Structure of PDB 3r5f Chain A

Receptor sequence

>3r5fA (length=343) Species: 291331 (Xanthomonas oryzae pv. oryzae KACC 10331)

KIRVGLIFGGKSAEHEVSLQSARNILDALDPQRFEPVLIGIDKQGQWHVN
DPDSFLLHADDPARIALHRSGRGVALLPGAQQQQLRPIQALAQIDVVFPI
VHGTLGEDGSLQGLLRMANLPFVGSGVLGSAVAMDKDMAKRVLRDARLAV
APFVCFDRHTAAHADVDTLIAQLGLPLFVKPANQGSSVGVSQVRTADAFA
AALALALAYDHKVLVEAAVAGREIECAVLGNAVPHASVCGEVVVEIVIPA
DIDAQTQQRIQQIAVQAYQALGCAGMARVDVFLCADGRIVINEVNTLPGF
TRISVYPKLWQASGLDYRGLITRLIELALERHTDDQLLRSAVE

3D structure

• PDB: 3r5f Crystal structure of D-alanine-D-alanine ligase A from Xanthomonas oryzae pathovar oryzae with ATP
• Chain: A
• Resolution: 2.07 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): Q22 H107 S191 R300 D302 E315 N317 G321 I325
• Catalytic site (residue number reindexed from 1): Q20 H102 S186 R278 D280 E293 N295 G299 I303
• Enzyme Commision number: 6.3.2.4: D-alanine--D-alanine ligase.

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	ATP	A	F183 K185 S192 A223 V224 E228 F304 E315	F178 K180 S187 A218 V219 E223 F282 E293
BS02	MG	A	D302 E315	D280 E293

Gene Ontology

Molecular Function

• GO:0003824 catalytic activity
• GO:0005524 ATP binding
• GO:0008716 D-alanine-D-alanine ligase activity
• GO:0016874 ligase activity
• GO:0046872 metal ion binding

Biological Process

• GO:0008360 regulation of cell shape
• GO:0009252 peptidoglycan biosynthetic process
• GO:0071555 cell wall organization

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol

External links

• PDB: RCSB:3r5f, PDBe:3r5f, PDBj:3r5f
• PDBsum: 3r5f
• UniProt: Q5H614