DLTA_BACSU
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 03-AUG-2022, entry version 140.
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; Firmicutes; 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; P39581; -.
DR PRIDE; P39581; -.
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 OMA; VMDLYPC; -.
DR PhylomeDB; P39581; -.
DR BioCyc; BSUB:BSU38500-MON; -.
DR BioCyc; MetaCyc:BSU38500-MON; -.
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; -; 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.
DR InterPro; IPR042099; ANL_N_sf.
DR InterPro; IPR010072; DltA.
DR InterPro; IPR044507; DltA-like.
DR Pfam; PF00501; AMP-binding; 1.
DR Pfam; PF13193; AMP-binding_C; 1.
DR TIGRFAMs; TIGR01733; AA-adenyl-dom; 1.
DR TIGRFAMs; TIGR01734; D-ala-DACP-lig; 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
