Structure of PDB 2zdh Chain B

Receptor sequence

>2zdhB (length=312) Species: 300852 (Thermus thermophilus HB8)

MRVLLIAGGVSPEHEVSLLSAEGVLRHIPFPTDLAVIAQDGRWLLGEKAL
TALEAKAAPEGEHPFPPPLSWERYDVVFPLLHGRFGEDGTVQGFLELLGK
PYVGAGVAASALCMDKDLSKRVLAQAGVPVVPWVAVRKGEPPVVPFDPPF
FVKPANTGSSVGISRVERFQDLEAALALAFRYDEKAVVEKALSPVRELEV
GVLGNVFGEASPVGEVRYEAPFYPGRAELLIPAPLDPGTQETVQELALKA
YKVLGVRGMARVDFFLAEGELYLNELNTIPGFTPTSMYPRLFEAGGVAYP
ELLRRLVELALT

3D structure

• PDB: 2zdh Crystal structure of D-Alanine:D-Alanine Ligase with ADP and D-Alanine from Thermus thermophius HB8
• Chain: B
• Resolution: 1.9 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): E13 V16 L19 H82 S159 R268 D270 E282 N284 G288 T292
• Catalytic site (residue number reindexed from 1): E13 V16 L19 H82 S159 R261 D263 E275 N277 G281 T285
• 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	ADP	B	K116 F151 K153 S160 A191 L192 E197 F272 E282	K116 F151 K153 S160 A191 L192 E197 F265 E275

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:2zdh, PDBe:2zdh, PDBj:2zdh
• PDBsum: 2zdh
• UniProt: Q5SHZ3|DDL_THET8 D-alanine--D-alanine ligase (Gene Name=ddl)