Structure of PDB 3der Chain A

Receptor sequence

>3derA (length=341) Species: 243274 (Thermotoga maritima MSB8)

RIVNVKLSLKRYEYEKPFHITGSVSSESRNVEVEIVLESGVKGYGEASPS
FRVNGERVEALLAIENAVREMITGIDVRNYARIFEITDRLFGFPSLKAAV
QFATLDALSQELGTQVCYLLGGKRDEIETDKTVGIDTVENRVKEAKKIFE
EGFRVIKIKVGENLKEDIEAVEEIAKVTRGAKYIVDANMGYTQKEAVEFA
RAVYQKGIDIAVYEQPVRREDIEGLKFVRFHSPFPVAADESARTKFDVMR
LVKEEAVDYVNIKLMKSGISDALAIVEIAESSGLKLMIGCMGESSLGINQ
SVHFALGTGAFEFHDLDSHLMLKEEVFRGKFIQDGPRMRVK

3D structure

• PDB: 3der Discovery of a dipeptide epimerase enzymatic function guided by homology modeling and virtual screening.
• Chain: A
• Resolution: 1.9 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): F20 T134 K159 K161 D188 E216 D241 E242 S243 K265 G291 C292 M293 H316 D317 L318
• Catalytic site (residue number reindexed from 1): F18 T132 K157 K159 D186 E214 D239 E240 S241 K263 G289 C290 M291 H314 D315 L316
• Enzyme Commision number: 5.1.1.20: L-Ala-D/L-Glu epimerase.

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	MG	A	D188 E216 D241	D186 E214 D239
BS02	ALA	A	K161 C292 D317 D319	K159 C290 D315 D317
BS03	LYS	A	F20 K161 D188 K265 C292	F18 K159 D186 K263 C290

Gene Ontology

Molecular Function

• GO:0016853 isomerase activity
• GO:0016854 racemase and epimerase activity
• GO:0016855 racemase and epimerase activity, acting on amino acids and derivatives
• GO:0046872 metal ion binding
• GO:0103031 L-Ala-D/L-Glu epimerase activity

Biological Process

• GO:0016998 cell wall macromolecule catabolic process
• GO:0071555 cell wall organization

External links

• PDB: RCSB:3der, PDBe:3der, PDBj:3der
• PDBsum: 3der
• PubMed: 19000819
• UniProt: Q9WXM1|AEEP_THEMA L-Ala-D/L-Glu epimerase (Gene Name=TM_0006)