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6.3.2.9: UDP-N-acetylmuramoyl-L-alanine-D-glutamate ligase

This is an abbreviated version!
For detailed information about UDP-N-acetylmuramoyl-L-alanine-D-glutamate ligase, go to the full flat file.

Word Map on EC 6.3.2.9

Reaction

ATP
+
UDP-N-acetyl-alpha-D-muramoyl-L-alanine
 +
D-glutamate
=
ADP
 +
phosphate
 +
UDP-N-acetyl-alpha-D-muramoyl-L-alanyl-D-glutamate

Synonyms

D-Glutamate-adding enzyme, D-glutamic acid adding enzyme, D-Glutamic acid-adding enzyme, MurD, MurD cell wall enzyme, MurD ligase, Synthetase, uridine diphospho-N-acetylmuramoylalanyl-D-glutamate, UDP-Mur-Nac-L-Ala:L-Glu ligase, UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase, UDP-N-acetylmuramoyl-L-alanine:D-glutamateligase, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase, UDPMurNAc-L-alanine:D-glutamate ligase (ADP-forming), Uridine diphosphate N-acetylmuramoyl-L-alanine:D-glutamate ligase, Uridine diphospho-N-acetylmuramoylalanyl-D-glutamate synthetase

ECTree

     6 Ligases
         6.3 Forming carbon-nitrogen bonds
             6.3.2 Acid—amino-acid ligases (peptide synthases)
                6.3.2.9 UDP-N-acetylmuramoyl-L-alanine-D-glutamate ligase

Inhibitors

Inhibitors on EC 6.3.2.9 - UDP-N-acetylmuramoyl-L-alanine-D-glutamate ligase

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INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
(2R)-2-[((3-[(Z)-(4-oxo-2-thioxo-1,3-thiazolidin-5-ylidene)methyl]phenyl)carbonyl)amino]pentanedioic acid
-
(2R)-2-[((4-[(Z)-(4-oxo-2-thioxo-1,3-thiazolidin-5-ylidene)methyl]phenyl)carbonyl)amino]pentanedioic acid
-
(2R)-2-[[(7-(2-ethoxy-2-oxoethoxy)naphthalen-2-yl)sulfonyl]amino]pentanedioic acid
NMR and molecular dynamics analysis
(2R)-2-[[(7-(3-phenylpropoxy)naphthalen-2-yl)sulfonyl]amino]pentanedioic acid
NMR and molecular dynamics analysis
(2R)-2-[[(7-(4-cyanobenzyloxy)naphthalen-2-yl)sulfonyl]amino]pentanedioic acid
(2R)-2-[[(7-benzyloxynaphthalen-2-yl)sulfonyl]amino]pentanedioic acid
calculation of binding free energies. Main driving force for binding are non-polar van der Waals-interactions
(2R)-2-[[(7-butoxynaphthalen-2-yl)sulfonyl]amino]pentanedioic acid
NMR and molecular dynamics analysis
(2R)-2-[[(7-pentoxynaphthalen-2-yl)sulfonyl]amino]pentanedioic acid
calculation of binding free energies. Main driving force for binding are non-polar van der Waals-interactions
(2S)-2-[((4-[(Z)-(4-oxo-2-thioxo-1,3-thiazolidin-5-ylidene)methyl]phenyl)carbonyl)amino]pentanedioic acid
-
(R,Z)-2-(3-((1-carboxy-N-(4-((4-oxo-2-thioxothiazolidin-5-ylidene)-methyl)phenyl)formamido)methyl)benzamido)pentanedioic acid
-
(R,Z)-2-(3-((2-carboxy-N-(4-((4-oxo-2-thioxothiazolidin-5-ylidene)-methyl)phenyl)acetamido)methyl)benzamido)pentanedioic acid
in addition, weak activity against Gram-positive Staphylococcus aureus and Enterococcus faecalis
(R,Z)-2-(3-((3-carboxy-N-(4-((4-oxo-2-thioxothiazolidin-5-ylidene)-methyl)phenyl)propanamido)methyl)benzamido)pentanedioic acid
in addition, weak activity against Gram-positive Staphylococcus aureus and Enterococcus faecalis
(R,Z)-2-(3-((4-((2,4-dioxothiazolidin-5-ylidene)methyl)phenylamino)methyl)benzamido)pentanedioic acid
-
(R,Z)-2-(3-((4-((4-oxo-2-thioxothiazolidin-5-ylidene)methyl)phenylamino)methyl)benzamido)pentanedioic acid
-
1-phospho-N-acetylmuramoyl-L-Ala-D-Glu
-
-
2,3,4,5-tetrabromo-6-(3,6-dihydroxy-9H-xanthen-9-yl)benzoic acid
inhibitor identified by structure-based virtual screening
2,4,6-Trinitrobenzenesulfonic acid
-
-
2-((4-[(2S)-butan-2-ylamino]-6-(ethylamino)-1,3,5-triazin-2-yl)sulfanyl)-N-(2-chlorophenyl)acetamide
0.5 mM, 50% inhibition. Inhibitory to both MurC and MurD, ECs 6.3.2.8 and 6.3.2.9, respectively
2-([2-(2-naphthylsulfonyl)hydrazono)methyl]phenyl 2-nitrobenzenesulfonate
-
71% inhibition at 0.05 mM
2-([2-(2-naphthylsulfonyl)hydrazono)methyl]phenyl 3-nitrobenzenesulfonate
-
70% inhibition at 0.05 mM
2-([2-(2-naphthylsulfonyl)hydrazono)methyl]phenyl 4-nitrobenzenesulfonate
-
-
2-([2-(naphthalen-2-ylsulfonyl)hydrazono]methyl)phenyl 2-(benzo[d][1,3]dioxol-5-yl)acetate
-
49% inhibition at 0.10 mM
2-bromo-N-(4-([2-(2-naphthylsulfonyl)hydrazono]methyl)phenyl)benzamide
-
-
2-[([6-[(4-cyano-2-fluorobenzyl)oxy]naphthalen-2-yl]sulfonyl)amino]-5-hydroxybenzoic acid
-
2-[([6-[(4-cyano-2-fluorobenzyl)oxy]naphthalen-2-yl]sulfonyl)amino]benzene-1,4-dicarboxylic acid
-
3-([[(5-amino-1,3,4-thiadiazol-2-yl)sulfanyl]acetyl]amino)-4-methylbenzoic acid
-
-
3-bromo-N-(4-([2-(2-naphthylsulfonyl)hydrazono]methyl)phenyl)benzamide
-
-
4-([(5-methyl-1,3,4-thiadiazol-2-yl)sulfanyl]methyl)-6-(naphthalen-2-ylmethyl)-1,3,5-triazin-2-amine
0.5 mM, 33% inhibition. Inhibitory to both MurC and MurD, ECs 6.3.2.8 and 6.3.2.9, respectively
4-cyano-N-(4-([2-(2-naphthylsulfonyl)hydrazono]methyl)phenyl)benzamide
-
78% inhibition at 0.05 mM
4-[([6-[(4-cyano-2-fluorobenzyl)oxy]naphthalen-2-yl]sulfonyl)amino]benzene-1,3-dicarboxylic acid
-
4-[([6-[(4-cyano-2-fluorobenzyl)oxy]naphthalen-2-yl]sulfonyl)amino]cyclohexane-1,3-dicarboxylic acid
-
6-([(1,1-dioxidotetrahydrothiophen-3-yl)sulfanyl]methyl)-N-(2-phenylethyl)-1,3,5-triazine-2,4-diamine
0.25 mM, 11% inhibition. Inhibitory to both MurC and MurD, ECs 6.3.2.8 and 6.3.2.9, respectively
6-[(1-methyl-1H-imidazol-2-yl)sulfanyl]-N,N'-diphenyl-1,3,5-triazine-2,4-diamine
0.5 mM, 30% inhibition. Inhibitory to both MurC and MurD, ECs 6.3.2.8 and 6.3.2.9, respectively
benzylidene rhodanines
-
possess MurC inhibitory activity in the low micromolar range
-
beta,gamma-methyleneadenosine 5'-triphosphate
-
nonhydrolyzable ATP analogue
CPAHWPHPC
-
i.e. peptide MD-C7C_1, inhibits MurD
CSAWSNKFC
-
i.e. peptide MD-C7C_2, inhibits MurD
D-2-Aminoadipic acid
-
-
D-Asp
-
weak
D-erythro-3-Methylglutamic acid
-
-
D-erythro-4-Methylglutamic acid
-
-
D-Gln
-
weak
D-pyroglutamic acid
-
-
dihydrouridine 5'-diphosphate-N-acetylmuramoyl-L-Ala-D-Glu
-
-
DL-2-Amino-4-phosphonobutyric acid
-
-
DL-2-aminopimelic acid
-
-
DL-homocysteic acid
-
-
HLPTSSLFDTTG
-
-
HSSWYIQHFPPL
-
i.e. peptide MD-12, inhibits MurD
L-Glu
N'-((2-[(2-nitrobenzyl)oxy]phenyl)methylidene)-2-naphthalenesulfonohydrazide
-
-
N'-((2-[(3-nitrobenzyl)oxy]phenyl)methylidene)-2-naphthalenesulfonohydrazide
-
70% inhibition at 0.05 mM
N'-((2-[(4-cyanobenzyl)oxy]phenyl)methylidene)(2-fluorophenyl)methanesulfonohydrazide
-
39% inhibition at 0.10 mM
N'-((2-[(4-cyanobenzyl)oxy]phenyl)methylidene)(phenyl)methanesulfonohydrazide
-
58% inhibition at 0.10 mM
N'-((2-[(4-cyanobenzyl)oxy]phenyl)methylidene)-2-naphthalenesulfonohydrazide
-
-
N'-((2-[(4-cyanobenzyl)oxy]phenyl)methylidene)-2-nitrobenzenesulfonohydrazide
-
86% inhibition at 0.10 mM
N'-((2-[(4-cyanobenzyl)oxy]phenyl)methylidene)-3-nitrobenzenesulfonohydrazide
-
74% inhibition at 0.10 mM
N'-((2-[(4-cyanobenzyl)oxy]phenyl)methylidene)[4-(trifluoromethyl)phenyl]methanesulfonohydrazide
-
57% inhibition at 0.10 mM
N'-((3-[(3-nitrobenzyl)oxy]phenyl)methylidene)-2-naphthalenesulfonohydrazide
-
61% inhibition at 0.05 mM
N-(2-([2-(2-naphthylsulfonyl)hydrazono]methyl)phenyl)-3,5-dinitrobenzamide
-
-
N-(2-([2-(2-naphthylsulfonyl)hydrazono]methyl)phenyl)-4-nitrobenzamide
-
-
N-(3-[[(carboxyacetyl)[4-[(Z)-(2,4-dioxo-1,3-thiazolidin-5-ylidene)methyl]phenyl]amino]methyl]benzoyl)-D-glutamic acid
-
N-(4-([2-(2-naphthylsulfonyl)hydrazono]methyl)phenyl)-2-naphthamide
-
19% inhibition at 0.01 mM
N-(4-([2-(2-naphthylsulfonyl)hydrazono]methyl)phenyl)-2-nitrobenzamide
-
-
N-(4-([2-(2-naphthylsulfonyl)hydrazono]methyl)phenyl)-3,5-dinitrobenzamide
-
78% inhibition at 0.10 mM
N-(4-([2-(2-naphthylsulfonyl)hydrazono]methyl)phenyl)-4-nitrobenzamide
-
81% inhibition at 0.05 mM
N-(4-([2-(2-naphthylsulfonyl)hydrazono]methyl)phenyl)benzamide
-
56% inhibition at 0.10 mM
N-(6-butoxy-naphthalene-2-sulfonyl)-D-glutamic acid
competitive versus D-Glu, non-competitive versus ATP and UDP-N-acetylmuramoyl-L-Ala
N-(6-butoxy-naphthalene-2-sulfonyl)-L-glutamic acid
competitive versus D-Glu, non-competitive versus UDP-N-acetylmuramoyl-L-Ala
N-([(2S)-2-[(2-naphthylsulfonyl)amino]propyl]-sulfonyl)-D-glutamic acid
-
1 mM, 75% residual activity
N-([(2S)-2-[([1,1'-biphenyl]-4-yl-sulfonyl)amino]-propyl]sulfonyl)-D-glutamic acid
-
1 mM, 70% residual activity
N-[((2S)-2-[[(E)-3-(1,3-benzodioxol-5-yl)-2-propenoyl]amino]propyl)sulfonyl]-D-glutamic acid
-
1 mM, 80% residual activity
N-[2-fluoro-5-[([4-[(Z)-(4-oxo-2-thioxo-1,3-thiazolidin-5-ylidene)methyl]phenyl]amino)methyl]benzoyl]-D-glutamic acid
-
N-[[(2S)-2-(1,3-dioxo-1,3-dihydro-2H-isoindol-2-yl)propyl]sulfonyl]-D-glutamic acid
-
1 mM, 74% residual activity
N-[[(2S)-2-([2-[2-(acetylamino)phenoxy]acetyl]-amino)propyl]sulfonyl]-D-glutamic acid
-
1 mM, 93% residual activity
N-[[2-(1,3-dioxo-1,3-dihydro-2H-isoindol-2-yl)-ethyl]sulfonyl]-D-glutamic acid
-
1 mM, 77% residual activity
Phosphinate
-
an analogue of UDP-N-acetylmuramoyl-dipeptide, the N-acetylmuramoyl moiety being replaced by a hexanoyl chain and the peptide bond between L-Ala and D-Glu by a tetrahedral phosphinate bond
potassium phosphate
-
highly dependent on, optimal concentration: 11-16 mM, inhibition above 20 mM, phosphate ion is responsible for inhibition
RPTHSPI
-
peptides are synthesized from consensus sequences to evaluate their inhibitory potential against the essential MurD enzyme. The C-7-C mers MurDp1 (RPTHSPI) gives a decrease of MurD ATPase activity with a significant IC50 value of 4 mM. The 12 mers MurDp2 (HLPTSSLFDTTG) inhibits MurD with an IC50 value of 15 mM indicating a weak inhibition. Both peptides show a correlation between an increase in concentration versus an increase in inhibition values
UDP-N-acetylmuramoyl-L-Ala-D-Glu
-
-
[1-[(6-Uridinediphospho)hexanamido]ethyl](2,4-dicarboxybutyl)phosphinate pentasodium salt
-
good inhibitor, closely resembles the tetrahedral intermediate that is presumed to form the ligation reaction
additional information
-