Structure of PDB 5c1p Chain D

Receptor sequence
>5c1pD (length=302) Species: 632 (Yersinia pestis) [Search protein sequence]
AEKVAVLLGGTSAEREVSLLSGQAVLAGLKEAGIDAYGVDTKDFPVTQLK
EQGFDKVFIALHGRGGEDGTLQGVLEFLQLPYTGSGVMASALTMDKLRTK
LVWQALGLPISPYVALNRQQFETLSPEELVACVAKLGLPLIVKPSHEVGM
SKVDHASELQKALVEAFQHDSDVLIEKWLSGPEFTVAILGDEVLPSIRIQ
PPGVFYDYDAKYLSDKTQYFCPSGLSDESEQQLAALALQAYHALDCSGWG
RVDVMQDRDGHFYLLEVNTSPGMTSHSLVPMAARQYGLSFSQLVARILML
AD
3D structure
PDB5c1p Structure of D-alanine-D-alanine ligase from Yersinia pestis: nucleotide phosphate recognition by the serine loop.
ChainD
Resolution2.4 Å
3D
structure
Catalytic site residues are labeled in the structure
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Enzymatic activity
Catalytic site (original residue number in PDB) E15 V18 L21 H63 D213 Y216 R255 D257 E270 N272 G276 H280
Catalytic site (residue number reindexed from 1) E14 V17 L20 H62 D209 Y212 R251 D253 E266 N268 G272 H276
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 D K97 I142 K144 E148 E180 W182 L183 E187 Y210 M259 E270 K96 I141 K143 E147 E176 W178 L179 E183 Y206 M255 E266
BS02 DAL D Y216 R255 N272 P275 G276 Y212 R251 N268 P271 G272
BS03 DAL D K215 Y216 S281 L282 K211 Y212 S277 L278
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

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5c1p, PDBe:5c1p, PDBj:5c1p
PDBsum5c1p
PubMed26894530
UniProtQ8ZIE7|DDL_YERPE D-alanine--D-alanine ligase (Gene Name=ddl)

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