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Information on EC 6.2.1.54 - D-alanine-[D-alanyl-carrier protein] ligase and Organism(s) Bacillus cereus and UniProt Accession Q81G39

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EC Tree
     6 Ligases
         6.2 Forming carbon-sulfur bonds
             6.2.1 Acid-thiol ligases
                6.2.1.54 D-alanine-[D-alanyl-carrier protein] ligase
IUBMB Comments
The enzyme is involved in the modification of wall teichoic acids, as well as type I and IV lipoteichoic acids, with D-alanine residues. It activates D-alanine using ATP to form a high-energy (D-alanyl)adenylate intermediate and subsequently transfers the alanyl moiety to the phosphopantheinyl prosthetic group of a D-alanyl-carrier protein (DltC).
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Bacillus cereus
UNIPROT: Q81G39
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Word Map
The taxonomic range for the selected organisms is: Bacillus cereus
The enzyme appears in selected viruses and cellular organisms
Reaction Schemes
hide(Overall reactions are displayed. Show all >>)
+
+
holo-[D-alanyl-carrier protein]
=
+
+
D-alanyl-[D-alanyl-carrier protein]
Synonyms
d-alanyl carrier protein ligase, d-alanine:d-alanyl carrier protein ligase, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
D-alanyl carrier protein ligase
-
Dcl
-
-
-
-
DltA
-
-
-
-
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Acid-thiol ligation
-
adenylation
-
PATHWAY SOURCE
PATHWAYS
-
-, -, -, -, -, -, -
SYSTEMATIC NAME
IUBMB Comments
D-alanine:[D-alanyl-carrier protein] ligase
The enzyme is involved in the modification of wall teichoic acids, as well as type I and IV lipoteichoic acids, with D-alanine residues. It activates D-alanine using ATP to form a high-energy (D-alanyl)adenylate intermediate and subsequently transfers the alanyl moiety to the phosphopantheinyl prosthetic group of a D-alanyl-carrier protein (DltC).
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
(D-alanyl)adenylate + holo-[D-alanyl-carrier protein]
AMP + D-alanyl-[D-alanyl-carrier protein]
show the reaction diagram
-
-
-
?
ATP + D-Ala + diphosphate
?
show the reaction diagram
-
-
-
?
ATP + D-alanine
(D-alanyl)adenylate + diphosphate
show the reaction diagram
-
-
-
?
ATP + D-alanine + holo-[D-alaninyl-carrier protein]
AMP + diphosphate + D-alanyl-[D-alanyl-carrier protein]
show the reaction diagram
-
-
-
?
ATP + D-alanine + poly(ribitol phosphate)
AMP + diphosphate + O-D-alanyl-poly(ribitol phosphate)
show the reaction diagram
ATP + L-Ala + diphosphate
?
show the reaction diagram
-
-
-
?
ATP + L-alanine + holo-[D-alaninyl-carrier protein]
AMP + diphosphate + L-alanyl-[D-alanyl-carrier protein]
show the reaction diagram
-
-
-
?
ATP + L-alanine + poly(ribitol phosphate)
AMP + diphosphate + O-L-alanyl-poly(ribitol phosphate)
show the reaction diagram
low activity
-
-
?
additional information
?
-
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
ATP + D-alanine + poly(ribitol phosphate)
AMP + diphosphate + O-D-alanyl-poly(ribitol phosphate)
show the reaction diagram
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
5'-O-[N-(D-alanyl)-sulfamoyl]adenosine
-
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
coenzyme A
CoA can mimic D-alanyl carrier protein DltC. The resulting Michaelis constants in the presence of saturating CoA for both ATP and D-alanine are reduced more than 10fold as compared to the values obtained in the absence of CoA. The presence of CoA also made DltA about 100fold more selective on D-alanine over L-alanine
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.01 - 0.75
ATP
1.1 - 3.1
D-Ala
0.02 - 1
D-alanine
6.6 - 14.4
L-Ala
0.109 - 109
L-alanine
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.011 - 0.24
ATP
0.025 - 0.103
D-Ala
0.18 - 0.33
D-alanine
0.11 - 0.12
L-Ala
0.14 - 0.41
L-alanine
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.05
ATP
wild type enzyme, at pH 7.2 and 37°C
0.33 - 9.2
D-alanine
0.003 - 0.03
L-alanine
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
crystal structure of a DltA is determined at 2.0 A resolution in complex with the D-alanine adenylate intermediate of the first reaction. Despite the low level of sequence similarity, the DltA structure resembles known structures of adenylation domains such as the acetyl-CoA synthetase. The enantiomer selection appears to be enhanced by the medium-sized side chain of Cys-269
hanging drop vapor diffusion method, using 0.1 M MgCl2, 0.5 M KCl, 16% (w/v) polyethylene glycol 3350 and 0.05 M HEPES-NaOH buffer at pH 7.2
substrate-free form, to 1.9 A resolution, space group P21
the crystal structure of Bacillus cereus D-alanyl carrier protein ligase (DltA) is determined in complex with ATP to 1.9 A resolution
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
C269A
D383N
mutant, an invariant amino residue in the ATP-binding pocket is choosen for mutagenesis studies
E298Q
mutant, an invariant amino residue in the ATP-binding pocket is choosen for mutagenesis studies
R397Q
mutant, an invariant amino residue in the ATP-binding pocket is choosen for mutagenesis studies
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
nickel affinity column chromatography and gel filtration
using Ni-NTA chromatography
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expressed in Escherichia coli as a His-tagged fusion protein
the pET28a vector is used
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Du, L.; He, Y.; Luo, Y.
Crystal Structure and Enantiomer Selection by D-Alanyl Carrier Protein Ligase DltA from Bacillus cereus
Biochemistry
47
11473-11480
2008
Bacillus cereus (Q81G39), Bacillus cereus
Manually annotated by BRENDA team
Osman, K.T.; Du, L.; He, Y.; Luo, Y.
Crystal structure of Bacillus cereus D-alanyl carrier protein ligase (DltA) in complex with ATP
J. Mol. Biol.
388
345-355
2009
Bacillus cereus (Q81G39), Bacillus cereus
Manually annotated by BRENDA team
Luo, Y.; Du, L.
Thiolation-enhanced substrate recognition by D-alanyl carrier protein ligase DltA from Bacillus cereus
F1000Res.
3
106
2014
Bacillus cereus (Q81G39), Bacillus cereus, Bacillus cereus DSM 31 (Q81G39)
Manually annotated by BRENDA team