6.3.2.4: D-Alanine-D-alanine ligase
This is an abbreviated version!
For detailed information about D-Alanine-D-alanine ligase, go to the full flat file.
Word Map on EC 6.3.2.4
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6.3.2.4
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peptidoglycan
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vancomycin
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enterococci
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d-cycloserine
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vancomycin-resistant
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faecium
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d-alanyl-d-lactate
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teicoplanin
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depsipeptide
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d-ala-d-lac
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drug development
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vanrs
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atp-grasp
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vancomycin-dependent
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vand-type
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d-ala-d-lactate
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d-ala2
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analysis
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synthesis
- 6.3.2.4
- peptidoglycan
- vancomycin
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enterococci
- d-cycloserine
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vancomycin-resistant
- faecium
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d-alanyl-d-lactate
- teicoplanin
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depsipeptide
- d-ala-d-lac
- drug development
-
vanrs
-
atp-grasp
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vancomycin-dependent
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vand-type
- d-ala-d-lactate
-
d-ala2
- analysis
- synthesis
Reaction
Synonyms
AbDDL, ATP-dependent D-Ala:D-Ala ligase, BBR47_20440, BMD_0213, BMQ_0219, BMWSH_5013, D-Ala-D-Ala ligase, D-Ala-D-Ala synthetase, D-Ala:D-Ala ligase, D-alanine:D-alanine (D-lactate) ligase (ADP), D-Alanine:D-alanine ligase, D-alanyl-D-alanine ligase B, D-Alanyl-D-alanine synthetase, D-Alanylalanine synthetase, DD1, DDI, Ddl, DdlA, DdlB, DdlB ligase, dll, dllB, EcDdlB, More, Rv2981c, SsDdl, Synthetase, D-alanylalanine, Tb-DdlA, TmDdl, TtDdL, TTHA1587, VanA, VanB ligase, YpDDL
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Substrates Products
Substrates Products on EC 6.3.2.4 - D-Alanine-D-alanine ligase
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REACTION DIAGRAM
ATP + beta-Ala
ADP + phosphate + ?
at 60°C activity is 1.3% of the activity with D-Ala, no activity at 37°C
-
-
?
ATP + D-Ala + 2-aminopentanoate
ADP + phosphate + D-Ala-2-aminopentanoate
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-
-
-
?
ATP + D-Ala + 2-hydroxybutanoate
ADP + phosphate + D-Ala-D-2-hydroxybutanoate
-
-
-
?
ATP + D-Ala + 2-hydroxypentanoate
ADP + phosphate + D-Ala-D-2-hydroxypentanoate
-
-
-
?
ATP + D-alanine + D-serine
ADP + D-alanyl-D-serine + D-alanyl-D-alanine + D-seryl-D-serine
ATP + D-Arg
ADP + phosphate + D-Arg-D-Arg
at 60°C activity is 0.43% of the activity with D-Ala, no activity at 37°C
-
-
?
ATP + D-Asn
ADP + phosphate + D-Asn-D-Asn
at 60°C activity is 0.22% of the activity with D-Ala, no activity at 37°C
-
-
?
ATP + D-Asp
ADP + phosphate + D-Asp-D-Asp
at 60°C activity is 0.051% of the activity with D-Ala, no activity at 37°C
-
-
?
ATP + D-Cys
ADP + phosphate + D-Cys-D-Cys
at 60°C activity is 29% of the activity with D-Ala
-
-
?
ATP + D-Gln
ADP + phosphate + D-Gln-D-Gln
at 60°C activity is 0.56% of the activity with D-Ala, no activity at 37°C
-
-
?
ATP + D-Glu
ADP + phosphate + D-Glu-D-Glu
at 60°C activity is 0.012% of the activity with D-Ala, no activity at 37°C
-
-
?
ATP + D-His
ADP + phosphate + D-His-D-His
at 60°C activity is 0.49% of the activity with D-Ala, no activity at 37°C
-
-
?
ATP + D-Ile
ADP + phosphate + D-Ile-D-Ile
at 60°C activity is 0.36% of the activity with D-Ala, no activity at 37°C
-
-
?
ATP + D-Leu
ADP + phosphate + D-Leu-D-Leu
at 60°C activity is 0.31% of the activity with D-Ala, no activity at 37°C
-
-
?
ATP + D-Lys
ADP + phosphate + D-Lys-D-Lys
at 60°C activity is 0.6% of the activity with D-Ala, no activity at 37°C
-
-
?
ATP + D-Met
ADP + phosphate + D-Met-D-Met
at 60°C activity is 0.34% of the activity with D-Ala, no activity at 37°C
-
-
?
ATP + D-Phe
ADP + phosphate + D-Phe-D-Phe
at 60°C activity is 0.31% of the activity with D-Ala, no activity at 37°C
-
-
?
ATP + D-Pro
ADP + phosphate + D-Pro-D-Pro
at 60°C activity is 0.29% of the activity with D-Ala, no activity at 37°C
-
-
?
ATP + D-Ser
ADP + phosphate + D-Ser-D-Ser
at 60°C activity is 16% of the activity with D-Ala
-
-
?
ATP + D-Thr
ADP + phosphate + D-Thr-D-Thr
at 60°C activity is 2.2% of the activity with D-Ala
-
-
?
ATP + D-Trp
ADP + phosphate + D-Trp-D-Trp
at 60°C activity is 0.1% of the activity with D-Ala, no activity at 37°C
-
-
?
ATP + D-Val
ADP + phosphate + D-Val-D-Val
at 60°C activity is 0.43% of the activity with D-Ala, no activity at 37°C
-
-
?
ATP + Gly
ADP + phosphate + Gly-Gly
at 60°C activity is 3.6% of the activity with D-Ala
-
-
?
beta-alanine + beta-alanine + ATP
beta-alanyl-beta-alanine + ADP + phosphate
-
1.3% of the activity with D-serine
-
?
D-alanine + D-alanine + ATP
D-alanyl-D-alanine + ADP + phosphate
-
-
-
?
D-cysteine + D-cysteine + ATP
D-cysteinyl-D-cysteine + ADP + phosphate
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29% of the activity with D-serine
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?
D-serine + D-serine + ATP
D-seryl-D-serine + ADP + phosphate
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16% of the activity with D-serine
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?
D-threonine + D-threonine + ATP
D-threonyl-D-threonine + ADP + phosphate
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2.2% of the activity with D-serine
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?
glycine + D-alanine + ATP
glycyl-D-alanine + ADP + phosphate
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3.6% of the activity with D-serine
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?
ATP + 2 D-alanine
ADP + phosphate + D-alanyl-D-alanine
Y216, S150, and E15 form a hydrogen-bonding triad that orients an omega-loop to close over the active site and also to orient substrate D-Ala1 (the first molecule of substrate that is activated by the enzyme protein). The bifunctional enzyme also catalyzes the formation of D-alanyl-D-lactate (D-alanine-(R)-lactate ligase)
-
-
?
ATP + 2 D-alanine
ADP + phosphate + D-alanyl-D-alanine
-
-
-
?
ATP + 2 D-alanine
ADP + phosphate + D-alanyl-D-alanine
DdlA catalyzes the dimerization of two D-alanine molecules and typically couples ATP hydrolysis to provide a thermodynamic driving force and exhibits a cleavage of ATP to ADP and phosphate. D-Alanine is completely converted into D-alanyl-D-alanine, so no remaining D-alanine is detected
-
-
?
ATP + 2 D-alanine
ADP + phosphate + D-alanyl-D-alanine
Mycobacterium tuberculosis ATCC 25618 / H37Rv
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-
-
?
ATP + 2 D-alanine
ADP + phosphate + D-alanyl-D-alanine
Mycobacterium tuberculosis ATCC 25618 / H37Rv
DdlA catalyzes the dimerization of two D-alanine molecules and typically couples ATP hydrolysis to provide a thermodynamic driving force and exhibits a cleavage of ATP to ADP and phosphate. D-Alanine is completely converted into D-alanyl-D-alanine, so no remaining D-alanine is detected
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-
?
ATP + 2 D-alanine
ADP + phosphate + D-alanyl-D-alanine
-
-
-
-
?
ATP + 2 D-alanine
ADP + phosphate + D-alanyl-D-alanine
Thermus thermophilus HB8 / ATCC 27634 / DSM 579
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-
-
?
?
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the finding that the reactions of EC 6.3.2.4 and EC 6.3.2.10 are reversible may represent a functional regulatory mechanism which determines the level of the lysine-containing UDPMurNAc-pentapeptide depending on the intracellular ATP/ADP ratio
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-
?
ATP + Ala + Ala
?
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second step in the biosynthesis of bacterial peptidoglycan
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-
?
ATP + Ala + Ala
?
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a possible cellular role of VanA is to synthesize a modified cell-wall component, with D-Ala-D-Met or D-Ala-Phe instead of D-Ala-D-Ala, which is subsequently not recognized by vancomycin
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-
?
ATP + Ala + Ala
?
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enzyme involved in peptidoglycan precursor synthesis during sporulation
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-
?
ATP + Ala + Ala
?
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enzyme involved in peptidoglycan precursor synthesis during sporulation
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-
?
ATP + Ala + Ala
?
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one step in peptidoglycan synthesis: the formation of D-Ala-D-Ala, the terminal dipeptide of the UDP-N-acetylmuramylpentapeptide
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-
?
ATP + Ala + Ala
?
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second enzyme in the three enzyme D-alanine branch of peptidoglycan biosynthesis
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-
?
ATP + Ala + Ala
?
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the finding that the reactions of EC 6.3.2.4 and EC 6.3.2.10 are reversible may represent a functional regulatory mechanism which determines the level of the lysine-containing UDPMurNAc-pentapeptide depending on the intracellular ATP/ADP ratio
-
-
?
ATP + Ala + Ala
?
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one step in peptidoglycan synthesis: the formation of D-Ala-D-Ala, the terminal dipeptide of the UDP-N-acetylmuramylpentapeptide
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-
?
ADP + phosphate + D-Ala-D-2-aminopentanoate
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-
-
-
?
ATP + D-Ala + D-2-aminopentanoate
ADP + phosphate + D-Ala-D-2-aminopentanoate
-
-
-
-
?
ATP + D-Ala + D-Ala
ADP + phosphate + D-Ala-D-Ala
-
-
-
?
ATP + D-Ala + D-Ala
ADP + phosphate + D-Ala-D-Ala
-
-
-
?
ATP + D-Ala + D-Ala
ADP + phosphate + D-Ala-D-Ala
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-
-
?
ATP + D-Ala + D-Ala
ADP + phosphate + D-Ala-D-Ala
-
-
-
?
ATP + D-Ala + D-Ala
ADP + phosphate + D-Ala-D-Ala
-
-
-
?
ATP + D-Ala + D-Ala
ADP + phosphate + D-Ala-D-Ala
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-
-
?
ATP + D-Ala + D-lactate
ADP + phosphate + D-Ala-D-lactate
-
enzyme uses both D-Ala and D-lactate as a substrate
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-
?
ATP + D-Ala + D-lactate
ADP + phosphate + D-Ala-D-lactate
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-
?
ATP + D-Ala + D-lactate
ADP + phosphate + D-Ala-D-lactate
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-
depsipeptide D-Ala-D-lactate is responsible for the intrinsic resistance of Leuconostoc mesenteroides to vancomycin
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?
ATP + D-Ala + D-lactate
ADP + phosphate + D-Ala-D-lactate
-
D-lactate is not a substrate for wild-type, but for mutants S137A/Y207F, S137F/Y207F, S137T/Y207F, S137G/Y207F, Y207F
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-
?
ATP + D-Ala + D-lactate
ADP + phosphate + D-Ala-D-lactate
-
D-lactate is not a substrate for wild-type, but for mutants S137A/Y207F, S137F/Y207F, S137T/Y207F, S137G/Y207F, Y207F
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-
?
ADP + phosphate + D-Ala-D-norleucine
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-
-
-
?
ATP + D-Ala + D-norleucine
ADP + phosphate + D-Ala-D-norleucine
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-
-
-
?
ADP + phosphate + D-AlaNH2
the D-AlaNH2 production of enzyme S293X mutants is optimized, the S293E variant, which is selected as the best enzyme for D-AlaNH2 production, exhibits an optimal activity at pH 9.0 and 40°C for D-AlaNH2 production. The S293E variant catalyzes the synthesis of 9.3 and 35.7 mM of D-AlaNH2 from 10 and 50 mM D-Ala and 3 M NH4Cl with conversion yields of 93% and 71.4%, respectively. The S293E variant exhibits higher reaction specificity to D-AlaNH2 production compared with the S293D variant and the other variants
-
-
?
ATP + D-Ala + NH3
ADP + phosphate + D-AlaNH2
Thermus thermophilus HB8 / ATCC 27634 / DSM 579
the D-AlaNH2 production of enzyme S293X mutants is optimized, the S293E variant, which is selected as the best enzyme for D-AlaNH2 production, exhibits an optimal activity at pH 9.0 and 40°C for D-AlaNH2 production. The S293E variant catalyzes the synthesis of 9.3 and 35.7 mM of D-AlaNH2 from 10 and 50 mM D-Ala and 3 M NH4Cl with conversion yields of 93% and 71.4%, respectively. The S293E variant exhibits higher reaction specificity to D-AlaNH2 production compared with the S293D variant and the other variants
-
-
?
ATP + D-alanine
ADP + phosphate + D-alanyl-D-alanine
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essential enzyme
-
?
ATP + D-alanine
ADP + phosphate + D-alanyl-D-alanine
-
-
-
?
ATP + D-alanine
ADP + phosphate + D-alanyl-D-alanine
the enzyme shows relatively weak binding affinity and poor catalytic activity against the substrate D-Ala in vitro, active site structure, overview
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-
?
ATP + D-alanine
ADP + phosphate + D-alanyl-D-alanine
-
-
-
?
ATP + D-alanine
ADP + phosphate + D-alanyl-D-alanine
-
-
?
ATP + D-alanine
ADP + phosphate + D-alanyl-D-alanine
-
-
-
-
?
ATP + D-alanine
ADP + phosphate + D-alanyl-D-alanine
D-alanine:D-alanine ligase is an essential enzyme in bacterial cell wall biosynthesis and an important target for developing new antibiotics
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-
?
ATP + D-alanine
ADP + phosphate + D-alanyl-D-alanine
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-
-
-
?
ADP + D-alanyl-D-serine + D-alanyl-D-alanine + D-seryl-D-serine
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-
-
-
?
ATP + D-alanine + D-serine
ADP + D-alanyl-D-serine + D-alanyl-D-alanine + D-seryl-D-serine
-
-
-
-
?
ATP + D-alanine + D-serine
ADP + D-alanyl-D-serine + D-alanyl-D-alanine + D-seryl-D-serine
-
-
-
-
?
?
-
-
the enzyme is also capable of synthesizing fluorinated dipeptides
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-
?
additional information
?
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DDl is an essential enzyme in bacterial cell wall biosynthesis
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-
?
additional information
?
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no activity with D-Ser, Gly, and D-lactate
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-
?
additional information
?
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no activity with D-Ser, Gly, and D-lactate
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-
?
additional information
?
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putative protein interaction partners of enzyme DdlA from Mycobacterium tuberculosis, overview
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-
?
additional information
?
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putative protein interaction partners of enzyme DdlA from Mycobacterium tuberculosis, overview
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-
?
additional information
?
-
Mycobacterium tuberculosis ATCC 25618 / H37Rv
putative protein interaction partners of enzyme DdlA from Mycobacterium tuberculosis, overview
-
-
?
additional information
?
-
-
substrate specificity expands at high temperature. At 37°C, enzyme shows reactivity only for D-alanine, D-serine, D-threonine, D-cysteine and glycine. At 60°C, substrates additionally include D-lysine, D-glutamine, D-histidine, D-arginine, D-valine, D-isoleucine, D-methionine, D-leucine, D-phenylalanine, D-proline, and D-asparagine, all below 1% of the activity with D-alanine
-
-
?
additional information
?
-
substrate specificity expands at high temperature. At 37°C, enzyme shows reactivity only for D-alanine, D-serine, D-threonine, D-cysteine and glycine. At 60°C, substrates additionally include D-lysine, D-glutamine, D-histidine, D-arginine, D-valine, D-isoleucine, D-methionine, D-leucine, D-phenylalanine, D-proline, and D-asparagine, all below 1% of the activity with D-alanine
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-
?
additional information
?
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substrate-binding mechanism of enzyme YpDDL involving conformational changes of the loops, overview. Two D-alanine-binding sites are located next to each other between the N-terminal domain and the C-terminal domain, and an ATP-binding site exists between the central and the C-terminal domains
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-
?
additional information
?
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-
substrate-binding mechanism of enzyme YpDDL involving conformational changes of the loops, overview. Two D-alanine-binding sites are located next to each other between the N-terminal domain and the C-terminal domain, and an ATP-binding site exists between the central and the C-terminal domains
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-
?