Structure of PDB 3dod Chain A

Receptor sequence

>3dodA (length=417) Species: 1423 (Bacillus subtilis)

HDLIEKSKKHLWLPFTQMKDYDENPLIIESGTGIKVKDINGKEYYDGFSS
VWLNVHGHRKKELDDAIKKQLGKIAHSTLLGMTNVPATQLAETLIDISPK
KLTRVFYSDSGAEAMEIALKMAFQYWKNIGKPEKQKFIAMKSYKAPIPYV
YRSESGDPDECRDQCLRELAQLLEEHHEEIAALSIESMVQGASGMIVMPE
GYLAGVRELCTTYDVLMIVDEVATGFGRTGKMFACEHENVQPDLMAAGKG
ITGGYLPIAVTFATEDIYKAFYDDYENLKTFFHGHSYTGNQLGCAVALEN
LALFESENIVEQVAEKSKKLHFLLQDLHALPHVGDIRQLGFMCGAELVRS
KETKEPYPADRRIGYKVSLKMRELGMLTRPLGDVIAFLPPLASTAEELSE
MVAIMKQAIHEVTSLED

3D structure

• PDB: 3dod Structural characterization of the Mycobacterium tuberculosis biotin biosynthesis enzymes 7,8-diaminopelargonic acid synthase and dethiobiotin synthetase .
• Chain: A
• Resolution: 1.9 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): F17 E217 D251 A254 K280 A417
• Catalytic site (residue number reindexed from 1): F15 E186 D220 A223 K249 A386
• Enzyme Commision number: 2.6.1.105: lysine--8-amino-7-oxononanoate transaminase.

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	W54 S112 G113 A114 D251 V253 K280	W52 S110 G111 A112 D220 V222 K249
BS02	PLP	A	H316 S317	H285 S286

Gene Ontology

Molecular Function

• GO:0003824 catalytic activity
• GO:0004015 adenosylmethionine-8-amino-7-oxononanoate transaminase activity
• GO:0008483 transaminase activity
• GO:0030170 pyridoxal phosphate binding

Biological Process

• GO:0009102 biotin biosynthetic process

Cellular Component

• GO:0005737 cytoplasm

External links

• PDB: RCSB:3dod, PDBe:3dod, PDBj:3dod
• PDBsum: 3dod
• PubMed: 20565114
• UniProt: P53555|BIOK_BACSU L-Lysine--8-amino-7-oxononanoate transaminase (Gene Name=bioK)