1PVD
CRYSTAL STRUCTURE OF THE THIAMIN DIPHOSPHATE DEPENDENT ENZYME PYRUVATE DECARBOXYLASE FROM THE YEAST SACCHAROMYCES CEREVISIAE AT 2.3 ANGSTROMS RESOLUTION
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0000287 | molecular_function | magnesium ion binding |
| A | 0000949 | biological_process | aromatic amino acid family catabolic process to alcohol via Ehrlich pathway |
| A | 0000955 | biological_process | amino acid catabolic process via Ehrlich pathway |
| A | 0003824 | molecular_function | catalytic activity |
| A | 0004737 | molecular_function | pyruvate decarboxylase activity |
| A | 0005634 | cellular_component | nucleus |
| A | 0005737 | cellular_component | cytoplasm |
| A | 0005829 | cellular_component | cytosol |
| A | 0006090 | biological_process | pyruvate metabolic process |
| A | 0006559 | biological_process | L-phenylalanine catabolic process |
| A | 0006569 | biological_process | tryptophan catabolic process |
| A | 0009083 | biological_process | branched-chain amino acid catabolic process |
| A | 0016831 | molecular_function | carboxy-lyase activity |
| A | 0019655 | biological_process | glycolytic fermentation to ethanol |
| A | 0030976 | molecular_function | thiamine pyrophosphate binding |
| A | 0046872 | molecular_function | metal ion binding |
| A | 0047433 | molecular_function | branched-chain-2-oxoacid decarboxylase activity |
| A | 0047434 | molecular_function | indolepyruvate decarboxylase activity |
| A | 0050177 | molecular_function | phenylpyruvate decarboxylase activity |
| B | 0000287 | molecular_function | magnesium ion binding |
| B | 0000949 | biological_process | aromatic amino acid family catabolic process to alcohol via Ehrlich pathway |
| B | 0000955 | biological_process | amino acid catabolic process via Ehrlich pathway |
| B | 0003824 | molecular_function | catalytic activity |
| B | 0004737 | molecular_function | pyruvate decarboxylase activity |
| B | 0005634 | cellular_component | nucleus |
| B | 0005737 | cellular_component | cytoplasm |
| B | 0005829 | cellular_component | cytosol |
| B | 0006090 | biological_process | pyruvate metabolic process |
| B | 0006559 | biological_process | L-phenylalanine catabolic process |
| B | 0006569 | biological_process | tryptophan catabolic process |
| B | 0009083 | biological_process | branched-chain amino acid catabolic process |
| B | 0016831 | molecular_function | carboxy-lyase activity |
| B | 0019655 | biological_process | glycolytic fermentation to ethanol |
| B | 0030976 | molecular_function | thiamine pyrophosphate binding |
| B | 0046872 | molecular_function | metal ion binding |
| B | 0047433 | molecular_function | branched-chain-2-oxoacid decarboxylase activity |
| B | 0047434 | molecular_function | indolepyruvate decarboxylase activity |
| B | 0050177 | molecular_function | phenylpyruvate decarboxylase activity |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE MG A 558 |
| Chain | Residue |
| A | ASP444 |
| A | ASN471 |
| A | GLY473 |
| A | TPP557 |
| A | HOH559 |
| site_id | AC2 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE MG B 558 |
| Chain | Residue |
| B | ASP444 |
| B | ASN471 |
| B | GLY473 |
| B | TPP557 |
| B | HOH559 |
| site_id | AC3 |
| Number of Residues | 23 |
| Details | BINDING SITE FOR RESIDUE TPP A 557 |
| Chain | Residue |
| A | GLY389 |
| A | THR390 |
| A | GLY413 |
| A | SER414 |
| A | ILE415 |
| A | GLY443 |
| A | ASP444 |
| A | GLY445 |
| A | SER446 |
| A | ASN471 |
| A | GLY473 |
| A | TYR474 |
| A | THR475 |
| A | ILE476 |
| A | GLU477 |
| A | MG558 |
| A | HOH559 |
| A | HOH583 |
| A | HOH647 |
| B | PRO26 |
| B | GLY27 |
| B | GLU51 |
| B | VAL76 |
| site_id | AC4 |
| Number of Residues | 23 |
| Details | BINDING SITE FOR RESIDUE TPP B 557 |
| Chain | Residue |
| A | PRO26 |
| A | GLU51 |
| A | VAL76 |
| B | GLY389 |
| B | THR390 |
| B | GLY413 |
| B | SER414 |
| B | ILE415 |
| B | GLY443 |
| B | ASP444 |
| B | GLY445 |
| B | SER446 |
| B | ASN471 |
| B | GLY473 |
| B | TYR474 |
| B | THR475 |
| B | ILE476 |
| B | GLU477 |
| B | MG558 |
| B | HOH559 |
| B | HOH612 |
| B | HOH791 |
| B | HOH861 |
| site_id | TPA |
| Number of Residues | 20 |
| Details |
| Chain | Residue |
| A | GLY413 |
| A | GLY473 |
| A | GLU477 |
| A | LEU449 |
| B | GLU51 |
| B | ASP28 |
| B | THR73 |
| B | VAL76 |
| B | ASN83 |
| B | LEU25 |
| B | HIS114 |
| A | ILE415 |
| B | HIS115 |
| A | THR388 |
| A | THR390 |
| A | SER446 |
| A | ILE476 |
| A | LEU469 |
| A | ASN471 |
| A | ASP444 |
| site_id | TPB |
| Number of Residues | 20 |
| Details |
| Chain | Residue |
| B | GLY413 |
| B | ILE415 |
| B | THR388 |
| B | THR390 |
| B | SER446 |
| B | ILE476 |
| B | LEU469 |
| B | ASN471 |
| B | ASP444 |
| B | GLY473 |
| B | GLU477 |
| B | LEU449 |
| A | GLU51 |
| A | ASP28 |
| A | THR73 |
| A | VAL76 |
| A | ASN83 |
| A | LEU25 |
| A | HIS114 |
| A | HIS115 |
Functional Information from PROSITE/UniProt
| site_id | PS00187 |
| Number of Residues | 20 |
| Details | TPP_ENZYMES Thiamine pyrophosphate enzymes signature. FAaeeidPkkrvIlFiGDGS |
| Chain | Residue | Details |
| A | PHE427-SER446 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 6 |
| Details | BINDING: BINDING => ECO:0000305|PubMed:10651824 |
| Chain | Residue | Details |
| A | PHE29 | |
| A | VAL158 | |
| A | LYS478 | |
| B | PHE29 | |
| B | VAL158 | |
| B | LYS478 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 4 |
| Details | BINDING: BINDING => ECO:0000305|PubMed:10651824, ECO:0007744|PDB:1QPB |
| Chain | Residue | Details |
| A | THR116 | |
| A | HIS225 | |
| B | THR116 | |
| B | HIS225 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 12 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:10651824, ECO:0007744|PDB:1QPB |
| Chain | Residue | Details |
| A | SER391 | |
| B | SER446 | |
| B | ASP472 | |
| B | TYR474 | |
| A | SER414 | |
| A | GLY445 | |
| A | SER446 | |
| A | ASP472 | |
| A | TYR474 | |
| B | SER391 | |
| B | SER414 | |
| B | GLY445 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 2 |
| Details | MOD_RES: N-acetylserine => ECO:0000269|PubMed:10545125, ECO:0000269|PubMed:9298649 |
| Chain | Residue | Details |
| A | GLU3 | |
| B | GLU3 |
| site_id | SWS_FT_FI5 |
| Number of Residues | 2 |
| Details | MOD_RES: Omega-N-methylarginine => ECO:0000269|PubMed:26046779 |
| Chain | Residue | Details |
| A | PRO162 | |
| B | PRO162 |
| site_id | SWS_FT_FI6 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:17330950, ECO:0007744|PubMed:18407956, ECO:0007744|PubMed:19779198 |
| Chain | Residue | Details |
| A | ARG224 | |
| B | ARG224 |
| site_id | SWS_FT_FI7 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphothreonine => ECO:0007744|PubMed:18407956 |
| Chain | Residue | Details |
| A | LEU267 | |
| B | LEU267 |
| site_id | SWS_FT_FI8 |
| Number of Residues | 4 |
| Details | MOD_RES: Phosphothreonine => ECO:0007744|PubMed:19779198 |
| Chain | Residue | Details |
| A | ILE337 | |
| A | GLN523 | |
| B | ILE337 | |
| B | GLN523 |
| site_id | SWS_FT_FI9 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphothreonine => ECO:0007744|PubMed:17330950, ECO:0007744|PubMed:19779198 |
| Chain | Residue | Details |
| A | PRO354 | |
| B | PRO354 |
| site_id | SWS_FT_FI10 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:18407956 |
| Chain | Residue | Details |
| A | PHE527 | |
| B | PHE527 |
| site_id | SWS_FT_FI11 |
| Number of Residues | 16 |
| Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0007744|PubMed:22106047 |
| Chain | Residue | Details |
| A | ASN213 | |
| B | LEU234 | |
| B | PRO270 | |
| B | LEU333 | |
| B | ALA485 | |
| B | ASP506 | |
| B | LEU521 | |
| A | LEU234 | |
| A | PRO270 | |
| A | LEU333 | |
| A | ALA485 | |
| A | ASP506 | |
| A | LEU521 | |
| B | ASN213 |
Catalytic Information from CSA
| site_id | CSA1 |
| Number of Residues | 4 |
| Details | a catalytic site defined by CSA, PubMed 11412090 |
| Chain | Residue | Details |
| A | ASP28 | |
| A | HIS114 | |
| A | HIS115 | |
| A | GLU477 |
| site_id | CSA2 |
| Number of Residues | 4 |
| Details | a catalytic site defined by CSA, PubMed 11412090 |
| Chain | Residue | Details |
| B | ASP28 | |
| B | HIS114 | |
| B | HIS115 | |
| B | GLU477 |
| site_id | MCSA1 |
| Number of Residues | 9 |
| Details | M-CSA 215 |
| Chain | Residue | Details |
| A | PHE29 | hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton relay |
| A | LEU52 | hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor |
| A | HIS115 | activator, electrostatic stabiliser, hydrogen bond donor, polar interaction |
| A | THR116 | electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, polar interaction, proton acceptor, proton donor |
| A | SER414 | activator, electrostatic stabiliser, hydrogen bond acceptor |
| A | GLY445 | metal ligand |
| A | ASP472 | metal ligand |
| A | TYR474 | metal ligand |
| A | LYS478 | electrostatic stabiliser, polar interaction |
| site_id | MCSA2 |
| Number of Residues | 9 |
| Details | M-CSA 215 |
| Chain | Residue | Details |
| B | PHE29 | hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton relay |
| B | LEU52 | hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor |
| B | HIS115 | activator, electrostatic stabiliser, hydrogen bond donor, polar interaction |
| B | THR116 | electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, polar interaction, proton acceptor, proton donor |
| B | SER414 | activator, electrostatic stabiliser, hydrogen bond acceptor |
| B | GLY445 | metal ligand |
| B | ASP472 | metal ligand |
| B | TYR474 | metal ligand |
| B | LYS478 | electrostatic stabiliser, polar interaction |
