Structure of PDB 2vbg Chain B

Receptor sequence

>2vbgB (length=544) Species: 1358 (Lactococcus lactis)

HSSGLMYTVGDYLLDRLHELGIEEIFGVPGDYNLQFLDQIISREDMKWIG
NANELNASYMADGYARTKKAAAFLTTFGVGELSAINGLAGSYAENLPVVE
IVGSPTSKVQNDGKFVHHTLADGDFKHFMKMHEPVTAARTLLTAENATYE
IDRVLSQLLKERKPVYINLPVDVAAAKAEKPALSLENTTEQVILSKIEES
LKNAQKPVVIAGHEVISFGLEKTVTQFVSETKLPITTLNFGKSAVDESLP
SFLGIYNGKLSEISLKNFVESADFILMLGVKLTDSSTGAFTHHLDENKMI
SLNIDEGIIFNKVVEDFDFRAVVSSLSELKGIEYEGQYIDKEEFIPSSAP
LSQDRLWQAVESLTQSNETIVAEQGTSFFGASTIFLKSNSRFIGQPLWGS
IGYTFPAALGSQIADKESRHLLFIGDGSLQLTVQELGLSIREKLNPICFI
INNDGYTVEREIHGPTQSYNDIPMWNYSKLPETFGATEDRVVSKIVRTEN
EFVSVMKEAQADVNRMYWIELVLEKEDAPKLLKKMGKLFAEQNK

3D structure

• PDB: 2vbg Crystal Structure of the Branched-Chain Keto Acid Decarboxylase (Kdca) from Lactococcus Lactis Provides Insights Into the Structural Basis for the Chemo- and Enantioselective Carboligation Reaction
• Chain: B
• Resolution: 1.8 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): V23 G25 D26 Y27 N28 N48 E49 T71 F110 V111 H112 H113 L115 A116 V166 K260 S287 E376 Q377 G402 I404 D429 N456 G458 Y459 V461 E462 K528
• Catalytic site (residue number reindexed from 1): V28 G30 D31 Y32 N33 N53 E54 T76 F115 V116 H117 H118 L120 A121 V171 K259 S286 E373 Q374 G399 I401 D426 N453 G455 Y456 V458 E459 K525

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	R1T	B	P24 E49 V74 H113	P29 E54 V79 H118
BS02	MG	B	D429 N456 G458	D426 N453 G455
BS03	R1T	B	T379 G402 S403 I404 G428 G430 S431 N456 G458 Y459 T460 V461 E462	T376 G399 S400 I401 G425 G427 S428 N453 G455 Y456 T457 V458 E459

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
• GO:0047433 branched-chain-2-oxoacid decarboxylase activity

Biological Process

• GO:0000949 aromatic amino acid family catabolic process to alcohol via Ehrlich pathway
• GO:0009082 branched-chain amino acid biosynthetic process

Cellular Component

• GO:0005829 cytosol

External links

• PDB: RCSB:2vbg, PDBe:2vbg, PDBj:2vbg
• PDBsum: 2vbg
• PubMed: 18084069
• UniProt: Q6QBS4