ID   DLTA_BACSU              Reviewed;         503 AA.
AC   P39581;
DT   01-FEB-1995, integrated into UniProtKB/Swiss-Prot.
DT   01-FEB-1995, sequence version 1.
DT   27-MAR-2024, entry version 147.
DE   RecName: Full=D-alanine--D-alanyl carrier protein ligase {ECO:0000255|HAMAP-Rule:MF_00593};
DE            Short=DCL {ECO:0000255|HAMAP-Rule:MF_00593};
DE            EC=6.2.1.54 {ECO:0000255|HAMAP-Rule:MF_00593};
DE   AltName: Full=D-alanine--poly(phosphoribitol) ligase subunit 1 {ECO:0000255|HAMAP-Rule:MF_00593};
DE   AltName: Full=D-alanine-activating enzyme {ECO:0000255|HAMAP-Rule:MF_00593};
DE            Short=DAE {ECO:0000255|HAMAP-Rule:MF_00593};
GN   Name=dltA {ECO:0000255|HAMAP-Rule:MF_00593}; Synonyms=dae;
GN   OrderedLocusNames=BSU38500; ORFNames=ipa-5r;
OS   Bacillus subtilis (strain 168).
OC   Bacteria; Bacillota; Bacilli; Bacillales; Bacillaceae; Bacillus.
OX   NCBI_TaxID=224308;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC   STRAIN=168;
RX   PubMed=7934828; DOI=10.1111/j.1365-2958.1993.tb01963.x;
RA   Glaser P., Kunst F., Arnaud M., Coudart M.P., Gonzales W., Hullo M.-F.,
RA   Ionescu M., Lubochinsky B., Marcelino L., Moszer I., Presecan E.,
RA   Santana M., Schneider E., Schweizer J., Vertes A., Rapoport G., Danchin A.;
RT   "Bacillus subtilis genome project: cloning and sequencing of the 97 kb
RT   region from 325 degrees to 333 degrees.";
RL   Mol. Microbiol. 10:371-384(1993).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=168;
RX   PubMed=9384377; DOI=10.1038/36786;
RA   Kunst F., Ogasawara N., Moszer I., Albertini A.M., Alloni G., Azevedo V.,
RA   Bertero M.G., Bessieres P., Bolotin A., Borchert S., Borriss R.,
RA   Boursier L., Brans A., Braun M., Brignell S.C., Bron S., Brouillet S.,
RA   Bruschi C.V., Caldwell B., Capuano V., Carter N.M., Choi S.-K.,
RA   Codani J.-J., Connerton I.F., Cummings N.J., Daniel R.A., Denizot F.,
RA   Devine K.M., Duesterhoeft A., Ehrlich S.D., Emmerson P.T., Entian K.-D.,
RA   Errington J., Fabret C., Ferrari E., Foulger D., Fritz C., Fujita M.,
RA   Fujita Y., Fuma S., Galizzi A., Galleron N., Ghim S.-Y., Glaser P.,
RA   Goffeau A., Golightly E.J., Grandi G., Guiseppi G., Guy B.J., Haga K.,
RA   Haiech J., Harwood C.R., Henaut A., Hilbert H., Holsappel S., Hosono S.,
RA   Hullo M.-F., Itaya M., Jones L.-M., Joris B., Karamata D., Kasahara Y.,
RA   Klaerr-Blanchard M., Klein C., Kobayashi Y., Koetter P., Koningstein G.,
RA   Krogh S., Kumano M., Kurita K., Lapidus A., Lardinois S., Lauber J.,
RA   Lazarevic V., Lee S.-M., Levine A., Liu H., Masuda S., Mauel C.,
RA   Medigue C., Medina N., Mellado R.P., Mizuno M., Moestl D., Nakai S.,
RA   Noback M., Noone D., O'Reilly M., Ogawa K., Ogiwara A., Oudega B.,
RA   Park S.-H., Parro V., Pohl T.M., Portetelle D., Porwollik S.,
RA   Prescott A.M., Presecan E., Pujic P., Purnelle B., Rapoport G., Rey M.,
RA   Reynolds S., Rieger M., Rivolta C., Rocha E., Roche B., Rose M., Sadaie Y.,
RA   Sato T., Scanlan E., Schleich S., Schroeter R., Scoffone F., Sekiguchi J.,
RA   Sekowska A., Seror S.J., Serror P., Shin B.-S., Soldo B., Sorokin A.,
RA   Tacconi E., Takagi T., Takahashi H., Takemaru K., Takeuchi M.,
RA   Tamakoshi A., Tanaka T., Terpstra P., Tognoni A., Tosato V., Uchiyama S.,
RA   Vandenbol M., Vannier F., Vassarotti A., Viari A., Wambutt R., Wedler E.,
RA   Wedler H., Weitzenegger T., Winters P., Wipat A., Yamamoto H., Yamane K.,
RA   Yasumoto K., Yata K., Yoshida K., Yoshikawa H.-F., Zumstein E.,
RA   Yoshikawa H., Danchin A.;
RT   "The complete genome sequence of the Gram-positive bacterium Bacillus
RT   subtilis.";
RL   Nature 390:249-256(1997).
RN   [3]
RP   FUNCTION, AND PATHWAY.
RX   PubMed=7797557; DOI=10.1074/jbc.270.26.15598;
RA   Perego M., Glaser P., Minutello A., Strauch M.A., Leopold K., Fischer W.;
RT   "Incorporation of D-alanine into lipoteichoic acid and wall teichoic acid
RT   in Bacillus subtilis. Identification of genes and regulation.";
RL   J. Biol. Chem. 270:15598-15606(1995).
RN   [4]
RP   X-RAY CRYSTALLOGRAPHY (2.28 ANGSTROMS) IN COMPLEX WITH AMP.
RX   PubMed=18784082; DOI=10.1074/jbc.m800557200;
RA   Yonus H., Neumann P., Zimmermann S., May J.J., Marahiel M.A., Stubbs M.T.;
RT   "Crystal structure of DltA. Implications for the reaction mechanism of non-
RT   ribosomal peptide synthetase adenylation domains.";
RL   J. Biol. Chem. 283:32484-32491(2008).
CC   -!- FUNCTION: Catalyzes the first step in the D-alanylation of lipoteichoic
CC       acid (LTA), the activation of D-alanine and its transfer onto the D-
CC       alanyl carrier protein (Dcp) DltC. In an ATP-dependent two-step
CC       reaction, forms a high energy D-alanyl-AMP intermediate, followed by
CC       transfer of the D-alanyl residue as a thiol ester to the
CC       phosphopantheinyl prosthetic group of the Dcp. D-alanylation of LTA
CC       plays an important role in modulating the properties of the cell wall
CC       in Gram-positive bacteria, influencing the net charge of the cell wall.
CC       {ECO:0000255|HAMAP-Rule:MF_00593, ECO:0000269|PubMed:7797557}.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=ATP + D-alanine + holo-[D-alanyl-carrier protein] = AMP + D-
CC         alanyl-[D-alanyl-carrier protein] + diphosphate;
CC         Xref=Rhea:RHEA:55132, Rhea:RHEA-COMP:14102, Rhea:RHEA-COMP:14103,
CC         ChEBI:CHEBI:30616, ChEBI:CHEBI:33019, ChEBI:CHEBI:57416,
CC         ChEBI:CHEBI:64479, ChEBI:CHEBI:138620, ChEBI:CHEBI:456215;
CC         EC=6.2.1.54; Evidence={ECO:0000255|HAMAP-Rule:MF_00593};
CC   -!- PATHWAY: Cell wall biogenesis; lipoteichoic acid biosynthesis.
CC       {ECO:0000255|HAMAP-Rule:MF_00593, ECO:0000269|PubMed:7797557}.
CC   -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_00593}.
CC   -!- SIMILARITY: Belongs to the ATP-dependent AMP-binding enzyme family.
CC       DltA subfamily. {ECO:0000255|HAMAP-Rule:MF_00593}.
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DR   EMBL; X73124; CAA51561.1; -; Genomic_DNA.
DR   EMBL; AL009126; CAB15876.1; -; Genomic_DNA.
DR   PIR; S39660; S39660.
DR   RefSeq; NP_391729.1; NC_000964.3.
DR   RefSeq; WP_003242511.1; NZ_JNCM01000034.1.
DR   PDB; 3E7W; X-ray; 2.28 A; A=1-503.
DR   PDB; 3E7X; X-ray; 2.60 A; A=1-503.
DR   PDBsum; 3E7W; -.
DR   PDBsum; 3E7X; -.
DR   AlphaFoldDB; P39581; -.
DR   SMR; P39581; -.
DR   IntAct; P39581; 1.
DR   MINT; P39581; -.
DR   STRING; 224308.BSU38500; -.
DR   jPOST; P39581; -.
DR   PaxDb; 224308-BSU38500; -.
DR   EnsemblBacteria; CAB15876; CAB15876; BSU_38500.
DR   GeneID; 937358; -.
DR   KEGG; bsu:BSU38500; -.
DR   PATRIC; fig|224308.179.peg.4169; -.
DR   eggNOG; COG1020; Bacteria.
DR   InParanoid; P39581; -.
DR   OrthoDB; 9765680at2; -.
DR   PhylomeDB; P39581; -.
DR   BioCyc; BSUB:BSU38500-MONOMER; -.
DR   BioCyc; MetaCyc:BSU38500-MONOMER; -.
DR   BRENDA; 6.2.1.54; 658.
DR   SABIO-RK; P39581; -.
DR   UniPathway; UPA00556; -.
DR   EvolutionaryTrace; P39581; -.
DR   Proteomes; UP000001570; Chromosome.
DR   GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR   GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR   GO; GO:0047473; F:D-alanine [D-alanyl carrier protein] ligase activity; IEA:UniProtKB-UniRule.
DR   GO; GO:0070395; P:lipoteichoic acid biosynthetic process; IEA:UniProtKB-UniRule.
DR   CDD; cd05945; DltA; 1.
DR   Gene3D; 3.30.300.30; -; 1.
DR   Gene3D; 3.40.50.12780; N-terminal domain of ligase-like; 1.
DR   HAMAP; MF_00593; DltA; 1.
DR   InterPro; IPR010071; AA_adenyl_domain.
DR   InterPro; IPR025110; AMP-bd_C.
DR   InterPro; IPR045851; AMP-bd_C_sf.
DR   InterPro; IPR020845; AMP-binding_CS.
DR   InterPro; IPR000873; AMP-dep_Synth/Lig_com.
DR   InterPro; IPR042099; ANL_N_sf.
DR   InterPro; IPR010072; DltA.
DR   InterPro; IPR044507; DltA-like.
DR   NCBIfam; TIGR01733; AA-adenyl-dom; 1.
DR   NCBIfam; TIGR01734; D-ala-DACP-lig; 1.
DR   PANTHER; PTHR45398; ENZYME, PUTATIVE (JCVI)-RELATED; 1.
DR   PANTHER; PTHR45398:SF1; ENZYME, PUTATIVE (JCVI)-RELATED; 1.
DR   Pfam; PF00501; AMP-binding; 1.
DR   Pfam; PF13193; AMP-binding_C; 1.
DR   SUPFAM; SSF56801; Acetyl-CoA synthetase-like; 1.
DR   PROSITE; PS00455; AMP_BINDING; 1.
PE   1: Evidence at protein level;
KW   3D-structure; ATP-binding; Cytoplasm; Ligase; Nucleotide-binding;
KW   Reference proteome.
FT   CHAIN           1..503
FT                   /note="D-alanine--D-alanyl carrier protein ligase"
FT                   /id="PRO_0000213142"
FT   BINDING         151..152
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00593"
FT   BINDING         196
FT                   /ligand="D-alanine"
FT                   /ligand_id="ChEBI:CHEBI:57416"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00593"
FT   BINDING         291..296
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00593,
FT                   ECO:0000269|PubMed:18784082, ECO:0007744|PDB:3E7W,
FT                   ECO:0007744|PDB:3E7X"
FT   BINDING         300
FT                   /ligand="D-alanine"
FT                   /ligand_id="ChEBI:CHEBI:57416"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00593"
FT   BINDING         382
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00593,
FT                   ECO:0000269|PubMed:18784082, ECO:0007744|PDB:3E7W,
FT                   ECO:0007744|PDB:3E7X"
FT   BINDING         407
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000269|PubMed:18784082,
FT                   ECO:0007744|PDB:3E7W, ECO:0007744|PDB:3E7X"
FT   BINDING         491
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00593"
FT   BINDING         491
FT                   /ligand="D-alanine"
FT                   /ligand_id="ChEBI:CHEBI:57416"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00593"
FT   HELIX           3..13
FT                   /evidence="ECO:0007829|PDB:3E7W"
FT   STRAND          17..22
FT                   /evidence="ECO:0007829|PDB:3E7W"
FT   STRAND          25..28
FT                   /evidence="ECO:0007829|PDB:3E7W"
FT   HELIX           29..43
FT                   /evidence="ECO:0007829|PDB:3E7W"
FT   TURN            44..46
FT                   /evidence="ECO:0007829|PDB:3E7W"
FT   STRAND          49..51
FT                   /evidence="ECO:0007829|PDB:3E7W"
FT   STRAND          55..61
FT                   /evidence="ECO:0007829|PDB:3E7W"
FT   HELIX           63..75
FT                   /evidence="ECO:0007829|PDB:3E7W"
FT   STRAND          79..83
FT                   /evidence="ECO:0007829|PDB:3E7W"
FT   HELIX           88..98
FT                   /evidence="ECO:0007829|PDB:3E7W"
FT   STRAND          102..108
FT                   /evidence="ECO:0007829|PDB:3E7W"
FT   STRAND          120..122
FT                   /evidence="ECO:0007829|PDB:3E7W"
FT   HELIX           123..127
FT                   /evidence="ECO:0007829|PDB:3E7W"
FT   HELIX           136..138
FT                   /evidence="ECO:0007829|PDB:3E7W"
FT   STRAND          144..151
FT                   /evidence="ECO:0007829|PDB:3E7W"
FT   STRAND          159..164
FT                   /evidence="ECO:0007829|PDB:3E7W"
FT   HELIX           165..178
FT                   /evidence="ECO:0007829|PDB:3E7W"
FT   TURN            180..184
FT                   /evidence="ECO:0007829|PDB:3E7W"
FT   STRAND          186..189
FT                   /evidence="ECO:0007829|PDB:3E7W"
FT   HELIX           197..207
FT                   /evidence="ECO:0007829|PDB:3E7W"
FT   STRAND          211..214
FT                   /evidence="ECO:0007829|PDB:3E7W"
FT   HELIX           217..221
FT                   /evidence="ECO:0007829|PDB:3E7W"
FT   HELIX           223..233
FT                   /evidence="ECO:0007829|PDB:3E7W"
FT   STRAND          236..240
FT                   /evidence="ECO:0007829|PDB:3E7W"
FT   HELIX           242..249
FT                   /evidence="ECO:0007829|PDB:3E7W"
FT   TURN            256..258
FT                   /evidence="ECO:0007829|PDB:3E7W"
FT   STRAND          264..267
FT                   /evidence="ECO:0007829|PDB:3E7W"
FT   HELIX           274..283
FT                   /evidence="ECO:0007829|PDB:3E7W"
FT   STRAND          288..291
FT                   /evidence="ECO:0007829|PDB:3E7W"
FT   HELIX           296..298
FT                   /evidence="ECO:0007829|PDB:3E7W"
FT   STRAND          302..307
FT                   /evidence="ECO:0007829|PDB:3E7W"
FT   HELIX           309..312
FT                   /evidence="ECO:0007829|PDB:3E7W"
FT   STRAND          321..323
FT                   /evidence="ECO:0007829|PDB:3E7W"
FT   STRAND          328..332
FT                   /evidence="ECO:0007829|PDB:3E7W"
FT   STRAND          345..351
FT                   /evidence="ECO:0007829|PDB:3E7W"
FT   HELIX           362..368
FT                   /evidence="ECO:0007829|PDB:3E7W"
FT   STRAND          369..387
FT                   /evidence="ECO:0007829|PDB:3E7W"
FT   STRAND          390..403
FT                   /evidence="ECO:0007829|PDB:3E7W"
FT   STRAND          406..409
FT                   /evidence="ECO:0007829|PDB:3E7W"
FT   HELIX           410..419
FT                   /evidence="ECO:0007829|PDB:3E7W"
FT   STRAND          423..431
FT                   /evidence="ECO:0007829|PDB:3E7W"
FT   STRAND          433..436
FT                   /evidence="ECO:0007829|PDB:3E7W"
FT   STRAND          439..446
FT                   /evidence="ECO:0007829|PDB:3E7W"
FT   HELIX           454..468
FT                   /evidence="ECO:0007829|PDB:3E7W"
FT   HELIX           471..473
FT                   /evidence="ECO:0007829|PDB:3E7W"
FT   STRAND          476..480
FT                   /evidence="ECO:0007829|PDB:3E7W"
FT   HELIX           488..490
FT                   /evidence="ECO:0007829|PDB:3E7X"
FT   HELIX           494..503
FT                   /evidence="ECO:0007829|PDB:3E7W"
SQ   SEQUENCE   503 AA;  55809 MW;  76604AA90C812644 CRC64;
     MKLLHAIQTH AETYPQTDAF RSQGQSLTYQ ELWEQSDRAA AAIQKRISGE KKSPILVYGH
     MEPHMIVSFL GSVKAGHPYI PVDLSIPSER IAKIIESSGA ELLIHAAGLS IDAVGQQIQT
     VSAEELLENE GGSVSQDQWV KEHETFYIIY TSGSTGNPKG VQISAANLQS FTDWICADFP
     VSGGKIFLNQ APFSFDLSVM DLYPCLQSGG TLHCVTKDAV NKPKVLFEEL KKSGLNVWTS
     TPSFVQMCLM DPGFSQDLLP HADTFMFCGE VLPVSVAKAL LERFPKAKIF NTYGPTEATV
     AVTSVEITND VISRSESLPV GFAKPDMNIF IMDEEGQPLP EGEKGEIVIA GPSVSRGYLG
     EPELTEKAFF SHEGQWAYRT GDAGFIQDGQ IFCQGRLDFQ IKLHGYRMEL EEIEFHVRQS
     QYVRSAVVIP YQPNGTVEYL IAAIVPEEHE FEKEFQLTSA IKKELAASLP AYMIPRKFIY
     QDHIQMTANG KIDRKRIGEE VLV
//