Structure of PDB 5bph Chain A

Receptor sequence

>5bphA (length=306) Species: 632 (Yersinia pestis)

MAEKVAVLLGGTSAEREVSLLSGQAVLAGLKEAGIDAYGVDTKDFPVTQL
KEQGFDKVFIALHGRGGEDGTLQGVLEFLQLPYTGSGVMASALTMDKLRT
KLVWQALGLPISPYVALNRQQFETLSPEELVACVAKLGLPLIVKPSHEGS
SVGMSKVDHASELQKALVEAFQHDSDVLIEKWLSGPEFTVAILGDEVLPS
IRIQPPGVFYDYDAKYLSDKTQYFCPSGLSDESEQQLAALALQAYHALDC
SGWGRVDVMQDRDGHFYLLEVNTSPGMTSHSLVPMAARQYGLSFSQLVAR
ILMLAD

3D structure

• PDB: 5bph Structure of D-alanine-D-alanine ligase from Yersinia pestis: nucleotide phosphate recognition by the serine loop.
• Chain: A
• Resolution: 1.7 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): E15 V18 L21 H63 S150 D213 R255 D257 E270 N272 G276 H280
• Catalytic site (residue number reindexed from 1): E15 V18 L21 H63 S150 D213 R255 D257 E270 N272 G276 H280
• 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	AMP	A	K97 I142 K144 M154 E180 W182 L183 E187 F209 Y210 M259 E270	K97 I142 K144 M154 E180 W182 L183 E187 F209 Y210 M259 E270

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:5bph, PDBe:5bph, PDBj:5bph
• PDBsum: 5bph
• PubMed: 26894530
• UniProt: Q8ZIE7|DDL_YERPE D-alanine--D-alanine ligase (Gene Name=ddl)