Reference on EC 6.3.2.4 - D-Alanine-D-alanine ligase
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REF. 
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Oppenheim, B.; Patchornik, A.
Formation of D-alanyl-D-alanine and D-alanine from UDPMurNAc-L-Ala-D-isoGlu-L-Lys-D-Ala-D-Ala by extracts of Staphylococcus aureus and Streptococcus faecalis
FEBS Lett.
48
172-175
1974
Enterococcus faecalis, Staphylococcus aureus
Linnett, P.E.; Tipper, D.J.
Cell wall polymers of Bacillus sphaericus: activities of enzymes involved in peptidoglycan precursor synthesis during sporulation
J. Bacteriol.
120
342-354
1974
Lysinibacillus sphaericus, Lysinibacillus sphaericus 9602
Duncan, K.; Walsh, C.T.
ATP-dependent inactivation and slow binding inhibition of Salmonella typhimurium D-alanine:D-alanine ligase (ADP) by (aminoalkyl)phosphinate and aminophosphonate analogues of D-alanine
Biochemistry
27
3709-3714
1988
Salmonella enterica subsp. enterica serovar Typhimurium
Daub, E.; Zawadzke, L.E.; Botstein, D.; Walsh, C.T.
Isolation, cloning, and sequencing of the Salmonella typhimurium ddlA gene with purification and characterization of its product, D-alanine:D-alanine ligase (ADP forming)
Biochemistry
27
3701-3708
1988
Salmonella enterica subsp. enterica serovar Typhimurium
Vicario, P.P.; Green, B.G.; Katzen, H.M.
A single assay for simultaneously testing effectors of alanine racemase and/or D-alanine:D-alanine ligase
J. Antibiot.
15
209-216
1987
Enterococcus faecalis, Enterococcus faecalis R / ATCC 8043
Shi, Y.; Walsh, C.T.
Active site mapping of Escherichia coli D-Ala-D-Ala ligase by structure-based mutagenesis
Biochemistry
34
2768-2776
1995
Escherichia coli
Buxton, R.S.; Ward, J.B.
Heat-sensitive lysis mutants of Bacillus subtilis 168 blocked at three different stages of peptidoglycan synthesis
J. Gen. Microbiol.
120
283-293
1980
Bacillus subtilis, Bacillus subtilis 168
Lacoste, A.M.; Poulsen, M.; Cassaigne, A.; Neuzil, E.
Inhibition of D-alanyl-D-alanine ligase in different bacterial species by amino phosphonic acids
Curr. Microbiol.
2
113-117
1979
Staphylococcus aureus, Pseudomonas aeruginosa
-
Lugtenberg, E.J.J.; van Schijndel-van Dam, A.
Temperature-sensitive mutant of Escherichia coli K-12 with an impaired D-alanine:D-alanine ligase
J. Bacteriol.
113
96-104
1973
Escherichia coli
Bugg, T.D.H.; Dutka-Malen, S.; Athur, M.; Courvalin, P.; Walsh, C.T.
Identification of vancomycin resistance protein VanA as a D-alanine:D-alanine ligase of altered substrate specificity
Biochemistry
30
2017-2021
1991
Escherichia coli, Escherichia coli JM105
Pandhi, P.N.; Panos, C.
Biosynthesis of D-alanyl-D-alanine from L-alanine by extracts of a stabilized L-form fro Streptococcus pyogenes
J. Gen. Microbiol.
71
487-494
1972
Streptococcus pyogenes
Lugtenberg, E.J.J.
Studies on Escherichia coli enzymes involved in the synthesis of uridine diphosphate-N-acetyl-muramyl-pentapeptide
J. Bacteriol.
110
26-34
1972
Escherichia coli
Zawadzke, L.E.; Bugg, T.D.H.; Walsh, C.T.
Existence of two D-alanine:D-alanine ligases in Escherichia coli: cloning and sequencing of the ddlA gene and purification and characterization of the DdlA and DdlB enzymes
Biochemistry
30
1673-1682
1991
Escherichia coli
McDermott, A.E.; Creuzet, F.; Griffin, R.G.
Rotational resonance determination of the structure of an enzyme-inhibitor complex: phosphorylation of an (aminoalkyl)phosphinate inhibitor of D-alanyl-D-alanine ligase by ATP
Biochemistry
29
5767-5775
1990
Salmonella enterica subsp. enterica serovar Typhimurium
Knox, J.R.; Liu, H.; Walsh, C.T.; Zawadzke, L.E.
D-Alanine-D-alanine ligase (ADP) from Salmonella typhimurium. Overproduction, purification, crystallization and preliminary X-ray analysis
J. Mol. Biol.
205
461-463
1989
Salmonella enterica subsp. enterica serovar Typhimurium
Fan, C.; Park, I.S.; Walsh, C.T.; Knox, J.R.
D-Alanine:D-alanine ligase: phosphonate and phosphinate intermediates with wild type and the Y216F mutant
Biochemistry
36
2531-2538
1997
Escherichia coli (P07862), Escherichia coli
Duncan, K.; van Heijenoort, J.; Walsh, C.T.
Purification and characterization of the D-alanyl-D-alanine-adding enzyme from Escherichia coli
Biochemistry
29
2379-2386
1990
Escherichia coli
Chakravarty, P.K.; Greenlee, W.J.; Parsons, W.H.; Patchett, A.A.; Combs, P.; Roth, A.; Busch, R.D.; Mellin, T.N.
(3-Amino-2-oxoalkyl)phosphonic acids and their analogues as novel inhibitors of D-alanine:D-alanine ligase
J. Med. Chem.
32
1886-1890
1989
Enterococcus faecalis
Greenlee, W.J.; Springer, J.P.; Patchett, A.A.
Synthesis of an analogue of tabtoxinine as a potential inhibitor of the D-alanine:D-alanine ligase (ADP forming)
J. Med. Chem.
32
165-170
1989
Enterococcus faecalis
Lacoste, A.M.; Chollet-Gravey, A.M.; Quang, L.V.; Quang, Y.V.; le Goffic, F.
Time-dependent inhibition of Streptococcus faecalis D-alanine:D-alanine ligase by alpha-aminophosphonamidic acids
Eur. J. Med. Chem.
26
255-260
1991
Enterococcus faecalis
-
Ellsworth, B.A.; Tom, N.J.; Bartlett, P.A.
Synthesis and evaluation of inhibitors of bacterial D-alanine:D-alanine ligases
Chem. Biol.
3
37-44
1996
Escherichia coli, Enterococcus faecium
Al-Bar, O.A.M.; OConnor, C.D.; Giles, I.G.; Akhtar, M.
D-Alanine:D-alanine ligase of Escherichia coli. Expression, purification and inhibitory studies on the cloned enzyme
Biochem. J.
282
747-752
1992
Escherichia coli
Fan, C.; Moews, P.C.; Walsh, C.T.; Knox, J.R.
Vancomycin resistance: structure of D-alanine:D-alanine ligase at 2.3 A resolution
Science
266
439-443
1994
Escherichia coli
Park, I.S.; Walsh, C.T.
D-Alanyl-D-lactate and D-alanyl-D-alanine synthesis by D-alanyl-D-alanine ligase from vancomycin-resistant Leuconostoc mesenteroides. Effects of a phenylalanine 261 to tyrosine mutation
J. Biol. Chem.
272
9210-9214
1997
Leuconostoc mesenteroides (P71454), Leuconostoc mesenteroides
Meziane-Cherif, D.; Badet-Denisot, M.A.; Evers, S.; Courvalin, P.; Badet, B.
Purification and characterization of the VanB ligase associated with type B vancomycin resistance in Enterococcus faecalis V583
FEBS Lett.
354
140-142
1994
Bacteria, Enterococcus faecalis
Duncan, K.; Faraci, W.S.; Matteson, D.S.; Walsh, C.T.
(1-Aminoethyl)boronic acid: a novel inhibitor for Bacillus stearothermophilus alanine racemase and Salmonella typhimurium D-alanine:D-alanine ligase (ADP-forming)
Biochemistry
28
3541-3549
1989
Salmonella enterica subsp. enterica serovar Typhimurium
Perichon, B.; Casadewall, B.; Reynolds, P.; Courvalin, P.
Glycopeptide-resistant Enterococcus faecium BM4416 is a VanD-type strain with an impaired D-alanine:D-alanine ligase
Antimicrob. Agents Chemother.
44
1346-1348
2000
Enterococcus faecium, Enterococcus faecium BM4416
Feng, Z.; Barletta, R.G.
Roles of Mycobacterium smegmatis D-alanine:D-alanine ligase and D-alanine racemase in the mechanisms of action of and resistance to the peptidoglycan inhibitor D-cycloserine
Antimicrob. Agents Chemother.
47
283-291
2003
Mycobacterium tuberculosis, Mycolicibacterium smegmatis (Q9ZGN0), Mycolicibacterium smegmatis
Healy, V.L.; Park, I.S.; Walsh, C.T.
Active-site mutants of the VanC2 D-alanyl-D-serine ligase, characteristic of one vancomycin-resistant bacterial phenotype, revert towards wild-type D-alanyl-D-alanine ligases
Chem. Biol.
5
197-207
1998
Escherichia coli
Prevost, M.; Van Belle, D.; Tulkens, P.M.; Courvalin, P.; Van Bambeke, F.
Modeling of Enterococcus faecalis D-alanine:D-alanine ligase: structure-based study of the active site in the wild-type enzyme and in glycopeptide-dependent mutants
J. Mol. Microbiol. Biotechnol.
2
321-330
2000
Enterococcus faecalis
Gholizadeh, Y.; Prevost, M.; Van Bambeke, F.; Casadewall, B.; Tulkens, P.M.; Courvalin, P.
Sequencing of the ddl gene and modeling of the mutated D-alanine:D-alanine ligase in glycopeptide-dependent strains of Enterococcus faecium
Protein Sci.
10
836-844
2001
Enterococcus faecium
Noda, M.; Kawahara, Y.; Ichikawa, A.; Matoba, Y.; Matsuo, H.; Lee, D.G.; Kumagai, T.; Sugiyama, M.
Self-protection mechanism in D-cycloserine-producing Streptomyces lavendulae. Gene cloning, characterization, and kinetics of its alanine racemase and D-alanyl-D-alanine ligase, which are target enzymes of D-cycloserine
J. Biol. Chem.
279
46143-46152
2004
Streptomyces lavendulae, Streptomyces lavendulae ATCC 25233
Sato, M.; Kirimura, K.; Kino, K.
D-Amino acid dipeptide production utilizing D-alanine-D-alanine ligases with novel substrate specificity
J. Biosci. Bioeng.
99
623-628
2005
Escherichia coli, Oceanobacillus iheyensis, Synechocystis sp. PCC 6803, Thermotoga maritima, Oceanobacillus iheyensis JCM 11309
McCoy, A.J.; Maurelli, A.T.
Characterization of Chlamydia MurC-Ddl, a fusion protein exhibiting D-alanyl-D-alanine ligase activity involved in peptidoglycan synthesis and D-cycloserine sensitivity
Mol. Microbiol.
57
41-52
2005
Chlamydia trachomatis
Lu, Y.; Sheng, Y.; Li, L.; Tang, D.; Liu, X.; Zhao, X.; Liang, Y.; Su, X.
Crystallization and preliminary crystallographic analysis of D-alanine-D-alanine ligase from Streptococcus mutans
Acta Crystallogr. Sect. F
63
807-808
2007
Streptococcus mutans
Kovac, A.; Majce, V.; Lenarsic, R.; Bombek, S.; Bostock, J.M.; Chopra, I.; Polanc, S.; Gobec, S.
Diazenedicarboxamides as inhibitors of D-alanine-D-alanine ligase (Ddl)
Bioorg. Med. Chem. Lett.
17
2047-2054
2007
Escherichia coli (P07862), Escherichia coli
Sato, M.; Kirimura, K.; Kino, K.
Substrate specificity of thermostable D-alanine-D-alanine ligase from Thermotoga maritima ATCC 43589
Biosci. Biotechnol. Biochem.
70
2790-2792
2006
Thermotoga maritima, Thermotoga maritima (P46805)
Sato, M.; Masuda, Y.; Kirimura, K.; Kino, K.
Thermostable ATP regeneration system using polyphosphate kinase from Thermosynechococcus elongatus BP-1 for D-amino acid dipeptide synthesis
J. Biosci. Bioeng.
103
179-184
2007
Thermosynechococcus vestitus
Liu, S.; Chang, J.S.; Herberg, J.T.; Horng, M.M.; Tomich, P.K.; Lin, A.H.; Marotti, K.R.
Allosteric inhibition of Staphylococcus aureus D-alanine:D-alanine ligase revealed by crystallographic studies
Proc. Natl. Acad. Sci. USA
103
15178-15183
2006
Staphylococcus aureus (Q5HEB7), Staphylococcus aureus
Lee, J.H.; Na, Y.; Song, H.; Kim, D.; Park, B.; Rho, S.; Im, Y.J.; Kim, M.; Kang, G.B.; Lee, D.; Eom, S.H.
Crystal structure of the apo form of D-alanine: D-alanine ligase from Thermus caldophilus: A basis for the substrate-induced conformation changes
Proteins Struct. Funct. Bioinform.
64
1078-1082
2006
Thermus caldophilus
Triola, G.; Wetzel, S.; Ellinger, B.; Koch, M.; Huebel, K.; Rauh, D.; Waldmann, H.
ATP competitive inhibitors of D-alanine-D-alanine ligase based on protein kinase inhibitor scaffolds
Bioorg. Med. Chem.
17
1079-1087
2008
Escherichia coli (P07862)
Wu, D.; Kong, Y.; Han, C.; Chen, J.; Hu, L.; Jiang, H.; Shen, X.
D-Alanine:D-alanine ligase as a new target for the flavonoids quercetin and apigenin
Int. J. Antimicrob. Agents
32
421-426
2008
Escherichia coli, Helicobacter pylori
Wu, D.; Zhang, L.; Kong, Y.; Du, J.; Chen, S.; Chen, J.; Ding, J.; Jiang, H.; Shen, X.
Enzymatic characterization and crystal structure analysis of the D-alanine-D-alanine ligase from Helicobacter pylori
Proteins
72
1148-1160
2008
Helicobacter pylori (Q2N4T5), Helicobacter pylori
Kitamura, Y.; Ebihara, A.; Agari, Y.; Shinkai, A.; Hirotsu, K.; Kuramitsu, S.
Structure of D-alanine-D-alanine ligase from Thermus thermophilus HB8: cumulative conformational change and enzyme-ligand interactions
Acta Crystallogr. Sect. D
65
1098-1106
2009
Thermus thermophilus HB8 (Q5SHZ3), Thermus thermophilus HB8
Batson, S.; Rea, D.; Fueloep, V.; Roper, D.I.
Crystallization and preliminary X-ray analysis of a D-alanyl-D-alanine ligase (EcDdlB) from Escherichia coli
Acta Crystallogr. Sect. F
66
405-408
2010
Escherichia coli
Sova, M.; Cadez, G.; Turk, S.; Majce, V.; Polanc, S.; Batson, S.; Lloyd, A.J.; Roper, D.I.; Fishwick, C.W.; Gobec, S.
Design and synthesis of new hydroxyethylamines as inhibitors of D-alanyl-D-lactate ligase (VanA) and D-alanyl-D-alanine ligase (DdlB)
Bioorg. Med. Chem. Lett.
19
1376-1379
2009
Escherichia coli, Enterococcus faecium
Jofre, E.; Fischer, S.; Principe, A.; Castro, M.; Ferrari, W.; Lagares, A.; Mori, G.
Mutation in a D-alanine-D-alanine ligase of Azospirillum brasilense Cd results in an overproduction of exopolysaccharides and a decreased tolerance to saline stress
FEMS Microbiol. Lett.
290
236-246
2009
Azospirillum brasilense
Neuhaus, F.C.
Role of Arg301 in substrate orientation and catalysis in subsite 2 of D-alanine:D-alanine (D-lactate) ligase from Leuconostoc mesenteroides: A molecular docking study
J. Mol. Graph. Model.
28
728-734
2010
Leuconostoc mesenteroides
Park, I.-S.; Lin, C.-H.; Walsh, C.T.
Gain of D-alanyl-D-lactate or D-lactyl-D-alanine synthetase activities in three active-site mutants of the Escherichia coli D-alanyl-D-alanine ligase B
Biochemistry
35
10464-10471
1996
Escherichia coli (P07862), Escherichia coli
Bruning, J.B.; Murillo, A.C.; Chacon, O.; Barletta, R.G.; Sacchettini, J.C.
Structure of the Mycobacterium tuberculosis D-alanine:D-alanine ligase, a target of the antituberculosis drug D-cycloserine
Antimicrob. Agents Chemother.
55
291-301
2011
Mycobacterium tuberculosis (P9WP31), Mycobacterium tuberculosis, Mycobacterium tuberculosis H37Rv (P9WP31)
Nakagawa, T.; Satake, R.; Sato, M.; Kino, K.
Structure-based modification of D-alanine-D-alanine ligase from Thermotoga maritima ATCC 43589 for depsipeptide synthesis
Biosci. Biotechnol. Biochem.
75
700-704
2011
Thermotoga maritima, Thermotoga maritima ATCC 43589
Doan, T.T.; Kim, J.K.; Ngo, H.P.; Tran, H.T.; Cha, S.S.; Min Chung, K.; Huynh, K.H.; Ahn, Y.J.; Kang, L.W.
Crystal structures of D-alanine-D-alanine ligase from Xanthomonas oryzae pv. oryzae alone and in complex with nucleotides
Arch. Biochem. Biophys.
545C
92-99
2014
Xanthomonas oryzae (Q5H614)
Prosser, G.A.; de Carvalho, L.P.
Reinterpreting the mechanism of inhibition of Mycobacterium tuberculosis D-alanine:D-alanine ligase by D-cycloserine
Biochemistry
52
7145-7149
2013
Mycobacterium tuberculosis
Vehar, B.; Hrast, M.; Kovac, A.; Konc, J.; Mariner, K.; Chopra, I.; O'Neill, A.; Janezic, D.; Gobec, S.
Ellipticines and 9-acridinylamines as inhibitors of D-alanine:D-alanine ligase
Bioorg. Med. Chem.
19
5137-5146
2011
Escherichia coli
Neuhaus, F.C.
Role of the omega loop in specificity determination in subsite 2 of the D-alanine:D-alanine (D-lactate) ligase from Leuconostoc mesenteroides: a molecular docking study
J. Mol. Graph. Model.
30
31-37
2011
Leuconostoc mesenteroides
Halouska, S.; Fenton, R.; Zinniel, D.; Marshall, D.; Barletta, R.; Powers, R.
Metabolomics analysis identifies D-alanine-D-alanine ligase as the primary lethal target of D-cycloserine in mycobacteria
J. Proteome Res.
13
1065-1076
2014
Mycobacterium tuberculosis, Mycobacterium tuberculosis H37Rv
Skedelj, V.; Arsovska, E.; Tomasic, T.; Kroflic, A.; Hodnik, V.; Hrast, M.; Bester-Rogac, M.; Anderluh, G.; Gobec, S.; Bostock, J.; Chopra, I.; O'Neill, A.J.; Randall, C.; Zega, A.
6-Arylpyrido[2,3-d]pyrimidines as novel ATP-competitive inhibitors of bacterial D-alanine:D-alanine ligase
PLoS ONE
7
e39922
2012
Escherichia coli
Tran, H.T.; Hong, M.K.; Ngo, H.P.; Huynh, K.H.; Ahn, Y.J.; Wang, Z.; Kang, L.W.
Structure of D-alanine-D-alanine ligase from Yersinia pestis nucleotide phosphate recognition by the serine loop
Acta Crystallogr. Sect. D
72
12-21
2016
Yersinia pestis (Q8ZIE7), Yersinia pestis
Takenaka, T.; Ito, T.; Miyahara, I.; Hemmi, H.; Yoshimura, T.
A new member of MocR/GabR-type PLP-binding regulator of D-alanyl-D-alanine ligase in Brevibacillus brevis
FEBS J.
282
4201-4217
2015
Brevibacillus brevis (C0ZB62), Brevibacillus brevis 47 / JCM 6285 / NBRC 100599 (C0ZB62)
Asker, M.; Shady, H.; Soliman, M.; Gadalla, M.; Abd el-Nasser, S.
Cloning and expression of a D-alanine-D-alanine ligase gene from Bacillus megaterium in Escherichia coli
Int. J. Pharm. Sci. Rev. Res.
25
183-187
2014
Priestia megaterium (A0A1Q8TTZ0), Priestia megaterium (D5D9X4), Priestia megaterium (D5DWS5), Priestia megaterium DSM 319 (D5D9X4), Priestia megaterium WSH-002 (A0A1Q8TTZ0), Priestia megaterium ATCC 12872 / QM B1551 (D5DWS5)
-
Miki, Y.; Okazaki, S.; Asano, Y.
Engineering an ATP-dependent D-Ala D-Ala ligase for synthesizing amino acid amides from amino acids
J. Ind. Microbiol. Biotechnol.
44
667-675
2017
Thermus thermophilus (Q5SHZ3), Thermus thermophilus, Thermus thermophilus HB8 / ATCC 27634 / DSM 579 (Q5SHZ3)
Huynh, K.H.; Hong, M.K.; Lee, C.; Tran, H.T.; Lee, S.H.; Ahn, Y.J.; Cha, S.S.; Kang, L.W.
The crystal structure of the D-alanine-D-alanine ligase from Acinetobacter baumannii suggests a flexible conformational change in the central domain before nucleotide binding
J. Microbiol.
53
776-782
2015
Acinetobacter baumannii
Azam, S.; Abbasi, S.; Akhtar, A.; Mirza, M.
Comparative modeling and molecular docking studies of D-alanine D-alanine ligase a target of antibacterial drugs
Med. Chem. Res.
23
4108-4137
2014
Streptococcus sanguinis (A3CLS3), Streptococcus sanguinis SK36 (A3CLS3)
-
Yang, S.; Xu, Y.; Wang, Y.; Ren, F.; Li, S.; Ding, W.; Ma, Y.; Zhang, W.
The biological properties and potential interacting proteins of D-alanyl-D-alanine ligase a from Mycobacterium tuberculosis
Molecules
23
324-338
2018
Mycobacterium tuberculosis (P9WP31), Mycobacterium tuberculosis, Mycobacterium tuberculosis ATCC 25618 / H37Rv (P9WP31)
Batson, S.; de Chiara, C.; Majce, V.; Lloyd, A.J.; Gobec, S.; Rea, D.; Fueloep, V.; Thoroughgood, C.W.; Simmons, K.J.; Dowson, C.G.; Fishwick, C.W.G.; de Carvalho, L.P.S.; Roper, D.I.
Inhibition of D-Ala D-Ala ligase through a phosphorylated form of the antibiotic D-cycloserine
Nat. Commun.
8
1939
2017
Escherichia coli (P07862)
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