Structure of PDB 2dkb Chain A

Receptor sequence

>2dkbA (length=431) Species: 292 (Burkholderia cepacia)

LNDDATFWRNARHHLVRYGGTFEPMIIERAKGSFVYDADGRAILDFTSGQ
MSAVLGHCHPEIVSVIGEYAGKLDHLFSEMLSRPVVDLATRLANITPPGL
DRALLLSTGAESNEAAIRMAKLVTGKYEIVGFAQSWHGMTGAAASATYSA
GRKGVGPAAVGSFAIPAPFTYRPRFERNGAYDYLAELDYAFDLIDRQSSG
NLAAFIAEPILSSGGIIELPDGYMAALKRKCEARGMLLILDEAQTGVGRT
GTMFACQRDGVTPDILTLSKTLGAGLPLAAIVTSAAIEERAHELGYLFYT
THVSDPLPAAVGLRVLDVVQRDGLVARANVMGDRLRRGLLDLMERFDCIG
DVRGRGLLLGVEIVKDRRTKEPADGLGAKITRECMNLGLSMNIVQLPGMG
GVFRIAPPLTVSEDEIDLGLSLLGQAIERAL

3D structure

• PDB: 2dkb Dialkylglycine decarboxylase structure: bifunctional active site and alkali metal sites.
• Chain: A
• Resolution: 2.1 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): G21 W138 E210 D243 Q246 K272 T303 R406
• Catalytic site (residue number reindexed from 1): G19 W136 E208 D241 Q244 K270 T301 R404
• Enzyme Commision number: 4.1.1.64: 2,2-dialkylglycine decarboxylase (pyruvate).

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	PLP	A	G111 A112 W138 H139 E210 D243 A245 Q246 K272	G109 A110 W136 H137 E208 D241 A243 Q244 K270

Gene Ontology

Molecular Function

• GO:0008453 alanine-glyoxylate transaminase activity
• GO:0008483 transaminase activity
• GO:0016831 carboxy-lyase activity
• GO:0030170 pyridoxal phosphate binding
• GO:0047432 2,2-dialkylglycine decarboxylase (pyruvate) activity

Biological Process

• GO:0009436 glyoxylate catabolic process
• GO:0019481 L-alanine catabolic process, by transamination

External links

• PDB: RCSB:2dkb, PDBe:2dkb, PDBj:2dkb
• PDBsum: 2dkb
• PubMed: 8342040
• UniProt: P16932|DGDA_BURCE 2,2-dialkylglycine decarboxylase (Gene Name=dgdA)