Structure of PDB 2vjy Chain B

Receptor sequence

>2vjyB (length=562) Species: 28985 (Kluyveromyces lactis)

SEITLGRYLFERLKQVEVQTIFGLPGDFNLSLLDNIYEVPGMRWAGNANE
LNAAYAADGYARLKGMSCIITTFGVGELSALNGIAGSYAEHVGVLHVVGV
PSVSSQAKQLLLHHTLGNGDFTVFHRMSSNISETTAMITDINTAPAEIDR
CIRTTYVSQRPVYLGLPANLVDLTVPASLLDTPIDLSLKPNDPEAEEEVI
ENVLQLIKEAKNPVILADACCSRHDAKAETKKLIDLTQFPAFVTPMGKGS
IDEKHPRFGGVYVGTLSSPAVKEAVESADLVLSVGALLSDFNTGSFSYSY
KTKNIVEFHSDYTKIRSATFPGVQMKFALQKLLTKVADAAKGYKPVPVPS
EPEHNEAVADSTPLKQEWVWTQVGEFLREGDVVITETGTSAFGINQTHFP
NNTYGISQVLWGSIGFTTGATLGAAFAAEEIDPKKRVILFIGDGSLQLTV
QEISTMIRWGLKPYLFVLNNDGYTIERLIHGETAQYNCIQNWQHLELLPT
FGAKDYEAVRVSTTGEWNKLTTDEKFQDNTRIRLIEVMLPTMDAPSNLVK
QAQLTAATNAKN

3D structure

• PDB: 2vjy Covalently Bound Substrate at the Regulatory Site of Yeast Pyruvate Decarboxylases Triggers Allosteric Enzyme Activation.
• Chain: B
• Resolution: 2.3 Å

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 E477 I480 T542
• 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 E476 I479 T541
• Enzyme Commision number: 4.1.1.1: pyruvate 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	B	P26 E51 V76	P25 E50 V75
BS02	ALK	B	G27 D28 H114 H115	G26 D27 H113 H114
BS03	TPP	B	T390 G413 S414 I415 G443 G445 S446 N471 G473 Y474 T475 I476 E477	T389 G412 S413 I414 G442 G444 S445 N470 G472 Y473 T474 I475 E476
BS04	MG	B	D444 N471 G473	D443 N470 G472
BS05	ALK	B	F292 E477	F291 E476
BS06	ALK	B	H92 C221 H225 G286 A287 H310 S311	H91 C220 H224 G285 A286 H309 S310
BS07	ALU	B	V17 Y157	V16 Y156

Gene Ontology

Molecular Function

• GO:0000287 magnesium ion binding
• GO:0003824 catalytic activity
• GO:0004737 pyruvate decarboxylase activity
• GO:0016831 carboxy-lyase activity
• GO:0030976 thiamine pyrophosphate binding
• GO:0046872 metal ion binding

Biological Process

• GO:0000949 aromatic amino acid family catabolic process to alcohol via Ehrlich pathway

Cellular Component

• GO:0005634 nucleus
• GO:0005829 cytosol

External links

• PDB: RCSB:2vjy, PDBe:2vjy, PDBj:2vjy
• PDBsum: 2vjy
• PubMed: 19246454
• UniProt: Q12629|PDC1_KLULA Pyruvate decarboxylase (Gene Name=PDC1)