ISDA

Deposition Date 2013-09-10

Release Date 2015-01-21

Last Version Date 2023-12-20

Entry Detail

PDB ID:

4C5C

Keywords:

LIGASE

Title:

The X-ray crystal structure of D-alanyl-D-alanine ligase in complex with ADP and D-ala-D-ala

Biological Source:

Source Organism:

ESCHERICHIA COLI (Taxon ID: 83333)

Host Organism:

ESCHERICHIA COLI

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

1.40 Å

R-Value Free:

0.20

R-Value Work:

0.17

R-Value Observed:

0.18

Space Group:

P 21 21 21

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Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Molecule:D-ALANINE--D-ALANINE LIGASE
Chain IDs:A, B
Chain Length:330
Number of Molecules:2
Biological Source:ESCHERICHIA COLI

UniProt ID:P07862 Pfam ID:PF01820, PF07478

Ligand Molecules

ATP

DAL

GOL

Primary Citation

Inhibition of D-Ala:D-Ala ligase through a phosphorylated form of the antibiotic D-cycloserine.

Batson, S, de Chiara, C, Majce, V, Lloyd, A.J, Gobec, S, Rea, D, Fulop, V, Thoroughgood, C.W, Simmons, K.J, Dowson, C.G, Fishwick, C.W.G, de Carvalho, L.P.S, Roper, D.I.Show

Nat Commun 8 1939 1939 (2017)

PMID: 29208891 DOI: 10.1038/s41467-017-02118-7

Abstact

D-cycloserine is an antibiotic which targets sequential bacterial cell wall peptidoglycan biosynthesis enzymes: alanine racemase and D-alanine:D-alanine ligase. By a combination of structural, chemical and mechanistic studies here we show that the inhibition of D-alanine:D-alanine ligase by the antibiotic D-cycloserine proceeds via a distinct phosphorylated form of the drug. This mechanistic insight reveals a bimodal mechanism of action for a single antibiotic on different enzyme targets and has significance for the design of future inhibitor molecules based on this chemical structure.

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Protein

Chemical

Disease

Primary Citation of related structures