4WHQ
Alkylperoxo reaction intermediate trapped in Protocatechuate 3,4-dioxygenase (pseudomonas putida) at pH 6.5
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0003824 | molecular_function | catalytic activity |
| A | 0005506 | molecular_function | iron ion binding |
| A | 0006725 | biological_process | obsolete cellular aromatic compound metabolic process |
| A | 0008199 | molecular_function | ferric iron binding |
| A | 0016702 | molecular_function | oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen |
| A | 0018578 | molecular_function | protocatechuate 3,4-dioxygenase activity |
| A | 0019439 | biological_process | obsolete aromatic compound catabolic process |
| A | 0042952 | biological_process | beta-ketoadipate pathway |
| A | 0051213 | molecular_function | dioxygenase activity |
| B | 0003824 | molecular_function | catalytic activity |
| B | 0005506 | molecular_function | iron ion binding |
| B | 0006725 | biological_process | obsolete cellular aromatic compound metabolic process |
| B | 0008199 | molecular_function | ferric iron binding |
| B | 0016702 | molecular_function | oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen |
| B | 0018578 | molecular_function | protocatechuate 3,4-dioxygenase activity |
| B | 0019439 | biological_process | obsolete aromatic compound catabolic process |
| B | 0019619 | biological_process | 3,4-dihydroxybenzoate catabolic process |
| B | 0042952 | biological_process | beta-ketoadipate pathway |
| B | 0046872 | molecular_function | metal ion binding |
| B | 0051213 | molecular_function | dioxygenase activity |
| C | 0003824 | molecular_function | catalytic activity |
| C | 0005506 | molecular_function | iron ion binding |
| C | 0006725 | biological_process | obsolete cellular aromatic compound metabolic process |
| C | 0008199 | molecular_function | ferric iron binding |
| C | 0016702 | molecular_function | oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen |
| C | 0018578 | molecular_function | protocatechuate 3,4-dioxygenase activity |
| C | 0019439 | biological_process | obsolete aromatic compound catabolic process |
| C | 0042952 | biological_process | beta-ketoadipate pathway |
| C | 0051213 | molecular_function | dioxygenase activity |
| D | 0003824 | molecular_function | catalytic activity |
| D | 0005506 | molecular_function | iron ion binding |
| D | 0006725 | biological_process | obsolete cellular aromatic compound metabolic process |
| D | 0008199 | molecular_function | ferric iron binding |
| D | 0016702 | molecular_function | oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen |
| D | 0018578 | molecular_function | protocatechuate 3,4-dioxygenase activity |
| D | 0019439 | biological_process | obsolete aromatic compound catabolic process |
| D | 0019619 | biological_process | 3,4-dihydroxybenzoate catabolic process |
| D | 0042952 | biological_process | beta-ketoadipate pathway |
| D | 0046872 | molecular_function | metal ion binding |
| D | 0051213 | molecular_function | dioxygenase activity |
| E | 0003824 | molecular_function | catalytic activity |
| E | 0005506 | molecular_function | iron ion binding |
| E | 0006725 | biological_process | obsolete cellular aromatic compound metabolic process |
| E | 0008199 | molecular_function | ferric iron binding |
| E | 0016702 | molecular_function | oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen |
| E | 0018578 | molecular_function | protocatechuate 3,4-dioxygenase activity |
| E | 0019439 | biological_process | obsolete aromatic compound catabolic process |
| E | 0042952 | biological_process | beta-ketoadipate pathway |
| E | 0051213 | molecular_function | dioxygenase activity |
| F | 0003824 | molecular_function | catalytic activity |
| F | 0005506 | molecular_function | iron ion binding |
| F | 0006725 | biological_process | obsolete cellular aromatic compound metabolic process |
| F | 0008199 | molecular_function | ferric iron binding |
| F | 0016702 | molecular_function | oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen |
| F | 0018578 | molecular_function | protocatechuate 3,4-dioxygenase activity |
| F | 0019439 | biological_process | obsolete aromatic compound catabolic process |
| F | 0019619 | biological_process | 3,4-dihydroxybenzoate catabolic process |
| F | 0042952 | biological_process | beta-ketoadipate pathway |
| F | 0046872 | molecular_function | metal ion binding |
| F | 0051213 | molecular_function | dioxygenase activity |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 3 |
| Details | binding site for residue CL A 301 |
| Chain | Residue |
| A | ASN37 |
| A | THR105 |
| A | HIS107 |
| site_id | AC2 |
| Number of Residues | 5 |
| Details | binding site for residue 3N8 A 302 |
| Chain | Residue |
| A | PRO164 |
| A | ARG167 |
| A | GLU168 |
| A | ILE171 |
| A | HOH461 |
| site_id | AC3 |
| Number of Residues | 2 |
| Details | binding site for residue CL A 303 |
| Chain | Residue |
| A | LEU62 |
| A | HIS61 |
| site_id | AC4 |
| Number of Residues | 5 |
| Details | binding site for residue 3N8 E 301 |
| Chain | Residue |
| E | PRO164 |
| E | ARG167 |
| E | GLU168 |
| E | ILE171 |
| E | HOH488 |
| site_id | AC5 |
| Number of Residues | 5 |
| Details | binding site for residue FE F 601 |
| Chain | Residue |
| F | TYR408 |
| F | TYR447 |
| F | HIS460 |
| F | HIS462 |
| F | HOH865 |
| site_id | AC6 |
| Number of Residues | 5 |
| Details | binding site for residue 3N8 F 602 |
| Chain | Residue |
| F | LYS493 |
| F | ILE495 |
| F | ALA496 |
| F | VAL501 |
| F | BME606 |
| site_id | AC7 |
| Number of Residues | 5 |
| Details | binding site for residue 3N8 F 603 |
| Chain | Residue |
| D | PRO322 |
| D | ILE328 |
| F | ARG333 |
| F | HOH838 |
| F | HOH849 |
| site_id | AC8 |
| Number of Residues | 5 |
| Details | binding site for residue 3N8 F 604 |
| Chain | Residue |
| D | ARG450 |
| D | MET516 |
| F | SER338 |
| F | ILE339 |
| F | PRO340 |
| site_id | AC9 |
| Number of Residues | 4 |
| Details | binding site for residue BME F 605 |
| Chain | Residue |
| F | THR321 |
| F | PRO322 |
| F | ASP323 |
| F | HOH815 |
| site_id | AD1 |
| Number of Residues | 3 |
| Details | binding site for residue BME F 606 |
| Chain | Residue |
| F | GLN502 |
| F | ILE505 |
| F | 3N8602 |
| site_id | AD2 |
| Number of Residues | 3 |
| Details | binding site for residue BCT F 607 |
| Chain | Residue |
| F | ARG409 |
| F | PRO421 |
| F | HOH854 |
| site_id | AD3 |
| Number of Residues | 6 |
| Details | binding site for residue 3N8 F 608 |
| Chain | Residue |
| E | ASN28 |
| E | PRO29 |
| F | ASN366 |
| F | GLY424 |
| F | GLY425 |
| F | VAL426 |
| site_id | AD4 |
| Number of Residues | 3 |
| Details | binding site for residue BCT F 609 |
| Chain | Residue |
| F | ARG409 |
| F | HIS410 |
| F | LEU419 |
| site_id | AD5 |
| Number of Residues | 4 |
| Details | binding site for residue BME F 610 |
| Chain | Residue |
| F | GLN503 |
| F | ARG522 |
| F | PHE523 |
| F | ASP524 |
| site_id | AD6 |
| Number of Residues | 5 |
| Details | binding site for residue 3N8 C 301 |
| Chain | Residue |
| C | PRO164 |
| C | ARG167 |
| C | GLU168 |
| C | ILE171 |
| C | HOH434 |
| site_id | AD7 |
| Number of Residues | 6 |
| Details | binding site for residue BME C 302 |
| Chain | Residue |
| C | GLU168 |
| C | ILE171 |
| C | ARG184 |
| C | PHE185 |
| C | ASP186 |
| C | HOH517 |
| site_id | AD8 |
| Number of Residues | 3 |
| Details | binding site for residue CL C 303 |
| Chain | Residue |
| C | ASN37 |
| C | THR105 |
| C | HIS107 |
| site_id | AD9 |
| Number of Residues | 6 |
| Details | binding site for residue SO4 C 304 |
| Chain | Residue |
| C | HIS61 |
| C | LEU62 |
| C | ARG64 |
| C | HOH488 |
| E | GLN163 |
| E | GLN165 |
| site_id | AE1 |
| Number of Residues | 5 |
| Details | binding site for residue FE D 601 |
| Chain | Residue |
| D | TYR408 |
| D | TYR447 |
| D | HIS460 |
| D | HIS462 |
| D | HOH882 |
| site_id | AE2 |
| Number of Residues | 7 |
| Details | binding site for residue 3N8 D 602 |
| Chain | Residue |
| C | ASN28 |
| C | PRO29 |
| C | THR30 |
| D | ASN366 |
| D | GLY424 |
| D | GLY425 |
| D | VAL426 |
| site_id | AE3 |
| Number of Residues | 4 |
| Details | binding site for residue 3N8 D 603 |
| Chain | Residue |
| D | LYS493 |
| D | ILE495 |
| D | ALA496 |
| D | HOH831 |
| site_id | AE4 |
| Number of Residues | 4 |
| Details | binding site for residue 3N8 D 604 |
| Chain | Residue |
| B | PRO322 |
| B | ILE328 |
| D | ARG333 |
| D | HOH874 |
| site_id | AE5 |
| Number of Residues | 5 |
| Details | binding site for residue 3N8 D 605 |
| Chain | Residue |
| D | ARG531 |
| D | LYS532 |
| D | HOH810 |
| D | HOH869 |
| D | GLN530 |
| site_id | AE6 |
| Number of Residues | 3 |
| Details | binding site for residue BME D 606 |
| Chain | Residue |
| D | GLN503 |
| D | ARG522 |
| D | ASP524 |
| site_id | AE7 |
| Number of Residues | 4 |
| Details | binding site for residue NA D 607 |
| Chain | Residue |
| D | THR321 |
| D | PRO322 |
| D | ASP323 |
| D | HOH835 |
| site_id | AE8 |
| Number of Residues | 8 |
| Details | binding site for residue GOL D 608 |
| Chain | Residue |
| B | ASN514 |
| B | PRO515 |
| D | ARG307 |
| D | PHE308 |
| D | GLN341 |
| D | ARG531 |
| D | GLU536 |
| D | HOH729 |
| site_id | AE9 |
| Number of Residues | 5 |
| Details | binding site for residue FE B 601 |
| Chain | Residue |
| B | TYR408 |
| B | TYR447 |
| B | HIS460 |
| B | HIS462 |
| B | 3N9612 |
| site_id | AF1 |
| Number of Residues | 5 |
| Details | binding site for residue 3N8 B 602 |
| Chain | Residue |
| B | SER338 |
| B | PRO340 |
| F | ARG450 |
| F | PRO515 |
| F | MET516 |
| site_id | AF2 |
| Number of Residues | 3 |
| Details | binding site for residue 3N8 B 603 |
| Chain | Residue |
| B | ARG333 |
| B | HOH841 |
| F | ILE328 |
| site_id | AF3 |
| Number of Residues | 4 |
| Details | binding site for residue 3N8 B 604 |
| Chain | Residue |
| B | LYS493 |
| B | ILE495 |
| B | ALA496 |
| B | VAL501 |
| site_id | AF4 |
| Number of Residues | 5 |
| Details | binding site for residue 3N8 B 605 |
| Chain | Residue |
| B | ARG450 |
| B | MET516 |
| D | SER338 |
| D | PRO340 |
| D | HOH760 |
| site_id | AF5 |
| Number of Residues | 2 |
| Details | binding site for residue BME B 606 |
| Chain | Residue |
| B | SER306 |
| B | GLN530 |
| site_id | AF6 |
| Number of Residues | 4 |
| Details | binding site for residue 3N8 B 607 |
| Chain | Residue |
| B | ARG383 |
| B | ASP524 |
| B | HOH809 |
| B | HOH865 |
| site_id | AF7 |
| Number of Residues | 3 |
| Details | binding site for residue BME B 608 |
| Chain | Residue |
| B | GLN503 |
| B | ARG522 |
| B | ASP524 |
| site_id | AF8 |
| Number of Residues | 3 |
| Details | binding site for residue BME B 609 |
| Chain | Residue |
| B | GLY482 |
| B | ASP483 |
| B | PRO487 |
| site_id | AF9 |
| Number of Residues | 5 |
| Details | binding site for residue 3N8 B 610 |
| Chain | Residue |
| A | GLY27 |
| A | ASN28 |
| B | ARG409 |
| B | HIS410 |
| B | LEU419 |
| site_id | AG1 |
| Number of Residues | 2 |
| Details | binding site for residue BCT B 611 |
| Chain | Residue |
| B | ARG383 |
| D | LYS390 |
| site_id | AG2 |
| Number of Residues | 15 |
| Details | binding site for residue 3N9 B 612 |
| Chain | Residue |
| A | THR12 |
| A | GLY14 |
| A | PRO15 |
| A | TYR16 |
| A | HOH511 |
| B | TYR408 |
| B | TYR447 |
| B | TRP449 |
| B | ARG457 |
| B | HIS460 |
| B | HIS462 |
| B | GLN477 |
| B | ILE491 |
| B | FE601 |
| B | HOH872 |
Functional Information from PROSITE/UniProt
| site_id | PS00083 |
| Number of Residues | 29 |
| Details | INTRADIOL_DIOXYGENAS Intradiol ring-cleavage dioxygenases signature. LlGqVydgnGhlVrdsfLEVwqadanGeY |
| Chain | Residue | Details |
| A | LEU51-TYR79 | |
| F | VAL380-TYR408 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 12 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:7990141 |
| Chain | Residue | Details |
| F | TYR408 | |
| B | TYR447 | |
| B | HIS460 | |
| B | HIS462 | |
| F | TYR447 | |
| F | HIS460 | |
| F | HIS462 | |
| D | TYR408 | |
| D | TYR447 | |
| D | HIS460 | |
| D | HIS462 | |
| B | TYR408 |
Catalytic Information from CSA
| site_id | MCSA1 |
| Number of Residues | 5 |
| Details | M-CSA 936 |
| Chain | Residue | Details |
| F | TYR408 | metal ligand |
| F | TYR447 | metal ligand, proton shuttle (general acid/base) |
| F | ARG457 | electrostatic stabiliser |
| F | HIS460 | metal ligand |
| F | HIS462 | metal ligand |
| site_id | MCSA2 |
| Number of Residues | 5 |
| Details | M-CSA 936 |
| Chain | Residue | Details |
| D | TYR408 | metal ligand |
| D | TYR447 | metal ligand, proton shuttle (general acid/base) |
| D | ARG457 | electrostatic stabiliser |
| D | HIS460 | metal ligand |
| D | HIS462 | metal ligand |
| site_id | MCSA3 |
| Number of Residues | 5 |
| Details | M-CSA 936 |
| Chain | Residue | Details |
| B | TYR408 | metal ligand |
| B | TYR447 | metal ligand, proton shuttle (general acid/base) |
| B | ARG457 | electrostatic stabiliser |
| B | HIS460 | metal ligand |
| B | HIS462 | metal ligand |
