ID   DDL_RICAE               Reviewed;         321 AA.
AC   C3PMU6;
DT   22-SEP-2009, integrated into UniProtKB/Swiss-Prot.
DT   16-JUN-2009, sequence version 1.
DT   03-AUG-2022, entry version 74.
DE   RecName: Full=D-alanine--D-alanine ligase {ECO:0000255|HAMAP-Rule:MF_00047};
DE            EC=6.3.2.4 {ECO:0000255|HAMAP-Rule:MF_00047};
DE   AltName: Full=D-Ala-D-Ala ligase {ECO:0000255|HAMAP-Rule:MF_00047};
DE   AltName: Full=D-alanylalanine synthetase {ECO:0000255|HAMAP-Rule:MF_00047};
GN   Name=ddl {ECO:0000255|HAMAP-Rule:MF_00047}; OrderedLocusNames=RAF_ORF0310;
OS   Rickettsia africae (strain ESF-5).
OC   Bacteria; Proteobacteria; Alphaproteobacteria; Rickettsiales;
OC   Rickettsiaceae; Rickettsieae; Rickettsia; spotted fever group.
OX   NCBI_TaxID=347255;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ESF-5;
RX   PubMed=19379498; DOI=10.1186/1471-2164-10-166;
RA   Fournier P.-E., El Karkouri K., Leroy Q., Robert C., Giumelli B.,
RA   Renesto P., Socolovschi C., Parola P., Audic S., Raoult D.;
RT   "Analysis of the Rickettsia africae genome reveals that virulence
RT   acquisition in Rickettsia species may be explained by genome reduction.";
RL   BMC Genomics 10:166-166(2009).
CC   -!- FUNCTION: Cell wall formation. {ECO:0000255|HAMAP-Rule:MF_00047}.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=ATP + 2 D-alanine = ADP + D-alanyl-D-alanine + H(+) +
CC         phosphate; Xref=Rhea:RHEA:11224, ChEBI:CHEBI:15378,
CC         ChEBI:CHEBI:30616, ChEBI:CHEBI:43474, ChEBI:CHEBI:57416,
CC         ChEBI:CHEBI:57822, ChEBI:CHEBI:456216; EC=6.3.2.4;
CC         Evidence={ECO:0000255|HAMAP-Rule:MF_00047};
CC   -!- COFACTOR:
CC       Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Evidence={ECO:0000250};
CC       Name=Mn(2+); Xref=ChEBI:CHEBI:29035; Evidence={ECO:0000250};
CC       Note=Binds 2 magnesium or manganese ions per subunit. {ECO:0000250};
CC   -!- PATHWAY: Cell wall biogenesis; peptidoglycan biosynthesis.
CC       {ECO:0000255|HAMAP-Rule:MF_00047}.
CC   -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_00047}.
CC   -!- SIMILARITY: Belongs to the D-alanine--D-alanine ligase family.
CC       {ECO:0000255|HAMAP-Rule:MF_00047}.
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DR   EMBL; CP001612; ACP53256.1; -; Genomic_DNA.
DR   RefSeq; WP_012719510.1; NC_012633.1.
DR   AlphaFoldDB; C3PMU6; -.
DR   SMR; C3PMU6; -.
DR   EnsemblBacteria; ACP53256; ACP53256; RAF_ORF0310.
DR   KEGG; raf:RAF_ORF0310; -.
DR   HOGENOM; CLU_039268_1_1_5; -.
DR   OMA; NTTPGMT; -.
DR   UniPathway; UPA00219; -.
DR   Proteomes; UP000002305; Chromosome.
DR   GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR   GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR   GO; GO:0008716; F:D-alanine-D-alanine ligase activity; IEA:UniProtKB-UniRule.
DR   GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR   GO; GO:0071555; P:cell wall organization; IEA:UniProtKB-KW.
DR   GO; GO:0009252; P:peptidoglycan biosynthetic process; IEA:UniProtKB-UniRule.
DR   GO; GO:0008360; P:regulation of cell shape; IEA:UniProtKB-KW.
DR   Gene3D; 3.30.1490.20; -; 1.
DR   HAMAP; MF_00047; Dala_Dala_lig; 1.
DR   InterPro; IPR011761; ATP-grasp.
DR   InterPro; IPR013815; ATP_grasp_subdomain_1.
DR   InterPro; IPR000291; D-Ala_lig_Van_CS.
DR   InterPro; IPR005905; D_ala_D_ala.
DR   InterPro; IPR011095; Dala_Dala_lig_C.
DR   InterPro; IPR011127; Dala_Dala_lig_N.
DR   InterPro; IPR016185; PreATP-grasp_dom_sf.
DR   Pfam; PF07478; Dala_Dala_lig_C; 1.
DR   Pfam; PF01820; Dala_Dala_lig_N; 1.
DR   PIRSF; PIRSF039102; Ddl/VanB; 1.
DR   SUPFAM; SSF52440; SSF52440; 1.
DR   TIGRFAMs; TIGR01205; D_ala_D_alaTIGR; 1.
DR   PROSITE; PS50975; ATP_GRASP; 1.
DR   PROSITE; PS00843; DALA_DALA_LIGASE_1; 1.
DR   PROSITE; PS00844; DALA_DALA_LIGASE_2; 1.
PE   3: Inferred from homology;
KW   ATP-binding; Cell shape; Cell wall biogenesis/degradation; Cytoplasm;
KW   Ligase; Magnesium; Manganese; Metal-binding; Nucleotide-binding;
KW   Peptidoglycan synthesis.
FT   CHAIN           1..321
FT                   /note="D-alanine--D-alanine ligase"
FT                   /id="PRO_1000202204"
FT   DOMAIN          121..315
FT                   /note="ATP-grasp"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT   BINDING         147..199
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT   BINDING         268
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT   BINDING         282
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT   BINDING         282
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT   BINDING         284
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
SQ   SEQUENCE   321 AA;  36022 MW;  90C75F677CD30BBC CRC64;
     MHKYQTHWVE HSIVKILSST GKKHIALMVG GMSAEREVSL VSSEGVSKAL IELGYRVTFI
     DMGADIAVRL QEIKPDIVFN CLHGTYGEDG CLPGLLNIMR IPYTHSGMLS SALAFDKIHS
     RIWFLTNNIN MAESIVVNKS DNIKNDPMKR PYVIKPLTQG SSIGVEVIFA EDDFNFADYD
     FPYGDQVIIE QYIKGRELQV AVLNGKALGA LEIKLLKNRF YDYETKYTEG FADHLCPAPL
     PANLYEKLLI ESEKIYKTMN CKGPARAEFI LEEQTNKLYA LEINTHPGMT PLSIVPEIAA
     YAGINFTNLI EEIIKMASFE S