Structure of PDB 2vk8 Chain D

Receptor sequence
>2vk8D (length=562) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence]
SEITLGKYLFERLKQVNVNTVFGLPGDFNLSLLDKIYEVEGMRWAGNANE
LNAAYAADGYARIKGMSCIITTFGVGELSALNGIAGSYAEHVGVLHVVGV
PSISAQAKQLLLHHTLGNGDFTVFHRMSANISETTAMITDIATAPAEIDR
CIRTTYVTQRPVYLGLPANLVDLNVPAKLLQTPIDMSLKPNDAESEKEVI
DTILVLDKDAKNPVILADACCSRHDVKAETKKLIDLTQFPAFVTPMGKGS
IDEQHPRYGGVYVGTLSKPEVKEAVESADLILSVGALLSDFNTGSFSYSY
KTKNIVEFHSDHMKIRNATFPGVQMKFVLQKLLTTIADAAKGYKPVAVPA
RTPANAAVPASTPLKQEWMWNQLGNFLQEGDVVIAETGTSAFGINQTTFP
NNTYGISQVLWGSIGFTTGATLGAAFAAEEIDPKKRVILFIGDGSLQLTV
QEISTMIRWGLKPYLFVLNNDGYTIQKLIHGPKAQYNEIQGWDHLSLLPT
FGAKDYETHRVATTGEWDKLTQDKSFNDNSKIRMIEVMLPVFDAPQNLVE
QAKLTAATNAKQ
3D structure
PDB2vk8 Covalently Bound Substrate at the Regulatory Site of Yeast Pyruvate Decarboxylases Triggers Allosteric Enzyme Activation.
ChainD
Resolution1.42 Å
3D
structure
Catalytic site residues are labeled in the structure
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Enzymatic activity
Catalytic site (original residue number in PDB) L25 G27 D28 F29 N30 E51 T73 H114 H115 L117 G118 A169 T266 N293 T388 G413 I415 D444 N471 G473 Y474 I476 Q477 I480 V542
Catalytic site (residue number reindexed from 1) L24 G26 D27 F28 N29 E50 T72 H113 H114 L116 G117 A168 T265 N292 T387 G412 I414 D443 N470 G472 Y473 I475 Q476 I479 V541
Enzyme Commision number 4.1.1.-
4.1.1.43: phenylpyruvate decarboxylase.
4.1.1.72: branched-chain-2-oxoacid decarboxylase.
4.1.1.74: indolepyruvate decarboxylase.
Interaction with ligand
Site
#		 Ligand Ligand
chain		 Binding residues on receptor
(original residue number in PDB)		 Binding residues on receptor
(residue number reindexed from 1)		 Binding affinity
BS01 TPP D P26 E51 V76 P25 E50 V75
BS02 TPP D T390 G413 S414 I415 G443 G445 S446 N471 G473 Y474 T475 I476 Q477 T389 G412 S413 I414 G442 G444 S445 N470 G472 Y473 T474 I475 Q476
BS03 MG D D444 N471 G473 D443 N470 G472
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0003824 catalytic activity
GO:0004737 pyruvate decarboxylase activity
GO:0005515 protein binding
GO:0016831 carboxy-lyase activity
GO:0030976 thiamine pyrophosphate binding
GO:0046872 metal ion binding
GO:0047433 branched-chain-2-oxoacid decarboxylase activity
GO:0047434 indolepyruvate decarboxylase activity
GO:0050177 phenylpyruvate decarboxylase activity
Biological Process
GO:0000949 aromatic amino acid family catabolic process to alcohol via Ehrlich pathway
GO:0000955 amino acid catabolic process via Ehrlich pathway
GO:0006090 pyruvate metabolic process
GO:0006559 L-phenylalanine catabolic process
GO:0006569 tryptophan catabolic process
GO:0009083 branched-chain amino acid catabolic process
GO:0019655 glycolytic fermentation to ethanol
Cellular Component
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005829 cytosol

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:2vk8, PDBe:2vk8, PDBj:2vk8
PDBsum2vk8
PubMed19246454
UniProtP06169|PDC1_YEAST Pyruvate decarboxylase isozyme 1 (Gene Name=PDC1)

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