Structure of PDB 2dln Chain A

Receptor sequence

>2dlnA (length=306) Species: 562 (Escherichia coli)

MTDKIAVLLGGTSAEREVSLNSGAAVLAGLREGGIDAYPVDPKEVDVTQL
KSMGFQKVFIALHGRGGEDGTLQGMLELMGLPYTGSGVMASALSMDKLRS
KLLWQGAGLPVAPWVALTRAEFEKGLSDKQLAEISALGLPVIVKPSREGS
SVGMSKVVAENALQDALRLAFQHDEEVLIEKWLSGPEFTVAILGEEILPS
IRIQPSGTFYDYEAKYLSDETQYFCPAGLEASQEANLQALVLKAWTTLGC
KGWGRIDVMLDSDGQFYLLEANTSPGMTSHSLVPMAARQAGMSFSQLVVR
ILELAD

3D structure

• PDB: 2dln Vancomycin resistance: structure of D-alanine:D-alanine ligase at 2.3 A resolution.
• Chain: A
• Resolution: 2.3 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): E15 V18 N21 H63 S150 E213 Y216 R255 D257 E270 N272 G276 H280
• Catalytic site (residue number reindexed from 1): E15 V18 N21 H63 S150 E213 Y216 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	MG	A	D257 E270	D257 E270
BS02	MG	A	E270 N272	E270 N272
BS03	ADP	A	K97 K144 G149 S151 M154 E180 W182 L183 E187 Y210 M259 L269 E270	K97 K144 G149 S151 M154 E180 W182 L183 E187 Y210 M259 L269 E270
BS04	PHY	A	E15 S150 K215 Y216 R255 E270 N272 G276 S281 L282	E15 S150 K215 Y216 R255 E270 N272 G276 S281 L282

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:0042803 protein homodimerization 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:2dln, PDBe:2dln, PDBj:2dln
• PDBsum: 2dln
• PubMed: 7939684
• UniProt: P07862|DDLB_ECOLI D-alanine--D-alanine ligase B (Gene Name=ddlB)