2W93
Crystal structure of the Saccharomyces cerevisiae pyruvate decarboxylase variant E477Q in complex with the surrogate pyruvamide
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 | 0005515 | molecular_function | protein binding |
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 | 0005515 | molecular_function | protein binding |
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 |
C | 0000287 | molecular_function | magnesium ion binding |
C | 0000949 | biological_process | aromatic amino acid family catabolic process to alcohol via Ehrlich pathway |
C | 0000955 | biological_process | amino acid catabolic process via Ehrlich pathway |
C | 0003824 | molecular_function | catalytic activity |
C | 0004737 | molecular_function | pyruvate decarboxylase activity |
C | 0005515 | molecular_function | protein binding |
C | 0005634 | cellular_component | nucleus |
C | 0005737 | cellular_component | cytoplasm |
C | 0005829 | cellular_component | cytosol |
C | 0006090 | biological_process | pyruvate metabolic process |
C | 0006559 | biological_process | L-phenylalanine catabolic process |
C | 0006569 | biological_process | tryptophan catabolic process |
C | 0009083 | biological_process | branched-chain amino acid catabolic process |
C | 0016831 | molecular_function | carboxy-lyase activity |
C | 0019655 | biological_process | glycolytic fermentation to ethanol |
C | 0030976 | molecular_function | thiamine pyrophosphate binding |
C | 0046872 | molecular_function | metal ion binding |
C | 0047433 | molecular_function | branched-chain-2-oxoacid decarboxylase activity |
C | 0047434 | molecular_function | indolepyruvate decarboxylase activity |
C | 0050177 | molecular_function | phenylpyruvate decarboxylase activity |
D | 0000287 | molecular_function | magnesium ion binding |
D | 0000949 | biological_process | aromatic amino acid family catabolic process to alcohol via Ehrlich pathway |
D | 0000955 | biological_process | amino acid catabolic process via Ehrlich pathway |
D | 0003824 | molecular_function | catalytic activity |
D | 0004737 | molecular_function | pyruvate decarboxylase activity |
D | 0005515 | molecular_function | protein binding |
D | 0005634 | cellular_component | nucleus |
D | 0005737 | cellular_component | cytoplasm |
D | 0005829 | cellular_component | cytosol |
D | 0006090 | biological_process | pyruvate metabolic process |
D | 0006559 | biological_process | L-phenylalanine catabolic process |
D | 0006569 | biological_process | tryptophan catabolic process |
D | 0009083 | biological_process | branched-chain amino acid catabolic process |
D | 0016831 | molecular_function | carboxy-lyase activity |
D | 0019655 | biological_process | glycolytic fermentation to ethanol |
D | 0030976 | molecular_function | thiamine pyrophosphate binding |
D | 0046872 | molecular_function | metal ion binding |
D | 0047433 | molecular_function | branched-chain-2-oxoacid decarboxylase activity |
D | 0047434 | molecular_function | indolepyruvate decarboxylase activity |
D | 0050177 | molecular_function | phenylpyruvate decarboxylase activity |
Functional Information from PDB Data
site_id | AC1 |
Number of Residues | 22 |
Details | BINDING SITE FOR RESIDUE TPP A 600 |
Chain | Residue |
A | THR390 |
A | GLY473 |
A | TYR474 |
A | THR475 |
A | ILE476 |
A | GLN477 |
A | MG601 |
A | HOH2224 |
A | HOH2351 |
A | HOH2352 |
B | PRO26 |
A | GLY413 |
B | GLY27 |
B | GLU51 |
B | VAL76 |
A | SER414 |
A | ILE415 |
A | GLY443 |
A | ASP444 |
A | GLY445 |
A | SER446 |
A | ASN471 |
site_id | AC2 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE MG A 601 |
Chain | Residue |
A | ASP444 |
A | ASN471 |
A | GLY473 |
A | TPP600 |
A | HOH2351 |
site_id | AC3 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE PY0 A 603 |
Chain | Residue |
A | CYS221 |
A | HIS225 |
A | GLY286 |
A | ALA287 |
A | HIS310 |
A | SER311 |
site_id | AC4 |
Number of Residues | 2 |
Details | BINDING SITE FOR RESIDUE PY0 A 604 |
Chain | Residue |
A | GLN16 |
A | HOH2353 |
site_id | AC5 |
Number of Residues | 24 |
Details | BINDING SITE FOR RESIDUE TPP B 600 |
Chain | Residue |
A | PRO26 |
A | GLY27 |
A | GLU51 |
A | VAL76 |
A | HIS115 |
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 | GLN477 |
B | MG601 |
B | PY0602 |
B | HOH2313 |
B | HOH2408 |
B | HOH2409 |
site_id | AC6 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE MG B 601 |
Chain | Residue |
B | ASP444 |
B | ASN471 |
B | GLY473 |
B | TPP600 |
B | HOH2313 |
site_id | AC7 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE PY0 B 602 |
Chain | Residue |
A | ASP28 |
A | HIS115 |
B | THR388 |
B | GLN477 |
B | ILE480 |
B | TPP600 |
site_id | AC8 |
Number of Residues | 7 |
Details | BINDING SITE FOR RESIDUE PY0 B 603 |
Chain | Residue |
B | HIS92 |
B | CYS221 |
B | HIS225 |
B | GLY286 |
B | ALA287 |
B | HIS310 |
B | SER311 |
site_id | AC9 |
Number of Residues | 24 |
Details | BINDING SITE FOR RESIDUE TPP C 600 |
Chain | Residue |
D | VAL76 |
D | HIS115 |
C | THR390 |
C | GLY413 |
C | SER414 |
C | ILE415 |
C | GLY443 |
C | ASP444 |
C | GLY445 |
C | SER446 |
C | ASN471 |
C | GLY473 |
C | TYR474 |
C | THR475 |
C | ILE476 |
C | GLN477 |
C | MG601 |
C | PY0602 |
C | HOH2249 |
C | HOH2352 |
C | HOH2353 |
D | PRO26 |
D | GLY27 |
D | GLU51 |
site_id | BC1 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE MG C 601 |
Chain | Residue |
C | ASP444 |
C | ASN471 |
C | GLY473 |
C | TPP600 |
C | HOH2353 |
site_id | BC2 |
Number of Residues | 7 |
Details | BINDING SITE FOR RESIDUE PY0 C 602 |
Chain | Residue |
C | THR388 |
C | GLN477 |
C | TPP600 |
D | GLY27 |
D | ASP28 |
D | HIS114 |
D | HIS115 |
site_id | BC3 |
Number of Residues | 7 |
Details | BINDING SITE FOR RESIDUE PY0 C 603 |
Chain | Residue |
C | HIS92 |
C | CYS221 |
C | HIS225 |
C | GLY286 |
C | ALA287 |
C | HIS310 |
C | SER311 |
site_id | BC4 |
Number of Residues | 24 |
Details | BINDING SITE FOR RESIDUE TPP D 600 |
Chain | Residue |
C | PRO26 |
C | GLY27 |
C | GLU51 |
C | VAL76 |
C | HIS115 |
D | THR390 |
D | GLY413 |
D | SER414 |
D | ILE415 |
D | GLY443 |
D | ASP444 |
D | GLY445 |
D | SER446 |
D | ASN471 |
D | GLY473 |
D | TYR474 |
D | THR475 |
D | ILE476 |
D | GLN477 |
D | MG601 |
D | PY0602 |
D | HOH2295 |
D | HOH2296 |
D | HOH2297 |
site_id | BC5 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE MG D 601 |
Chain | Residue |
D | ASP444 |
D | ASN471 |
D | GLY473 |
D | TPP600 |
D | HOH2296 |
site_id | BC6 |
Number of Residues | 8 |
Details | BINDING SITE FOR RESIDUE PY0 D 602 |
Chain | Residue |
C | GLY27 |
C | ASP28 |
C | HIS115 |
C | HOH2069 |
D | THR388 |
D | GLN477 |
D | ILE480 |
D | TPP600 |
site_id | BC7 |
Number of Residues | 8 |
Details | BINDING SITE FOR RESIDUE PY0 D 603 |
Chain | Residue |
D | HIS92 |
D | CYS221 |
D | HIS225 |
D | GLY286 |
D | ALA287 |
D | HIS310 |
D | SER311 |
D | HOH2298 |
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 | 12 |
Details | BINDING: BINDING => ECO:0000305|PubMed:10651824 |
Chain | Residue | Details |
A | ASP28 | |
D | ASP28 | |
D | TYR157 | |
D | GLN477 | |
A | TYR157 | |
A | GLN477 | |
B | ASP28 | |
B | TYR157 | |
B | GLN477 | |
C | ASP28 | |
C | TYR157 | |
C | GLN477 |
site_id | SWS_FT_FI2 |
Number of Residues | 8 |
Details | BINDING: BINDING => ECO:0000305|PubMed:10651824, ECO:0007744|PDB:1QPB |
Chain | Residue | Details |
A | HIS115 | |
A | ARG224 | |
B | HIS115 | |
B | ARG224 | |
C | HIS115 | |
C | ARG224 | |
D | HIS115 | |
D | ARG224 |
site_id | SWS_FT_FI3 |
Number of Residues | 24 |
Details | BINDING: BINDING => ECO:0000269|PubMed:10651824, ECO:0007744|PDB:1QPB |
Chain | Residue | Details |
A | THR390 | |
B | GLY445 | |
B | ASN471 | |
B | GLY473 | |
C | THR390 | |
C | GLY413 | |
C | ASP444 | |
C | GLY445 | |
C | ASN471 | |
C | GLY473 | |
D | THR390 | |
A | GLY413 | |
D | GLY413 | |
D | ASP444 | |
D | GLY445 | |
D | ASN471 | |
D | GLY473 | |
A | ASP444 | |
A | GLY445 | |
A | ASN471 | |
A | GLY473 | |
B | THR390 | |
B | GLY413 | |
B | ASP444 |
site_id | SWS_FT_FI4 |
Number of Residues | 4 |
Details | MOD_RES: N-acetylserine => ECO:0000269|PubMed:10545125, ECO:0000269|PubMed:9298649 |
Chain | Residue | Details |
A | SER2 | |
B | SER2 | |
C | SER2 | |
D | SER2 |
site_id | SWS_FT_FI5 |
Number of Residues | 4 |
Details | MOD_RES: Omega-N-methylarginine => ECO:0000269|PubMed:26046779 |
Chain | Residue | Details |
A | ARG161 | |
B | ARG161 | |
C | ARG161 | |
D | ARG161 |
site_id | SWS_FT_FI6 |
Number of Residues | 4 |
Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:17330950, ECO:0007744|PubMed:18407956, ECO:0007744|PubMed:19779198 |
Chain | Residue | Details |
A | SER223 | |
B | SER223 | |
C | SER223 | |
D | SER223 |
site_id | SWS_FT_FI7 |
Number of Residues | 4 |
Details | MOD_RES: Phosphothreonine => ECO:0007744|PubMed:18407956 |
Chain | Residue | Details |
A | THR266 | |
B | THR266 | |
C | THR266 | |
D | THR266 |
site_id | SWS_FT_FI8 |
Number of Residues | 8 |
Details | MOD_RES: Phosphothreonine => ECO:0007744|PubMed:19779198 |
Chain | Residue | Details |
A | ASN336 | |
A | THR522 | |
B | ASN336 | |
B | THR522 | |
C | ASN336 | |
C | THR522 | |
D | ASN336 | |
D | THR522 |
site_id | SWS_FT_FI9 |
Number of Residues | 4 |
Details | MOD_RES: Phosphothreonine => ECO:0007744|PubMed:17330950, ECO:0007744|PubMed:19779198 |
Chain | Residue | Details |
A | THR353 | |
B | THR353 | |
C | THR353 | |
D | THR353 |
site_id | SWS_FT_FI10 |
Number of Residues | 4 |
Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:18407956 |
Chain | Residue | Details |
A | SER526 | |
B | SER526 | |
C | SER526 | |
D | SER526 |
site_id | SWS_FT_FI11 |
Number of Residues | 32 |
Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0007744|PubMed:22106047 |
Chain | Residue | Details |
A | LYS212 | |
B | LYS233 | |
B | LYS269 | |
B | LYS332 | |
B | LYS484 | |
B | LYS505 | |
B | LYS520 | |
C | LYS212 | |
C | LYS233 | |
C | LYS269 | |
C | LYS332 | |
C | LYS484 | |
C | LYS505 | |
C | LYS520 | |
D | LYS212 | |
D | LYS233 | |
D | LYS269 | |
D | LYS332 | |
A | LYS233 | |
D | LYS484 | |
D | LYS505 | |
D | LYS520 | |
A | LYS269 | |
A | LYS332 | |
A | LYS484 | |
A | LYS505 | |
A | LYS520 | |
B | LYS212 |
Catalytic Information from CSA
site_id | CSA1 |
Number of Residues | 4 |
Details | Annotated By Reference To The Literature 1pvd |
Chain | Residue | Details |
A | ASP28 | |
A | HIS114 | |
A | HIS115 | |
A | GLN477 |
site_id | CSA2 |
Number of Residues | 4 |
Details | Annotated By Reference To The Literature 1pvd |
Chain | Residue | Details |
B | ASP28 | |
B | HIS114 | |
B | HIS115 | |
B | GLN477 |
site_id | CSA3 |
Number of Residues | 4 |
Details | Annotated By Reference To The Literature 1pvd |
Chain | Residue | Details |
C | ASP28 | |
C | HIS114 | |
C | HIS115 | |
C | GLN477 |
site_id | CSA4 |
Number of Residues | 4 |
Details | Annotated By Reference To The Literature 1pvd |
Chain | Residue | Details |
D | ASP28 | |
D | HIS114 | |
D | HIS115 | |
D | GLN477 |
site_id | MCSA1 |
Number of Residues | 9 |
Details | M-CSA 215 |
Chain | Residue | Details |
A | ASP28 | hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton relay |
A | GLU51 | hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor |
A | HIS114 | activator, electrostatic stabiliser, hydrogen bond donor, polar interaction |
A | HIS115 | electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, polar interaction, proton acceptor, proton donor |
A | GLY413 | activator, electrostatic stabiliser, hydrogen bond acceptor |
A | ASP444 | metal ligand |
A | ASN471 | metal ligand |
A | GLY473 | metal ligand |
A | GLN477 | electrostatic stabiliser, polar interaction |
site_id | MCSA2 |
Number of Residues | 9 |
Details | M-CSA 215 |
Chain | Residue | Details |
B | ASP28 | hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton relay |
B | GLU51 | hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor |
B | HIS114 | activator, electrostatic stabiliser, hydrogen bond donor, polar interaction |
B | HIS115 | electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, polar interaction, proton acceptor, proton donor |
B | GLY413 | activator, electrostatic stabiliser, hydrogen bond acceptor |
B | ASP444 | metal ligand |
B | ASN471 | metal ligand |
B | GLY473 | metal ligand |
B | GLN477 | electrostatic stabiliser, polar interaction |
site_id | MCSA3 |
Number of Residues | 9 |
Details | M-CSA 215 |
Chain | Residue | Details |
C | ASP28 | hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton relay |
C | GLU51 | hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor |
C | HIS114 | activator, electrostatic stabiliser, hydrogen bond donor, polar interaction |
C | HIS115 | electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, polar interaction, proton acceptor, proton donor |
C | GLY413 | activator, electrostatic stabiliser, hydrogen bond acceptor |
C | ASP444 | metal ligand |
C | ASN471 | metal ligand |
C | GLY473 | metal ligand |
C | GLN477 | electrostatic stabiliser, polar interaction |
site_id | MCSA4 |
Number of Residues | 9 |
Details | M-CSA 215 |
Chain | Residue | Details |
D | ASP28 | hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton relay |
D | GLU51 | hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor |
D | HIS114 | activator, electrostatic stabiliser, hydrogen bond donor, polar interaction |
D | HIS115 | electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, polar interaction, proton acceptor, proton donor |
D | GLY413 | activator, electrostatic stabiliser, hydrogen bond acceptor |
D | ASP444 | metal ligand |
D | ASN471 | metal ligand |
D | GLY473 | metal ligand |
D | GLN477 | electrostatic stabiliser, polar interaction |