Structure of PDB 1yxd Chain A

Receptor sequence

>1yxdA (length=292) Species: 562 (Escherichia coli)

MFTGSIVAIVTPMDEKGNVCRASLKKLIDYHVASGTSAIVSVGTTGESAT
LNHDEHADVVMMTLDLADGRIPVIAGTGANATAEAISLTQRFNDSGIVGC
LTVTPYYNRPSQEGLYQHFKAIAEHTDLPQILYNVPSRTGCDLLPETVGR
LAKVKNIIGIKEATGNLTRVNQIKELVSDDFVLLSGDDASALDFMQLGGH
GVISVTANVAARDMAQMCKLAAEGHFAEARVINQRLMPLHNKLFVEPNPI
PVKWACKELGLVATDTLRLPMTPITDSGRETVRAALKHAGLL

3D structure

• PDB: 1yxd The crystal structures of native and (S)-lysine-bound dihydrodipicolinate synthase from Escherichia coli with improved resolution show new features of biological significance.
• Chain: A
• Resolution: 2.0 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): T44 Y107 Y133 R138 K161 I203
• Catalytic site (residue number reindexed from 1): T44 Y107 Y133 R138 K161 I203
• Enzyme Commision number: 4.3.3.7: 4-hydroxy-tetrahydrodipicolinate synthase.

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	LYS	A	A49 L51 H53 H56 Y106	A49 L51 H53 H56 Y106	PDBbind-CN: -logKd/Ki=5.30,Ki=5uM
BS02	LYS	A	N80 E84	N80 E84	PDBbind-CN: -logKd/Ki=5.30,Ki=5uM

Gene Ontology

Molecular Function

• GO:0008840 4-hydroxy-tetrahydrodipicolinate synthase activity
• GO:0016829 lyase activity
• GO:0042802 identical protein binding

Biological Process

• GO:0009085 lysine biosynthetic process
• GO:0009089 lysine biosynthetic process via diaminopimelate
• GO:0019877 diaminopimelate biosynthetic process
• GO:0044281 small molecule metabolic process

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol

External links

• PDB: RCSB:1yxd, PDBe:1yxd, PDBj:1yxd
• PDBsum: 1yxd
• PubMed: 16041077
• UniProt: P0A6L2|DAPA_ECOLI 4-hydroxy-tetrahydrodipicolinate synthase (Gene Name=dapA)