Structure of PDB 1xpy Chain D

Receptor sequence

>1xpyD (length=370) Species: 1299 (Deinococcus radiodurans)

RMFKIEAAEIVVARLPLKFRFETSFGVQTHKVVPLLILHGEGVQGVAEGT
MEARPMYREETIAGALDLLRGTFLPAILGQTFANPEAVSDALGSYRGNRM
ARAMVEMAAWDLWARTLGVPLGTLLGGHKEQVEVGVSLGIQADEQATVDL
VRRHVEQGYRRIKLKIKPGWDVQPVRATREAFPDIRLTVDANSAYTLADA
GRLRQLDEYDLTYIEQPLAWDDLVDHAELARRIRTPLCLDESVASASDAR
KALALGAGGVINLKVARVGGHAESRRVHDVAQSFGAPVWCGGMLESGIGR
AHNIHLSTLSNFRLPGDTSSASRYWERDLIQEPLEAVDGLMPVPQGPGTG
VTLDREFLATVTEAQEEHRA

3D structure

• PDB: 1xpy Structural basis for catalytic racemization and substrate specificity of an N-acylamino acid racemase homologue from Deinococcus radiodurans
• Chain: D
• Resolution: 2.3 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): F26 M56 R59 S142 K168 K170 R191 T193 D195 N197 E220 D245 E246 S247 K269 C295 G296 G297 M298 G321 D322 T323
• Catalytic site (residue number reindexed from 1): F21 M51 R54 S137 K163 K165 R186 T188 D190 N192 E215 D240 E241 S242 K264 C290 G291 G292 M293 G316 D317 T318
• Enzyme Commision number: 4.2.1.113: o-succinylbenzoate synthase.
  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	MG	D	D195 N197	D190 N192
BS02	NLQ	D	F26 K168 K170 K269 G297 L299 D322 Y329	F21 K163 K165 K264 G292 L294 D317 Y324

Gene Ontology

Molecular Function

• GO:0003824 catalytic activity
• GO:0016829 lyase activity
• GO:0016853 isomerase activity
• GO:0043748 O-succinylbenzoate synthase activity
• GO:0046872 metal ion binding

Biological Process

• GO:0009234 menaquinone biosynthetic process

External links

• PDB: RCSB:1xpy, PDBe:1xpy, PDBj:1xpy
• PDBsum: 1xpy
• PubMed: 15313614
• UniProt: Q9RYA6|NSAR_DEIRA N-succinylamino acid racemase (Gene Name=DR_0044)