Structure of PDB 3rit Chain D

Receptor sequence

>3ritD (length=354) Species: 414 (Methylococcus capsulatus)

MKIADIQVRTEHFPLTRPYRIAFRSIEEIDNLIVEIRTADGLLGLGAASP
ERHVTGETLEACHAALDHDRLGWLMGRDIRTLPRLCRELAERLPAAPAAR
AALDMALHDLVAQCLGLPLVEILGRAHDSLPTSVTIGIKPVEETLAEARE
HLALGFRVLKVKLCGDEEQDFERLRRLHETLAGRAVVRVDPNQSYDRDGL
LRLDRLVQELGIEFIEQPFPAGRTDWLRALPKAIRRRIAADESLLGPADA
FALAAPPAACGIFNIKLMKCGGLAPARRIATIAETAGIDLMWGCMDESRI
SIAAALHAALACPATRYLDLDGSFDLARDVAEGGFILEDGRLRVTERPGL
GLVY

3D structure

• PDB: 3rit Homology models guide discovery of diverse enzyme specificities among dipeptide epimerases in the enolase superfamily.
• Chain: D
• Resolution: 2.701 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): Y19 P50 H53 T135 K160 K162 D190 N192 E216 D241 E242 S243 K266 G293 C294 M295 L318 D319 L320
• Catalytic site (residue number reindexed from 1): Y19 P50 H53 T135 K160 K162 D190 N192 E216 D241 E242 S243 K266 G293 C294 M295 L318 D319 L320
• Enzyme Commision number: 5.1.1.-

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	ARG	D	Y19 T135 K162 D296 D319 D321	Y19 T135 K162 D296 D319 D321
BS02	DLY	D	E51 K160 K162 D190 E216 D241 K266 M295	E51 K160 K162 D190 E216 D241 K266 M295
BS03	MG	D	D190 E216 D241	D190 E216 D241

Gene Ontology

Molecular Function

• GO:0000287 magnesium ion binding
• 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

Biological Process

• GO:0006518 peptide metabolic process
• GO:0009063 amino acid catabolic process

External links

• PDB: RCSB:3rit, PDBe:3rit, PDBj:3rit
• PDBsum: 3rit
• PubMed: 22392983
• UniProt: Q607C7|KRDE_METCA L-Lys-D/L-Arg epimerase (Gene Name=MCA1834)