ID   DDL_PROM0               Reviewed;         355 AA.
AC   A3PEE0;
DT   15-JAN-2008, integrated into UniProtKB/Swiss-Prot.
DT   03-APR-2007, sequence version 1.
DT   02-SEP-2026, entry version 103.
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};
GN   OrderedLocusNames=P9301_14921;
OS   Prochlorococcus marinus (strain MIT 9301).
OC   Bacteria; Bacillati; Cyanobacteriota; Cyanophyceae; Synechococcales;
OC   Prochlorococcaceae; Prochlorococcus.
OX   NCBI_TaxID=167546;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=MIT 9301;
RX   PubMed=18159947; DOI=10.1371/journal.pgen.0030231;
RA   Kettler G.C., Martiny A.C., Huang K., Zucker J., Coleman M.L., Rodrigue S.,
RA   Chen F., Lapidus A., Ferriera S., Johnson J., Steglich C., Church G.M.,
RA   Richardson P., Chisholm S.W.;
RT   "Patterns and implications of gene gain and loss in the evolution of
RT   Prochlorococcus.";
RL   PLoS Genet. 3:2515-2528(2007).
CC   -!- FUNCTION: Cell wall formation. {ECO:0000255|HAMAP-Rule:MF_00047}.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=2 D-alanine + ATP = D-alanyl-D-alanine + ADP + phosphate +
CC         H(+); Xref=Rhea:RHEA:11224, ChEBI:CHEBI:15378, ChEBI:CHEBI:30616,
CC         ChEBI:CHEBI:43474, ChEBI:CHEBI:57416, ChEBI:CHEBI:57822,
CC         ChEBI:CHEBI:456216; EC=6.3.2.4; Evidence={ECO:0000255|HAMAP-
CC         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; CP000576; ABO18115.1; -; Genomic_DNA.
DR   RefSeq; WP_011863422.1; NC_009091.1.
DR   AlphaFoldDB; A3PEE0; -.
DR   SMR; A3PEE0; -.
DR   STRING; 167546.P9301_14921; -.
DR   KEGG; pmg:P9301_14921; -.
DR   eggNOG; COG1181; Bacteria.
DR   HOGENOM; CLU_039268_0_0_3; -.
DR   OrthoDB; 9813261at2; -.
DR   UniPathway; UPA00219; -.
DR   Proteomes; UP000001430; Chromosome.
DR   GO; GO:0005829; C:cytosol; IEA:TreeGrafter.
DR   GO; GO:0005524; F:ATP binding; IEA:InterPro.
DR   GO; GO:0008716; F:D-alanine-D-alanine ligase activity; IEA:UniProtKB-UniRule.
DR   GO; GO:0046872; F:metal ion binding; IEA:InterPro.
DR   GO; GO:0009252; P:peptidoglycan biosynthetic process; IEA:UniProtKB-UniRule.
DR   Gene3D; 3.40.50.20; -; 1.
DR   Gene3D; 3.30.1490.20; ATP-grasp fold, A domain; 1.
DR   Gene3D; 3.30.470.20; ATP-grasp fold, B domain; 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   NCBIfam; TIGR01205; D_ala_D_alaTIGR; 1.
DR   NCBIfam; NF002528; PRK01966.1-4; 1.
DR   PANTHER; PTHR23132; D-ALANINE--D-ALANINE LIGASE; 1.
DR   PANTHER; PTHR23132:SF25; D-ALANINE--D-ALANINE LIGASE A; 1.
DR   Pfam; PF07478; Dala_Dala_lig_C; 1.
DR   Pfam; PF01820; Dala_Dala_lig_N; 1.
DR   PIRSF; PIRSF039102; Ddl/VanB; 1.
DR   SUPFAM; SSF56059; Glutathione synthetase ATP-binding domain-like; 1.
DR   SUPFAM; SSF52440; PreATP-grasp domain; 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; Reference proteome.
FT   CHAIN           1..355
FT                   /note="D-alanine--D-alanine ligase"
FT                   /id="PRO_1000030478"
FT   DOMAIN          143..350
FT                   /note="ATP-grasp"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT   BINDING         178..233
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT   BINDING         303
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT   BINDING         317
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT   BINDING         317
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT   BINDING         319
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
SQ   SEQUENCE   355 AA;  40279 MW;  B2E6178D732D9CBF CRC64;
     MIGEKKKCIG LIFGGHSNEH EVSISSAKTV FKAFKAQINR ERFTVKAFYI NKYGDWLDSD
     ISEKILTGEI ENYKTKKQEI FNQEKINFLD GIEFQNIDVW FPLLHGFNGE DGSIHGLIRF
     TKKPLVGCGI IGSALGMDKI LMKTIFSNHK LPQVNYLVFQ NEDLNDKQVK NKIINEILKK
     LKFPVFVKPS NSGSSLGISK VKNESEILLA LEKAWGIDPR ILIEEGLEVR EIECGIIGNS
     KLITSEIGEV NYESDWYDYD SKYHSNNKII IPAEIDSKIT NEIKEIAIKS CRALNIFGFA
     RVDFFLEKSS NKILLNEINT IPGFTKNSMF PMLWEASGLK IEQLVAKLVD ISLDL
//