Structure of PDB 5bph Chain B

Receptor sequence
>5bphB (length=305) Species: 632 (Yersinia pestis) [Search protein sequence]
AEKVAVLLGGTSAEREVSLLSGQAVLAGLKEAGIDAYGVDTKDFPVTQLK
EQGFDKVFIALHGRGGEDGTLQGVLEFLQLPYTGSGVMASALTMDKLRTK
LVWQALGLPISPYVALNRQQFETLSPEELVACVAKLGLPLIVKPSHEGSS
VGMSKVDHASELQKALVEAFQHDSDVLIEKWLSGPEFTVAILGDEVLPSI
RIQPPGVFYDYDAKYLSDKTQYFCPSGLSDESEQQLAALALQAYHALDCS
GWGRVDVMQDRDGHFYLLEVNTSPGMTSHSLVPMAARQYGLSFSQLVARI
LMLAD
3D structure
PDB5bph Structure of D-alanine-D-alanine ligase from Yersinia pestis: nucleotide phosphate recognition by the serine loop.
ChainB
Resolution1.7 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 S150 D213 Y216 R255 D257 E270 N272 G276 H280
Catalytic site (residue number reindexed from 1) E14 V17 L20 H62 S149 D212 Y215 R254 D256 E269 N271 G275 H279
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 B K97 I142 K144 E180 W182 L183 E187 V208 Y210 M259 E270 K96 I141 K143 E179 W181 L182 E186 V207 Y209 M258 E269
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:5bph, PDBe:5bph, PDBj:5bph
PDBsum5bph
PubMed26894530
UniProtQ8ZIE7|DDL_YERPE D-alanine--D-alanine ligase (Gene Name=ddl)

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