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PDBsum entry 4zqi
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PDB id:
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Ligase
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Title:
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Crystal structure of apo d-alanine-d-alanine ligase(ddl) from yersinia pestis
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Structure:
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D-alanine--d-alanine ligase. Chain: a, b, c, d. Synonym: d-ala-d-ala ligase,d-alanylalanine synthetase. Engineered: yes
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Source:
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Yersinia pestis. Organism_taxid: 632. Gene: ddl, ddlb. Expressed in: escherichia coli. Expression_system_taxid: 562
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Resolution:
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2.30Å
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R-factor:
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0.206
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R-free:
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0.248
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Authors:
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H.-T.Tran,L.-W.Kang,M.-K.Hong,H.P.T.Ngo,K.H.Huynh,Y.J.Ahn
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Key ref:
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H.T.Tran
et al.
(2016).
Structure of D-alanine-D-alanine ligase from Yersinia pestis: nucleotide phosphate recognition by the serine loop.
Acta Crystallogr D Struct Biol,
72,
12-21.
PubMed id:
DOI:
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Date:
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10-May-15
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Release date:
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13-Jan-16
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PROCHECK
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Headers
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References
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Q8ZIE7
(DDL_YERPE) -
D-alanine--D-alanine ligase from Yersinia pestis
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Seq:
Struc:
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306 a.a.
292 a.a.
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Key: |
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PfamA domain |
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Secondary structure |
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CATH domain |
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Enzyme class:
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E.C.6.3.2.4
- D-alanine--D-alanine ligase.
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Pathway:
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Peptidoglycan Biosynthesis (Part 1)
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Reaction:
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2 D-alanine + ATP = D-alanyl-D-alanine + ADP + phosphate + H+
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2
×
D-alanine
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+
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ATP
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=
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D-alanyl-D-alanine
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+
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ADP
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+
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phosphate
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+
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H(+)
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Molecule diagrams generated from .mol files obtained from the
KEGG ftp site
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DOI no:
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Acta Crystallogr D Struct Biol
72:12-21
(2016)
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PubMed id:
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Structure of D-alanine-D-alanine ligase from Yersinia pestis: nucleotide phosphate recognition by the serine loop.
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H.T.Tran,
M.K.Hong,
H.P.Ngo,
K.H.Huynh,
Y.J.Ahn,
Z.Wang,
L.W.Kang.
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ABSTRACT
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D-Alanyl-D-alanine is an essential precursor of bacterial peptidoglycan and is
synthesized by D-alanine-D-alanine ligase (DDL) with hydrolysis of ATP; this
reaction makes DDL an important drug target for the development of antibacterial
agents. Five crystal structures of DDL from Yersinia pestis (YpDDL) were
determined at 1.7-2.5 Å resolution: apo, AMP-bound, ADP-bound, adenosine
5'-(β,γ-imido)triphosphate-bound, and D-alanyl-D-alanine- and ADP-bound
structures. YpDDL consists of three domains, in which four loops, loop 1, loop 2
(the serine loop), loop 3 (the ω-loop) and loop 4, constitute the binding sites
for two D-alanine molecules and one ATP molecule. Some of them, especially the
serine loop and the ω-loop, show flexible conformations, and the serine loop is
mainly responsible for the conformational change in substrate nucleotide
phosphates. Enzyme-kinetics assays were carried out for both the D-alanine and
ATP substrates and a substrate-binding mechanism was proposed for YpDDL
involving conformational changes of the loops.
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