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Alanine--anticapsin ligase (EC 6.3.2.49) (ATP-dependent dipeptide ligase) (Bacilysin synthetase) (L-Ala-L-amino acid dipeptide ligase) (L-alanine--L-anticapsin ligase) (L-amino acid ligase) (Lal)

 BACD_BACSU              Reviewed;         472 AA.
P39641;
01-FEB-1995, integrated into UniProtKB/Swiss-Prot.
01-FEB-1995, sequence version 1.
07-JUN-2017, entry version 117.
RecName: Full=Alanine--anticapsin ligase {ECO:0000303|PubMed:23317005};
EC=6.3.2.49 {ECO:0000269|PubMed:16030213, ECO:0000269|PubMed:22407814, ECO:0000269|PubMed:23317005, ECO:0000269|PubMed:24702628};
AltName: Full=ATP-dependent dipeptide ligase {ECO:0000303|PubMed:22407814};
AltName: Full=Bacilysin synthetase {ECO:0000303|PubMed:12372825};
AltName: Full=L-Ala-L-amino acid dipeptide ligase {ECO:0000303|PubMed:23317005};
AltName: Full=L-alanine--L-anticapsin ligase {ECO:0000303|PubMed:23317005};
AltName: Full=L-amino acid ligase {ECO:0000303|PubMed:16030213};
Short=Lal {ECO:0000303|PubMed:16030213};
Name=bacD {ECO:0000303|PubMed:15609023};
Synonyms=ywfE {ECO:0000303|PubMed:16030213};
OrderedLocusNames=BSU37710; ORFNames=ipa-83d;
Bacillus subtilis (strain 168).
Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Bacillus.
NCBI_TaxID=224308;
[1]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
STRAIN=168;
PubMed=7934828; DOI=10.1111/j.1365-2958.1993.tb01963.x;
Glaser P., Kunst F., Arnaud M., Coudart M.P., Gonzales W.,
Hullo M.-F., Ionescu M., Lubochinsky B., Marcelino L., Moszer I.,
Presecan E., Santana M., Schneider E., Schweizer J., Vertes A.,
Rapoport G., Danchin A.;
"Bacillus subtilis genome project: cloning and sequencing of the 97 kb
region from 325 degrees to 333 degrees.";
Mol. Microbiol. 10:371-384(1993).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=168;
PubMed=9384377; DOI=10.1038/36786;
Kunst F., Ogasawara N., Moszer I., Albertini A.M., Alloni G.,
Azevedo V., Bertero M.G., Bessieres P., Bolotin A., Borchert S.,
Borriss R., Boursier L., Brans A., Braun M., Brignell S.C., Bron S.,
Brouillet S., Bruschi C.V., Caldwell B., Capuano V., Carter N.M.,
Choi S.-K., Codani J.-J., Connerton I.F., Cummings N.J., Daniel R.A.,
Denizot F., Devine K.M., Duesterhoeft A., Ehrlich S.D., Emmerson P.T.,
Entian K.-D., Errington J., Fabret C., Ferrari E., Foulger D.,
Fritz C., Fujita M., Fujita Y., Fuma S., Galizzi A., Galleron N.,
Ghim S.-Y., Glaser P., Goffeau A., Golightly E.J., Grandi G.,
Guiseppi G., Guy B.J., Haga K., Haiech J., Harwood C.R., Henaut A.,
Hilbert H., Holsappel S., Hosono S., Hullo M.-F., Itaya M.,
Jones L.-M., Joris B., Karamata D., Kasahara Y., Klaerr-Blanchard M.,
Klein C., Kobayashi Y., Koetter P., Koningstein G., Krogh S.,
Kumano M., Kurita K., Lapidus A., Lardinois S., Lauber J.,
Lazarevic V., Lee S.-M., Levine A., Liu H., Masuda S., Mauel C.,
Medigue C., Medina N., Mellado R.P., Mizuno M., Moestl D., Nakai S.,
Noback M., Noone D., O'Reilly M., Ogawa K., Ogiwara A., Oudega B.,
Park S.-H., Parro V., Pohl T.M., Portetelle D., Porwollik S.,
Prescott A.M., Presecan E., Pujic P., Purnelle B., Rapoport G.,
Rey M., Reynolds S., Rieger M., Rivolta C., Rocha E., Roche B.,
Rose M., Sadaie Y., Sato T., Scanlan E., Schleich S., Schroeter R.,
Scoffone F., Sekiguchi J., Sekowska A., Seror S.J., Serror P.,
Shin B.-S., Soldo B., Sorokin A., Tacconi E., Takagi T., Takahashi H.,
Takemaru K., Takeuchi M., Tamakoshi A., Tanaka T., Terpstra P.,
Tognoni A., Tosato V., Uchiyama S., Vandenbol M., Vannier F.,
Vassarotti A., Viari A., Wambutt R., Wedler E., Wedler H.,
Weitzenegger T., Winters P., Wipat A., Yamamoto H., Yamane K.,
Yasumoto K., Yata K., Yoshida K., Yoshikawa H.-F., Zumstein E.,
Yoshikawa H., Danchin A.;
"The complete genome sequence of the Gram-positive bacterium Bacillus
subtilis.";
Nature 390:249-256(1997).
[3]
INDUCTION.
STRAIN=168 / 61884;
PubMed=12372825; DOI=10.1074/jbc.M208722200;
Inaoka T., Takahashi K., Ohnishi-Kameyama M., Yoshida M., Ochi K.;
"Guanine nucleotides guanosine 5'-diphosphate 3'-diphosphate and GTP
co-operatively regulate the production of an antibiotic bacilysin in
Bacillus subtilis.";
J. Biol. Chem. 278:2169-2176(2003).
[4]
FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, AND
BIOPHYSICOCHEMICAL PROPERTIES.
STRAIN=ATCC 15245 / 3349 / IAM 1-3;
PubMed=16030213; DOI=10.1128/JB.187.15.5195-5202.2005;
Tabata K., Ikeda H., Hashimoto S.;
"ywfE in Bacillus subtilis codes for a novel enzyme, L-amino acid
ligase.";
J. Bacteriol. 187:5195-5202(2005).
[5]
FUNCTION IN BACILYSIN PRODUCTION, AND GENE NAME.
PubMed=15609023; DOI=10.1007/s00203-004-0743-8;
Steinborn G., Hajirezaei M.-R., Hofemeister J.;
"bac genes for recombinant bacilysin and anticapsin production in
Bacillus host strains.";
Arch. Microbiol. 183:71-79(2005).
[6]
FUNCTION, CATALYTIC ACTIVITY, PATHWAY, AND SUBSTRATE SPECIFICITY.
PubMed=23317005; DOI=10.1021/bi3016229;
Parker J.B., Walsh C.T.;
"Action and timing of BacC and BacD in the late stages of biosynthesis
of the dipeptide antibiotic bacilysin.";
Biochemistry 52:889-901(2013).
[7]
X-RAY CRYSTALLOGRAPHY (2.50 ANGSTROMS) IN COMPLEX WITH SUBSTRATE
ANALOG; ADP AND MAGNESIUM, FUNCTION, CATALYTIC ACTIVITY,
BIOPHYSICOCHEMICAL PROPERTIES, MUTAGENESIS OF TYR-75 AND SER-184,
COFACTOR, REACTION MECHANISM, AND SUBUNIT.
PubMed=22407814; DOI=10.1002/pro.2058;
Shomura Y., Hinokuchi E., Ikeda H., Senoo A., Takahashi Y., Saito J.,
Komori H., Shibata N., Yonetani Y., Higuchi Y.;
"Structural and enzymatic characterization of BacD, an L-amino acid
dipeptide ligase from Bacillus subtilis.";
Protein Sci. 21:707-716(2012).
[8]
X-RAY CRYSTALLOGRAPHY (1.90 ANGSTROMS) OF 4-468 OF WILD-TYPE AND
MUTANT ALA-332 IN COMPLEX WITH ADP; ALANINE AND PHOSPHATE, FUNCTION,
CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, MUTAGENESIS OF
GLU-109; GLU-273; HIS-309; GLU-311; ARG-328 AND TRP-332, COFACTOR,
SUBUNIT, AND REACTION MECHANISM.
PubMed=24702628; DOI=10.1021/bi500292b;
Tsuda T., Asami M., Koguchi Y., Kojima S.;
"Single mutation alters the substrate specificity of L-amino acid
ligase.";
Biochemistry 53:2650-2660(2014).
-!- FUNCTION: Part of the bacABCDEFG operon responsible for the
biosynthesis of bacilysin, an irreversible inactivator of the
glutaminase domain of glucosamine synthetase. Catalyzes the
formation of alpha-dipeptides from various L-amino acids in the
presence of ATP. In vivo catalyzes the ligation of L-alanine and
L-anticapsin (epoxycyclohexanonyl-Ala) to produce the final
bacilysin antibiotic (L-Ala-L-4S-cyclohexenonyl-Ala dipeptide).
The substrate specificity is restricted to small amino acids such
as L-Ala, for the N-terminal end of the dipeptide, whereas a wide
range of hydrophobic amino acids such as L-Phe, L-Tyr and L-Met
are recognized for the C-terminal end.
{ECO:0000269|PubMed:15609023, ECO:0000269|PubMed:16030213,
ECO:0000269|PubMed:22407814, ECO:0000269|PubMed:23317005,
ECO:0000269|PubMed:24702628}.
-!- CATALYTIC ACTIVITY: ATP + L-alanine + L-anticapsin = ADP +
phosphate + bacilysin. {ECO:0000269|PubMed:16030213,
ECO:0000269|PubMed:22407814, ECO:0000269|PubMed:23317005,
ECO:0000269|PubMed:24702628}.
-!- COFACTOR:
Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
Evidence={ECO:0000269|PubMed:22407814,
ECO:0000269|PubMed:24702628};
Note=Binds 2 Mg(2+) ions per monomer.
{ECO:0000269|PubMed:22407814, ECO:0000269|PubMed:24702628};
-!- BIOPHYSICOCHEMICAL PROPERTIES:
Kinetic parameters:
KM=0.07 mM for ATP {ECO:0000269|PubMed:16030213};
KM=0.42 mM for L-alanine {ECO:0000269|PubMed:16030213};
KM=1.64 mM for L-alanine {ECO:0000269|PubMed:24702628};
KM=1.7 mM for L-alanine {ECO:0000269|PubMed:22407814};
KM=5.23 mM for L-phenylalanine {ECO:0000269|PubMed:24702628};
KM=20 mM for L-phenylalanine {ECO:0000269|PubMed:22407814};
KM=105.0 mM for L-glutamine {ECO:0000269|PubMed:16030213};
Vmax=0.764 umol/min/mg enzyme for Ala-Gln synthesis
{ECO:0000269|PubMed:16030213};
Note=Kcat is 9.32 sec(-1) for ligase activity with alanine as
substrate (PubMed:24702628). Kcat is 10.4 sec(-1) for ligase
activity with phenylalanine as substrate (PubMed:24702628). Kcat
is 630 min(-1) for ligase activity with alanine and
phenylalanine as substrate (PubMed:22407814).
{ECO:0000269|PubMed:22407814, ECO:0000269|PubMed:24702628};
pH dependence:
Optimum pH is 9.5. {ECO:0000269|PubMed:16030213};
Temperature dependence:
Optimum temperature is 37 degrees Celsius.
{ECO:0000269|PubMed:16030213};
-!- PATHWAY: Antibiotic biosynthesis; bacilysin biosynthesis.
{ECO:0000305|PubMed:23317005}.
-!- SUBUNIT: Monomer or homodimer. {ECO:0000269|PubMed:22407814,
ECO:0000269|PubMed:24702628}.
-!- INDUCTION: The compound guanosine 5'-diphosphate 3'-diphosphate
(ppGpp) is essential for the transcription of the bacABCDE operon
and GTP regulates the transcription of both this operon and ywfH
via the CodY-mediated regulation system.
{ECO:0000269|PubMed:12372825}.
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EMBL; X73124; CAA51639.1; -; Genomic_DNA.
EMBL; AL009126; CAB15798.1; -; Genomic_DNA.
PIR; S39738; S39738.
RefSeq; NP_391651.1; NC_000964.3.
RefSeq; WP_003242921.1; NZ_JNCM01000034.1.
PDB; 3VMM; X-ray; 2.50 A; A=1-472.
PDB; 3WNZ; X-ray; 1.90 A; A=4-468.
PDB; 3WO0; X-ray; 2.00 A; A=4-468.
PDB; 3WO1; X-ray; 2.30 A; A=4-468.
PDBsum; 3VMM; -.
PDBsum; 3WNZ; -.
PDBsum; 3WO0; -.
PDBsum; 3WO1; -.
ProteinModelPortal; P39641; -.
SMR; P39641; -.
STRING; 224308.Bsubs1_010100020371; -.
PaxDb; P39641; -.
DNASU; 937214; -.
EnsemblBacteria; CAB15798; CAB15798; BSU37710.
GeneID; 937214; -.
KEGG; bsu:BSU37710; -.
PATRIC; fig|224308.179.peg.4083; -.
eggNOG; ENOG4108V3M; Bacteria.
eggNOG; COG0439; LUCA.
HOGENOM; HOG000009191; -.
InParanoid; P39641; -.
KO; K13037; -.
OMA; ATHTEIK; -.
PhylomeDB; P39641; -.
BioCyc; BSUB:BSU37710-MONOMER; -.
BioCyc; MetaCyc:MONOMER-19123; -.
SABIO-RK; P39641; -.
UniPathway; UPA00100; -.
Proteomes; UP000001570; Chromosome.
GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
GO; GO:0016874; F:ligase activity; IEA:UniProtKB-KW.
GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
GO; GO:0017000; P:antibiotic biosynthetic process; IEA:UniProtKB-KW.
InterPro; IPR011761; ATP-grasp.
PROSITE; PS50975; ATP_GRASP; 1.
1: Evidence at protein level;
3D-structure; Antibiotic biosynthesis; ATP-binding; Complete proteome;
Ligase; Magnesium; Metal-binding; Nucleotide-binding;
Reference proteome.
CHAIN 1 472 Alanine--anticapsin ligase.
/FTId=PRO_0000064804.
DOMAIN 142 355 ATP-grasp. {ECO:0000255|PROSITE-
ProRule:PRU00409}.
NP_BIND 184 185 ATP. {ECO:0000269|PubMed:22407814,
ECO:0000269|PubMed:24702628}.
NP_BIND 226 229 ATP. {ECO:0000269|PubMed:22407814,
ECO:0000269|PubMed:24702628}.
REGION 309 311 Substrate binding.
{ECO:0000269|PubMed:22407814,
ECO:0000269|PubMed:24702628}.
REGION 328 331 Substrate binding.
{ECO:0000269|PubMed:22407814,
ECO:0000269|PubMed:24702628}.
METAL 109 109 Magnesium 1.
{ECO:0000269|PubMed:22407814}.
METAL 182 182 Magnesium 1; via carbonyl oxygen.
{ECO:0000269|PubMed:22407814}.
METAL 311 311 Magnesium 2.
{ECO:0000269|PubMed:22407814,
ECO:0000269|PubMed:24702628}.
METAL 324 324 Magnesium 1.
{ECO:0000269|PubMed:22407814,
ECO:0000269|PubMed:24702628}.
METAL 324 324 Magnesium 2.
{ECO:0000269|PubMed:22407814,
ECO:0000269|PubMed:24702628}.
BINDING 138 138 ATP. {ECO:0000269|PubMed:22407814,
ECO:0000269|PubMed:24702628}.
BINDING 178 178 ATP. {ECO:0000269|PubMed:22407814,
ECO:0000269|PubMed:24702628}.
BINDING 268 268 ATP. {ECO:0000269|PubMed:22407814,
ECO:0000269|PubMed:24702628}.
BINDING 273 273 Substrate. {ECO:0000269|PubMed:24702628}.
SITE 332 332 Plays a key role in restricting the N-
terminal substrate specificity to small
amino acids such as L-Ala.
{ECO:0000269|PubMed:24702628}.
MUTAGEN 75 75 Y->F: Almost no effect on catalytic
efficiency.
{ECO:0000269|PubMed:22407814}.
MUTAGEN 109 109 E->A: Loss of ligase activity.
{ECO:0000269|PubMed:24702628}.
MUTAGEN 184 184 S->A: Almost no effect on catalytic
efficiency.
{ECO:0000269|PubMed:22407814}.
MUTAGEN 273 273 E->A: Loss of ligase activity.
{ECO:0000269|PubMed:24702628}.
MUTAGEN 309 309 H->R: Loss of ligase activity.
{ECO:0000269|PubMed:24702628}.
MUTAGEN 311 311 E->D: Loss of ligase activity.
{ECO:0000269|PubMed:24702628}.
MUTAGEN 328 328 R->K: Loss of ligase activity.
{ECO:0000269|PubMed:24702628}.
MUTAGEN 332 332 W->A: Hydrolyzes ATP, even in the absence
of L-Ala, and the structure appears to
show a cavity in the N-terminal
substrate-binding pocket. Also alters the
substrate specificity and activity
depending on the size and shape of
substituted amino acids.
{ECO:0000269|PubMed:24702628}.
STRAND 5 9 {ECO:0000244|PDB:3WNZ}.
STRAND 12 15 {ECO:0000244|PDB:3WNZ}.
HELIX 17 27 {ECO:0000244|PDB:3WNZ}.
STRAND 28 35 {ECO:0000244|PDB:3WNZ}.
HELIX 37 39 {ECO:0000244|PDB:3WNZ}.
HELIX 42 51 {ECO:0000244|PDB:3WNZ}.
STRAND 53 57 {ECO:0000244|PDB:3WNZ}.
HELIX 59 61 {ECO:0000244|PDB:3WNZ}.
HELIX 65 68 {ECO:0000244|PDB:3WNZ}.
HELIX 85 99 {ECO:0000244|PDB:3WNZ}.
STRAND 102 107 {ECO:0000244|PDB:3WNZ}.
HELIX 109 111 {ECO:0000244|PDB:3WNZ}.
HELIX 112 122 {ECO:0000244|PDB:3WNZ}.
HELIX 129 134 {ECO:0000244|PDB:3WNZ}.
HELIX 138 147 {ECO:0000244|PDB:3WNZ}.
STRAND 155 158 {ECO:0000244|PDB:3WNZ}.
HELIX 161 171 {ECO:0000244|PDB:3WNZ}.
STRAND 173 181 {ECO:0000244|PDB:3WNZ}.
TURN 184 187 {ECO:0000244|PDB:3WNZ}.
STRAND 189 191 {ECO:0000244|PDB:3WNZ}.
TURN 194 196 {ECO:0000244|PDB:3WNZ}.
HELIX 197 208 {ECO:0000244|PDB:3WNZ}.
STRAND 220 227 {ECO:0000244|PDB:3WNZ}.
HELIX 233 236 {ECO:0000244|PDB:3WNZ}.
STRAND 238 242 {ECO:0000244|PDB:3WNZ}.
STRAND 244 253 {ECO:0000244|PDB:3WNZ}.
STRAND 256 265 {ECO:0000244|PDB:3WNZ}.
STRAND 275 279 {ECO:0000244|PDB:3WNZ}.
HELIX 284 301 {ECO:0000244|PDB:3WNZ}.
STRAND 305 315 {ECO:0000244|PDB:3WNZ}.
HELIX 316 318 {ECO:0000244|PDB:3WNZ}.
STRAND 319 328 {ECO:0000244|PDB:3WNZ}.
HELIX 334 342 {ECO:0000244|PDB:3WNZ}.
HELIX 346 356 {ECO:0000244|PDB:3WNZ}.
HELIX 357 359 {ECO:0000244|PDB:3WNZ}.
STRAND 364 366 {ECO:0000244|PDB:3WNZ}.
STRAND 371 379 {ECO:0000244|PDB:3WNZ}.
HELIX 381 386 {ECO:0000244|PDB:3WNZ}.
STRAND 395 403 {ECO:0000244|PDB:3WNZ}.
STRAND 414 420 {ECO:0000244|PDB:3WNZ}.
STRAND 426 431 {ECO:0000244|PDB:3WNZ}.
HELIX 433 435 {ECO:0000244|PDB:3WNZ}.
STRAND 439 446 {ECO:0000244|PDB:3WNZ}.
HELIX 448 461 {ECO:0000244|PDB:3WNZ}.
STRAND 463 467 {ECO:0000244|PDB:3WNZ}.
SEQUENCE 472 AA; 52267 MW; 0300F4FA6327976A CRC64;
MERKTVLVIA DLGGCPPHMF YKSAAEKYNL VSFIPRPFAI TASHAALIEK YSVAVIKDKD
YFKSLADFEH PDSIYWAHED HNKPEEEVVE QIVKVAEMFG ADAITTNNEL FIAPMAKACE
RLGLRGAGVQ AAENARDKNK MRDAFNKAGV KSIKNKRVTT LEDFRAALEE IGTPLILKPT
YLASSIGVTL ITDTETAEDE FNRVNDYLKS INVPKAVTFE APFIAEEFLQ GEYGDWYQTE
GYSDYISIEG IMADGEYFPI AIHDKTPQIG FTETSHITPS ILDEEAKKKI VEAAKKANEG
LGLQNCATHT EIKLMKNREP GLIESAARFA GWNMIPNIKK VFGLDMAQLL LDVLCFGKDA
DLPDGLLDQE PYYVADCHLY PQHFKQNGQI PETAEDLVIE AIDIPDGLLK GDTEIVSFSA
AAPGTSVDLT LFEAFNSIAA FELKGSNSQD VAESIRQIQQ HAKLTAKYVL PV


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