 |
| Chain | Residue |
| A | PRO10 |
| A | GLY79 |
| A | ALA80 |
| A | SER81 |
| A | ARG82 |
| A | SER85 |
| A | ASP108 |
| A | ALA109 |
| A | ALA110 |
| A | LYS215 |
| A | MG302 |
| A | CYS11 |
| A | HOH405 |
| A | HOH429 |
| A | ALA12 |
| A | GLY13 |
| A | THR14 |
| A | GLY15 |
| A | SER16 |
| A | ARG17 |
| A | LYS24 |
| site_id | AC2 |
| Number of Residues | 3 |
| Details | binding site for residue MG A 302 |
| Chain | Residue |
| A | CTP301 |
| A | HOH448 |
| A | HOH454 |
| site_id | AC3 |
| Number of Residues | 1 |
| Details | binding site for residue ACT A 303 |
| Chain | Residue |
| A | GLY69 |
| site_id | AC4 |
| Number of Residues | 6 |
| Details | binding site for residue ACT A 304 |
| Chain | Residue |
| A | ARG82 |
| A | ASP108 |
| A | ARG111 |
| A | THR191 |
| A | LYS215 |
| A | HOH420 |
| site_id | AC5 |
| Number of Residues | 3 |
| Details | binding site for residue ACT A 305 |
| Chain | Residue |
| A | VAL74 |
| A | ARG75 |
| A | HOH445 |
| site_id | AC6 |
| Number of Residues | 4 |
| Details | binding site for residue ACT A 306 |
| Chain | Residue |
| A | ASP141 |
| B | GLN166 |
| B | PHE214 |
| B | LYS215 |
| site_id | AC7 |
| Number of Residues | 3 |
| Details | binding site for residue ACT A 307 |
| Chain | Residue |
| A | ASP223 |
| B | ARG212 |
| B | HIS231 |
| site_id | AC8 |
| Number of Residues | 3 |
| Details | binding site for residue ACT C 301 |
| Chain | Residue |
| C | THR142 |
| D | ARG111 |
| D | ALA165 |
| site_id | AC9 |
| Number of Residues | 4 |
| Details | binding site for residue ACT C 302 |
| Chain | Residue |
| C | ASP100 |
| C | ALA101 |
| C | ARG172 |
| C | MET175 |
| site_id | AD1 |
| Number of Residues | 4 |
| Details | binding site for residue ACT C 303 |
| Chain | Residue |
| C | ALA12 |
| C | SER81 |
| C | ARG82 |
| C | SER85 |
| site_id | AD2 |
| Number of Residues | 3 |
| Details | binding site for residue CAD C 304 |
| Chain | Residue |
| C | GLY69 |
| C | LEU185 |
| C | GLU186 |
| site_id | AD3 |
| Number of Residues | 12 |
| Details | binding site for residue CTP D 301 |
| Chain | Residue |
| D | PRO10 |
| D | CYS11 |
| D | ALA12 |
| D | LYS24 |
| D | GLY79 |
| D | ALA80 |
| D | SER81 |
| D | ARG82 |
| D | SER85 |
| D | ALA109 |
| D | ALA110 |
| D | MG302 |
| site_id | AD4 |
| Number of Residues | 1 |
| Details | binding site for residue MG D 302 |
| Chain | Residue |
| D | CTP301 |
| site_id | AD5 |
| Number of Residues | 4 |
| Details | binding site for residue ACT D 303 |
| Chain | Residue |
| C | ARG111 |
| C | PHE214 |
| C | LYS215 |
| D | ASP141 |
| site_id | AD6 |
| Number of Residues | 3 |
| Details | binding site for residue ACT D 304 |
| Chain | Residue |
| C | ASN160 |
| D | PRO147 |
| D | ALA148 |
| site_id | AD7 |
| Number of Residues | 2 |
| Details | binding site for residue GOL D 305 |
| Chain | Residue |
| D | ASP43 |
| D | GLY69 |
Functional Information from PROSITE/UniProt
| site_id | PS01295 |
| Number of Residues | 8 |
| Details | ISPD 4-diphosphocytidyl-2C-methyl-D-erythritol synthase signature. VLVHDAAR |
| Chain | Residue | Details |
| A | VAL104-ARG111 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 8 |
| Details | SITE: Transition state stabilizer => ECO:0000255|HAMAP-Rule:MF_00108 |
| Chain | Residue | Details |
| A | ARG17 | |
| A | LYS24 | |
| B | ARG17 | |
| B | LYS24 | |
| C | ARG17 | |
| C | LYS24 | |
| D | ARG17 | |
| D | LYS24 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 8 |
| Details | SITE: Positions MEP for the nucleophilic attack => ECO:0000255|HAMAP-Rule:MF_00108 |
| Chain | Residue | Details |
| A | ARG159 | |
| A | LYS215 | |
| B | ARG159 | |
| B | LYS215 | |
| C | ARG159 | |
| C | LYS215 | |
| D | ARG159 | |
| D | LYS215 |
