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2VK4

Crystal structure of pyruvate decarboxylase from Kluyveromyces lactis

Replaces:  2G1I
Functional Information from GO Data
ChainGOidnamespacecontents
A0000287molecular_functionmagnesium ion binding
A0000949biological_processaromatic amino acid family catabolic process to alcohol via Ehrlich pathway
A0003824molecular_functioncatalytic activity
A0004737molecular_functionpyruvate decarboxylase activity
A0005634cellular_componentnucleus
A0005829cellular_componentcytosol
A0016829molecular_functionlyase activity
A0016831molecular_functioncarboxy-lyase activity
A0019752biological_processcarboxylic acid metabolic process
A0030976molecular_functionthiamine pyrophosphate binding
A0046872molecular_functionmetal ion binding
B0000287molecular_functionmagnesium ion binding
B0000949biological_processaromatic amino acid family catabolic process to alcohol via Ehrlich pathway
B0003824molecular_functioncatalytic activity
B0004737molecular_functionpyruvate decarboxylase activity
B0005634cellular_componentnucleus
B0005829cellular_componentcytosol
B0016829molecular_functionlyase activity
B0016831molecular_functioncarboxy-lyase activity
B0019752biological_processcarboxylic acid metabolic process
B0030976molecular_functionthiamine pyrophosphate binding
B0046872molecular_functionmetal ion binding
C0000287molecular_functionmagnesium ion binding
C0000949biological_processaromatic amino acid family catabolic process to alcohol via Ehrlich pathway
C0003824molecular_functioncatalytic activity
C0004737molecular_functionpyruvate decarboxylase activity
C0005634cellular_componentnucleus
C0005829cellular_componentcytosol
C0016829molecular_functionlyase activity
C0016831molecular_functioncarboxy-lyase activity
C0019752biological_processcarboxylic acid metabolic process
C0030976molecular_functionthiamine pyrophosphate binding
C0046872molecular_functionmetal ion binding
D0000287molecular_functionmagnesium ion binding
D0000949biological_processaromatic amino acid family catabolic process to alcohol via Ehrlich pathway
D0003824molecular_functioncatalytic activity
D0004737molecular_functionpyruvate decarboxylase activity
D0005634cellular_componentnucleus
D0005829cellular_componentcytosol
D0016829molecular_functionlyase activity
D0016831molecular_functioncarboxy-lyase activity
D0019752biological_processcarboxylic acid metabolic process
D0030976molecular_functionthiamine pyrophosphate binding
D0046872molecular_functionmetal ion binding
Functional Information from PDB Data
site_idAC1
Number of Residues23
DetailsBINDING SITE FOR RESIDUE TPP A 600
ChainResidue
AGLY389
AASN471
AGLY473
ATYR474
ATHR475
AILE476
AGLU477
AMG601
AHOH2238
AHOH2309
AHOH2310
ATHR390
BPRO26
BGLY27
BGLU51
BVAL76
AGLY413
ASER414
AILE415
AGLY443
AASP444
AGLY445
ASER446

site_idAC2
Number of Residues5
DetailsBINDING SITE FOR RESIDUE MG A 601
ChainResidue
AASP444
AASN471
AGLY473
ATPP600
AHOH2238

site_idAC3
Number of Residues24
DetailsBINDING SITE FOR RESIDUE TPP B 600
ChainResidue
APRO26
AGLY27
AGLU51
AVAL76
BGLY389
BTHR390
BGLY413
BSER414
BILE415
BGLY443
BASP444
BGLY445
BSER446
BASN471
BGLY473
BTYR474
BTHR475
BILE476
BGLU477
BMG601
BHOH2215
BHOH2256
BHOH2325
BHOH2326

site_idAC4
Number of Residues5
DetailsBINDING SITE FOR RESIDUE MG B 601
ChainResidue
BASP444
BASN471
BGLY473
BTPP600
BHOH2256

site_idAC5
Number of Residues23
DetailsBINDING SITE FOR RESIDUE TPP C 600
ChainResidue
CTHR390
CGLY413
CSER414
CILE415
CGLY443
CASP444
CGLY445
CSER446
CASN471
CGLY473
CTYR474
CTHR475
CILE476
CGLU477
CMG601
CHOH2260
CHOH2374
CHOH2375
CHOH2376
DPRO26
DGLY27
DGLU51
DVAL76

site_idAC6
Number of Residues5
DetailsBINDING SITE FOR RESIDUE MG C 601
ChainResidue
CASP444
CASN471
CGLY473
CTPP600
CHOH2374

site_idAC7
Number of Residues24
DetailsBINDING SITE FOR RESIDUE TPP D 600
ChainResidue
DGLY473
DTYR474
DTHR475
DILE476
DGLU477
DMG601
DHOH2196
DHOH2197
DHOH2237
DHOH2307
CPRO26
CGLY27
CGLU51
CVAL76
DGLY389
DTHR390
DGLY413
DSER414
DILE415
DGLY443
DASP444
DGLY445
DSER446
DASN471

site_idAC8
Number of Residues5
DetailsBINDING SITE FOR RESIDUE MG D 601
ChainResidue
DASP444
DASN471
DGLY473
DTPP600
DHOH2237

Functional Information from PROSITE/UniProt
site_idPS00187
Number of Residues20
DetailsTPP_ENZYMES Thiamine pyrophosphate enzymes signature. FAaeeidPkkrvIlFiGDGS
ChainResidueDetails
APHE427-SER446

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues60
DetailsBinding site: {"evidences":[{"source":"UniProtKB","id":"P06169","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails

Catalytic Information from CSA
site_idCSA1
Number of Residues4
DetailsAnnotated By Reference To The Literature 1pvd
ChainResidueDetails
AASP28
AHIS114
AHIS115
AGLU477

site_idCSA2
Number of Residues4
DetailsAnnotated By Reference To The Literature 1pvd
ChainResidueDetails
BASP28
BHIS114
BHIS115
BGLU477

site_idCSA3
Number of Residues4
DetailsAnnotated By Reference To The Literature 1pvd
ChainResidueDetails
CASP28
CHIS114
CHIS115
CGLU477

site_idCSA4
Number of Residues4
DetailsAnnotated By Reference To The Literature 1pvd
ChainResidueDetails
DASP28
DHIS114
DHIS115
DGLU477

246905

PDB entries from 2025-12-31

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