2PCD
STRUCTURE OF PROTOCATECHUATE 3,4-DIOXYGENASE FROM PSEUDOMONAS AERUGINOSA AT 2.15 ANGSTROMS RESOLUTION
Replaces: 1PCDFunctional Information from GO Data
Chain | GOid | namespace | contents |
A | 0003824 | molecular_function | catalytic activity |
A | 0005506 | molecular_function | iron ion binding |
A | 0008199 | molecular_function | ferric iron binding |
A | 0009056 | biological_process | catabolic process |
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 | 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 | 0008199 | molecular_function | ferric iron binding |
B | 0009056 | biological_process | catabolic process |
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 | 0042952 | biological_process | beta-ketoadipate pathway |
B | 0051213 | molecular_function | dioxygenase activity |
C | 0003824 | molecular_function | catalytic activity |
C | 0005506 | molecular_function | iron ion binding |
C | 0008199 | molecular_function | ferric iron binding |
C | 0009056 | biological_process | catabolic process |
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 | 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 | 0008199 | molecular_function | ferric iron binding |
D | 0009056 | biological_process | catabolic process |
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 | 0042952 | biological_process | beta-ketoadipate pathway |
D | 0051213 | molecular_function | dioxygenase activity |
E | 0003824 | molecular_function | catalytic activity |
E | 0005506 | molecular_function | iron ion binding |
E | 0008199 | molecular_function | ferric iron binding |
E | 0009056 | biological_process | catabolic process |
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 | 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 | 0008199 | molecular_function | ferric iron binding |
F | 0009056 | biological_process | catabolic process |
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 | 0042952 | biological_process | beta-ketoadipate pathway |
F | 0051213 | molecular_function | dioxygenase activity |
M | 0003824 | molecular_function | catalytic activity |
M | 0005506 | molecular_function | iron ion binding |
M | 0008199 | molecular_function | ferric iron binding |
M | 0009056 | biological_process | catabolic process |
M | 0016702 | molecular_function | oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen |
M | 0018578 | molecular_function | protocatechuate 3,4-dioxygenase activity |
M | 0019619 | biological_process | 3,4-dihydroxybenzoate catabolic process |
M | 0042952 | biological_process | beta-ketoadipate pathway |
M | 0046872 | molecular_function | metal ion binding |
M | 0051213 | molecular_function | dioxygenase activity |
N | 0003824 | molecular_function | catalytic activity |
N | 0005506 | molecular_function | iron ion binding |
N | 0008199 | molecular_function | ferric iron binding |
N | 0009056 | biological_process | catabolic process |
N | 0016702 | molecular_function | oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen |
N | 0018578 | molecular_function | protocatechuate 3,4-dioxygenase activity |
N | 0019619 | biological_process | 3,4-dihydroxybenzoate catabolic process |
N | 0042952 | biological_process | beta-ketoadipate pathway |
N | 0046872 | molecular_function | metal ion binding |
N | 0051213 | molecular_function | dioxygenase activity |
O | 0003824 | molecular_function | catalytic activity |
O | 0005506 | molecular_function | iron ion binding |
O | 0008199 | molecular_function | ferric iron binding |
O | 0009056 | biological_process | catabolic process |
O | 0016702 | molecular_function | oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen |
O | 0018578 | molecular_function | protocatechuate 3,4-dioxygenase activity |
O | 0019619 | biological_process | 3,4-dihydroxybenzoate catabolic process |
O | 0042952 | biological_process | beta-ketoadipate pathway |
O | 0046872 | molecular_function | metal ion binding |
O | 0051213 | molecular_function | dioxygenase activity |
P | 0003824 | molecular_function | catalytic activity |
P | 0005506 | molecular_function | iron ion binding |
P | 0008199 | molecular_function | ferric iron binding |
P | 0009056 | biological_process | catabolic process |
P | 0016702 | molecular_function | oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen |
P | 0018578 | molecular_function | protocatechuate 3,4-dioxygenase activity |
P | 0019619 | biological_process | 3,4-dihydroxybenzoate catabolic process |
P | 0042952 | biological_process | beta-ketoadipate pathway |
P | 0046872 | molecular_function | metal ion binding |
P | 0051213 | molecular_function | dioxygenase activity |
Q | 0003824 | molecular_function | catalytic activity |
Q | 0005506 | molecular_function | iron ion binding |
Q | 0008199 | molecular_function | ferric iron binding |
Q | 0009056 | biological_process | catabolic process |
Q | 0016702 | molecular_function | oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen |
Q | 0018578 | molecular_function | protocatechuate 3,4-dioxygenase activity |
Q | 0019619 | biological_process | 3,4-dihydroxybenzoate catabolic process |
Q | 0042952 | biological_process | beta-ketoadipate pathway |
Q | 0046872 | molecular_function | metal ion binding |
Q | 0051213 | molecular_function | dioxygenase activity |
R | 0003824 | molecular_function | catalytic activity |
R | 0005506 | molecular_function | iron ion binding |
R | 0008199 | molecular_function | ferric iron binding |
R | 0009056 | biological_process | catabolic process |
R | 0016702 | molecular_function | oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen |
R | 0018578 | molecular_function | protocatechuate 3,4-dioxygenase activity |
R | 0019619 | biological_process | 3,4-dihydroxybenzoate catabolic process |
R | 0042952 | biological_process | beta-ketoadipate pathway |
R | 0046872 | molecular_function | metal ion binding |
R | 0051213 | molecular_function | dioxygenase activity |
Functional Information from PDB Data
site_id | AC1 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE FE M 600 |
Chain | Residue |
M | TYR408 |
M | TYR447 |
M | HIS460 |
M | HIS462 |
M | HOH733 |
site_id | AC2 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE FE N 600 |
Chain | Residue |
N | TYR408 |
N | TYR447 |
N | HIS460 |
N | HIS462 |
N | HOH749 |
site_id | AC3 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE FE O 600 |
Chain | Residue |
O | TYR408 |
O | TYR447 |
O | HIS460 |
O | HIS462 |
O | HOH748 |
site_id | AC4 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE FE P 600 |
Chain | Residue |
P | TYR408 |
P | TYR447 |
P | HIS460 |
P | HIS462 |
P | HOH746 |
site_id | AC5 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE FE Q 600 |
Chain | Residue |
Q | TYR408 |
Q | TYR447 |
Q | HIS460 |
Q | HIS462 |
Q | HOH1183 |
site_id | AC6 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE FE R 600 |
Chain | Residue |
R | TYR408 |
R | TYR447 |
R | HIS460 |
R | HIS462 |
R | HOH1396 |
R | HOH1422 |
site_id | ACA |
Number of Residues | 29 |
Details | active site |
Chain | Residue |
A | THR12 |
M | TYR408 |
M | TYR447 |
M | TRP449 |
M | ARG450 |
M | ARG457 |
M | HIS460 |
M | HIS462 |
M | GLN477 |
M | ILE491 |
M | FE600 |
A | ALA13 |
A | HOH205 |
M | HOH620 |
M | HOH628 |
M | HOH629 |
M | HOH638 |
M | HOH677 |
M | HOH696 |
M | HOH718 |
M | HOH719 |
M | HOH733 |
A | GLY14 |
A | PRO15 |
A | TYR16 |
A | ARG133 |
A | GLY134 |
M | TYR324 |
M | THR326 |
site_id | ACB |
Number of Residues | 29 |
Details | active site |
Chain | Residue |
B | THR12 |
B | ALA13 |
B | GLY14 |
B | PRO15 |
B | TYR16 |
B | ARG133 |
B | GLY134 |
N | TYR324 |
N | THR326 |
N | TYR408 |
N | TYR447 |
N | TRP449 |
N | ARG450 |
N | ARG457 |
N | HIS460 |
N | HIS462 |
N | GLN477 |
N | ILE491 |
N | FE600 |
B | HOH245 |
N | HOH629 |
N | HOH638 |
N | HOH639 |
B | HOH317 |
N | HOH689 |
N | HOH708 |
N | HOH731 |
N | HOH733 |
N | HOH749 |
site_id | ACC |
Number of Residues | 29 |
Details | active site |
Chain | Residue |
C | THR12 |
C | ALA13 |
C | GLY14 |
C | PRO15 |
C | TYR16 |
C | ARG133 |
C | GLY134 |
O | TYR324 |
O | THR326 |
O | TYR408 |
O | TYR447 |
O | TRP449 |
O | ARG450 |
O | ARG457 |
O | HIS460 |
O | HIS462 |
O | GLN477 |
O | ILE491 |
O | FE600 |
C | HOH205 |
O | HOH629 |
O | HOH638 |
O | HOH639 |
O | HOH650 |
O | HOH689 |
O | HOH708 |
O | HOH731 |
O | HOH733 |
O | HOH748 |
site_id | ACD |
Number of Residues | 29 |
Details | active site |
Chain | Residue |
D | THR12 |
D | ALA13 |
D | GLY14 |
D | PRO15 |
D | TYR16 |
D | ARG133 |
D | GLY134 |
P | TYR324 |
P | THR326 |
O | TYR408 |
P | TYR447 |
P | TRP449 |
P | ARG450 |
O | ARG457 |
P | HIS460 |
P | HIS462 |
P | GLN477 |
P | ILE491 |
P | FE600 |
D | HOH723 |
P | HOH630 |
P | HOH638 |
P | HOH639 |
P | HOH650 |
P | HOH690 |
P | HOH709 |
P | HOH730 |
P | HOH731 |
P | HOH746 |
site_id | ACE |
Number of Residues | 29 |
Details | active site |
Chain | Residue |
E | THR12 |
E | ALA13 |
E | GLY14 |
E | PRO15 |
E | TYR16 |
E | ARG133 |
E | GLY134 |
Q | TYR324 |
Q | THR326 |
Q | TYR408 |
Q | TYR447 |
Q | TRP449 |
Q | ARG450 |
Q | ARG457 |
Q | HIS460 |
Q | HIS462 |
Q | GLN477 |
Q | ILE491 |
Q | FE600 |
E | HOH208 |
Q | HOH999 |
Q | HOH1015 |
Q | HOH1016 |
Q | HOH1034 |
Q | HOH1092 |
Q | HOH1119 |
Q | HOH1155 |
Q | HOH1157 |
Q | HOH1183 |
site_id | ACF |
Number of Residues | 29 |
Details | active site |
Chain | Residue |
F | THR12 |
F | ALA13 |
F | GLY14 |
F | PRO15 |
F | TYR16 |
F | ARG133 |
F | GLY134 |
R | TYR324 |
R | THR326 |
R | TYR408 |
R | TYR447 |
R | TRP449 |
R | ARG450 |
R | ARG457 |
R | HIS460 |
R | HIS462 |
R | GLN477 |
R | ILE491 |
R | FE600 |
E | HOH208 |
Q | HOH999 |
Q | HOH1015 |
Q | HOH1016 |
Q | HOH1034 |
Q | HOH1092 |
Q | HOH1119 |
Q | HOH1155 |
Q | HOH1157 |
Q | HOH1183 |
site_id | VEA |
Number of Residues | 29 |
Details | vestigial site |
Chain | Residue |
A | TYR79 |
A | VAL114 |
A | ASN115 |
A | ASN116 |
A | ALA117 |
A | ALA118 |
A | MET122 |
A | HIS125 |
A | ASN127 |
A | ARG142 |
A | VAL157 |
M | ASP304 |
M | ARG307 |
M | ILE339 |
M | PRO340 |
M | GLN341 |
M | SER342 |
M | ILE343 |
M | SER344 |
M | GLU345 |
A | HOH222 |
M | HOH626 |
M | HOH633 |
A | HOH234 |
M | HOH640 |
A | HOH237 |
M | HOH656 |
A | HOH249 |
M | HOH715 |
site_id | VEB |
Number of Residues | 29 |
Details | vestigial site |
Chain | Residue |
N | ARG307 |
N | ILE339 |
N | PRO340 |
N | GLN341 |
N | SER342 |
N | ILE343 |
N | SER344 |
N | GLU345 |
B | HOH285 |
N | HOH636 |
B | HOH305 |
B | HOH312 |
N | HOH650 |
B | HOH322 |
N | HOH666 |
B | HOH364 |
B | HOH434 |
B | TYR79 |
B | VAL114 |
B | ASN115 |
B | ASN116 |
B | ALA117 |
B | ALA118 |
B | MET122 |
B | HIS125 |
B | ASN127 |
B | ARG142 |
B | VAL157 |
N | ASP304 |
site_id | VEC |
Number of Residues | 29 |
Details | vestigial site |
Chain | Residue |
C | TYR79 |
C | VAL114 |
C | ASN115 |
C | ASN116 |
C | ALA117 |
C | ALA118 |
C | MET122 |
C | HIS125 |
C | ASN127 |
C | ARG142 |
C | VAL157 |
O | ASP304 |
O | ARG307 |
O | ILE339 |
O | PRO340 |
O | GLN341 |
O | SER342 |
O | ILE343 |
O | SER344 |
O | GLU345 |
C | HOH221 |
O | HOH636 |
O | HOH643 |
C | HOH232 |
O | HOH652 |
C | HOH235 |
O | HOH668 |
C | HOH247 |
C | HOH268 |
site_id | VED |
Number of Residues | 29 |
Details | vestigial site |
Chain | Residue |
D | TYR79 |
D | VAL114 |
D | ASN115 |
D | ASN116 |
D | ALA117 |
D | ALA118 |
D | MET122 |
D | HIS125 |
D | ASN127 |
D | ARG142 |
D | VAL157 |
P | ASP304 |
P | ARG307 |
P | ILE339 |
P | PRO340 |
P | GLN341 |
P | SER342 |
P | ILE343 |
P | SER344 |
P | GLU345 |
D | HOH763 |
P | HOH636 |
P | HOH643 |
D | HOH790 |
P | HOH652 |
D | HOH800 |
P | HOH668 |
D | HOH842 |
P | HOH727 |
site_id | VEE |
Number of Residues | 29 |
Details | vestigial site |
Chain | Residue |
E | TYR79 |
E | VAL114 |
E | ASN115 |
E | ASN116 |
E | ALA117 |
E | ALA118 |
E | MET122 |
E | HIS125 |
E | ASN127 |
E | ARG142 |
E | VAL157 |
Q | ASP304 |
Q | ARG307 |
Q | ILE339 |
Q | PRO340 |
Q | GLN341 |
Q | SER342 |
Q | ILE343 |
Q | SER344 |
Q | GLU345 |
E | HOH223 |
Q | HOH1011 |
Q | HOH1022 |
E | HOH233 |
Q | HOH1037 |
E | HOH236 |
Q | HOH1063 |
E | HOH246 |
Q | HOH1151 |
site_id | VEF |
Number of Residues | 29 |
Details | vestigial site |
Chain | Residue |
F | TYR79 |
F | VAL114 |
F | ASN115 |
F | ASN116 |
F | ALA117 |
F | ALA118 |
F | MET122 |
F | HIS125 |
F | ASN127 |
F | ARG142 |
F | VAL157 |
R | ASP304 |
R | ARG307 |
R | ILE339 |
R | PRO340 |
R | GLN341 |
R | SER342 |
R | ILE343 |
R | SER344 |
R | GLU345 |
E | HOH223 |
Q | HOH1011 |
Q | HOH1022 |
E | HOH233 |
Q | HOH1037 |
E | HOH236 |
Q | HOH1063 |
E | HOH246 |
Q | HOH1151 |
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 | |
M | VAL380-TYR408 |
Functional Information from SwissProt/UniProt
site_id | SWS_FT_FI1 |
Number of Residues | 24 |
Details | BINDING: BINDING => ECO:0000269|PubMed:7990141 |
Chain | Residue | Details |
M | ARG409 | |
O | PRO448 | |
O | ILE461 | |
O | PHE463 | |
P | ARG409 | |
P | PRO448 | |
P | ILE461 | |
P | PHE463 | |
Q | ARG409 | |
Q | PRO448 | |
Q | ILE461 | |
M | PRO448 | |
Q | PHE463 | |
R | ARG409 | |
R | PRO448 | |
R | ILE461 | |
R | PHE463 | |
M | ILE461 | |
M | PHE463 | |
N | ARG409 | |
N | PRO448 | |
N | ILE461 | |
N | PHE463 | |
O | ARG409 |
Catalytic Information from CSA
site_id | CSA1 |
Number of Residues | 2 |
Details | Annotated By Reference To The Literature 3pca |
Chain | Residue | Details |
M | TYR447 | |
M | ARG457 |
site_id | CSA2 |
Number of Residues | 2 |
Details | Annotated By Reference To The Literature 3pca |
Chain | Residue | Details |
N | TYR447 | |
N | ARG457 |
site_id | CSA3 |
Number of Residues | 2 |
Details | Annotated By Reference To The Literature 3pca |
Chain | Residue | Details |
O | TYR447 | |
O | ARG457 |
site_id | CSA4 |
Number of Residues | 2 |
Details | Annotated By Reference To The Literature 3pca |
Chain | Residue | Details |
P | TYR447 | |
P | ARG457 |
site_id | CSA5 |
Number of Residues | 2 |
Details | Annotated By Reference To The Literature 3pca |
Chain | Residue | Details |
Q | TYR447 | |
Q | ARG457 |
site_id | CSA6 |
Number of Residues | 2 |
Details | Annotated By Reference To The Literature 3pca |
Chain | Residue | Details |
R | TYR447 | |
R | ARG457 |
site_id | MCSA1 |
Number of Residues | 5 |
Details | M-CSA 936 |
Chain | Residue | Details |
M | ARG409 | metal ligand |
M | PRO448 | metal ligand, proton shuttle (general acid/base) |
M | PRO458 | electrostatic stabiliser |
M | ILE461 | metal ligand |
M | PHE463 | metal ligand |
site_id | MCSA2 |
Number of Residues | 5 |
Details | M-CSA 936 |
Chain | Residue | Details |
N | ARG409 | metal ligand |
N | PRO448 | metal ligand, proton shuttle (general acid/base) |
N | PRO458 | electrostatic stabiliser |
N | ILE461 | metal ligand |
N | PHE463 | metal ligand |
site_id | MCSA3 |
Number of Residues | 5 |
Details | M-CSA 936 |
Chain | Residue | Details |
O | ARG409 | metal ligand |
O | PRO448 | metal ligand, proton shuttle (general acid/base) |
O | PRO458 | electrostatic stabiliser |
O | ILE461 | metal ligand |
O | PHE463 | metal ligand |
site_id | MCSA4 |
Number of Residues | 5 |
Details | M-CSA 936 |
Chain | Residue | Details |
P | ARG409 | metal ligand |
P | PRO448 | metal ligand, proton shuttle (general acid/base) |
P | PRO458 | electrostatic stabiliser |
P | ILE461 | metal ligand |
P | PHE463 | metal ligand |
site_id | MCSA5 |
Number of Residues | 5 |
Details | M-CSA 936 |
Chain | Residue | Details |
Q | ARG409 | metal ligand |
Q | PRO448 | metal ligand, proton shuttle (general acid/base) |
Q | PRO458 | electrostatic stabiliser |
Q | ILE461 | metal ligand |
Q | PHE463 | metal ligand |
site_id | MCSA6 |
Number of Residues | 5 |
Details | M-CSA 936 |
Chain | Residue | Details |
R | ARG409 | metal ligand |
R | PRO448 | metal ligand, proton shuttle (general acid/base) |
R | PRO458 | electrostatic stabiliser |
R | ILE461 | metal ligand |
R | PHE463 | metal ligand |