ID   DDL_HELPY               Reviewed;         347 AA.
AC   P56191;
DT   01-NOV-1997, integrated into UniProtKB/Swiss-Prot.
DT   01-NOV-1997, sequence version 1.
DT   04-NOV-2026, entry version 151.
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}; Synonyms=ddlA;
GN   OrderedLocusNames=HP_0738;
OS   Helicobacter pylori (strain ATCC 700392 / 26695) (Campylobacter pylori).
OC   Bacteria; Pseudomonadati; Campylobacterota; Epsilonproteobacteria;
OC   Campylobacterales; Helicobacteraceae; Helicobacter.
OX   NCBI_TaxID=85962;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC 700392 / 26695;
RX   PubMed=9252185; DOI=10.1038/41483;
RA   Tomb J.-F., White O., Kerlavage A.R., Clayton R.A., Sutton G.G.,
RA   Fleischmann R.D., Ketchum K.A., Klenk H.-P., Gill S.R., Dougherty B.A.,
RA   Nelson K.E., Quackenbush J., Zhou L., Kirkness E.F., Peterson S.N.,
RA   Loftus B.J., Richardson D.L., Dodson R.J., Khalak H.G., Glodek A.,
RA   McKenney K., FitzGerald L.M., Lee N., Adams M.D., Hickey E.K., Berg D.E.,
RA   Gocayne J.D., Utterback T.R., Peterson J.D., Kelley J.M., Cotton M.D.,
RA   Weidman J.F., Fujii C., Bowman C., Watthey L., Wallin E., Hayes W.S.,
RA   Borodovsky M., Karp P.D., Smith H.O., Fraser C.M., Venter J.C.;
RT   "The complete genome sequence of the gastric pathogen Helicobacter
RT   pylori.";
RL   Nature 388:539-547(1997).
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; AE000511; AAD07784.1; -; Genomic_DNA.
DR   PIR; B64612; B64612.
DR   RefSeq; WP_000393659.1; NC_018939.1.
DR   PDB; 2PVP; X-ray; 2.40 A; A/B=1-347.
DR   AlphaFoldDB; P56191; -.
DR   SMR; P56191; -.
DR   FunCoup; P56191; 236.
DR   IntAct; P56191; 1.
DR   STRING; 85962.HP_0738; -.
DR   PaxDb; 85962-HP_0738; -.
DR   EnsemblBacteria; AAD07784; AAD07784; HP_0738.
DR   KEGG; heo:C694_03790; -.
DR   KEGG; hpy:HP_0738; -.
DR   PATRIC; fig|85962.47.peg.786; -.
DR   eggNOG; COG1181; Bacteria.
DR   InParanoid; P56191; -.
DR   OMA; AACMDKE; -.
DR   OrthoDB; 9813261at2; -.
DR   PhylomeDB; P56191; -.
DR   UniPathway; UPA00219; -.
DR   Proteomes; UP000000429; Chromosome.
DR   GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR   GO; GO:0005524; F:ATP binding; IEA:InterPro.
DR   GO; GO:0008716; F:D-alanine-D-alanine ligase activity; IBA:GO_Central.
DR   GO; GO:0046872; F:metal ion binding; IEA:InterPro.
DR   GO; GO:0009252; P:peptidoglycan biosynthetic process; IEA:UniProtKB-UniRule.
DR   FunFam; 3.40.50.20:FF:000040; D-alanine--D-alanine ligase; 1.
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; NF002527; PRK01966.1-3; 1.
DR   PANTHER; PTHR23132; D-ALANINE--D-ALANINE LIGASE; 1.
DR   PANTHER; PTHR23132:SF23; D-ALANINE--D-ALANINE LIGASE B; 1.
DR   Pfam; PF07478; Dala_Dala_lig_C; 1.
DR   Pfam; PF01820; Dala_Dala_lig_N; 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   1: Evidence at protein level;
KW   3D-structure; ATP-binding; Cell shape; Cell wall biogenesis/degradation;
KW   Cytoplasm; Ligase; Magnesium; Manganese; Metal-binding; Nucleotide-binding;
KW   Peptidoglycan synthesis; Reference proteome.
FT   CHAIN           1..347
FT                   /note="D-alanine--D-alanine ligase"
FT                   /id="PRO_0000177830"
FT   DOMAIN          134..332
FT                   /note="ATP-grasp"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT   BINDING         161..216
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT   BINDING         288
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT   BINDING         300
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT   BINDING         300
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT   BINDING         302
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT   STRAND          3..8
FT                   /evidence="ECO:0007829|PDB:2PVP"
FT   HELIX           14..28
FT                   /evidence="ECO:0007829|PDB:2PVP"
FT   HELIX           29..31
FT                   /evidence="ECO:0007829|PDB:2PVP"
FT   STRAND          32..38
FT                   /evidence="ECO:0007829|PDB:2PVP"
FT   STRAND          44..46
FT                   /evidence="ECO:0007829|PDB:2PVP"
FT   HELIX           49..51
FT                   /evidence="ECO:0007829|PDB:2PVP"
FT   HELIX           54..58
FT                   /evidence="ECO:0007829|PDB:2PVP"
FT   HELIX           60..62
FT                   /evidence="ECO:0007829|PDB:2PVP"
FT   STRAND          68..71
FT                   /evidence="ECO:0007829|PDB:2PVP"
FT   STRAND          74..79
FT                   /evidence="ECO:0007829|PDB:2PVP"
FT   STRAND          82..87
FT                   /evidence="ECO:0007829|PDB:2PVP"
FT   STRAND          90..93
FT                   /evidence="ECO:0007829|PDB:2PVP"
FT   TURN            98..101
FT                   /evidence="ECO:0007829|PDB:2PVP"
FT   HELIX           104..111
FT                   /evidence="ECO:0007829|PDB:2PVP"
FT   STRAND          116..118
FT                   /evidence="ECO:0007829|PDB:2PVP"
FT   HELIX           121..128
FT                   /evidence="ECO:0007829|PDB:2PVP"
FT   HELIX           130..140
FT                   /evidence="ECO:0007829|PDB:2PVP"
FT   STRAND          148..150
FT                   /evidence="ECO:0007829|PDB:2PVP"
FT   TURN            152..154
FT                   /evidence="ECO:0007829|PDB:2PVP"
FT   HELIX           155..157
FT                   /evidence="ECO:0007829|PDB:2PVP"
FT   HELIX           158..161
FT                   /evidence="ECO:0007829|PDB:2PVP"
FT   STRAND          168..174
FT                   /evidence="ECO:0007829|PDB:2PVP"
FT   TURN            177..180
FT                   /evidence="ECO:0007829|PDB:2PVP"
FT   STRAND          182..186
FT                   /evidence="ECO:0007829|PDB:2PVP"
FT   HELIX           190..197
FT                   /evidence="ECO:0007829|PDB:2PVP"
FT   TURN            198..200
FT                   /evidence="ECO:0007829|PDB:2PVP"
FT   STRAND          204..208
FT                   /evidence="ECO:0007829|PDB:2PVP"
FT   STRAND          214..223
FT                   /evidence="ECO:0007829|PDB:2PVP"
FT   STRAND          226..234
FT                   /evidence="ECO:0007829|PDB:2PVP"
FT   TURN            235..238
FT                   /evidence="ECO:0007829|PDB:2PVP"
FT   STRAND          239..241
FT                   /evidence="ECO:0007829|PDB:2PVP"
FT   HELIX           262..276
FT                   /evidence="ECO:0007829|PDB:2PVP"
FT   TURN            277..279
FT                   /evidence="ECO:0007829|PDB:2PVP"
FT   STRAND          285..292
FT                   /evidence="ECO:0007829|PDB:2PVP"
FT   STRAND          295..304
FT                   /evidence="ECO:0007829|PDB:2PVP"
FT   HELIX           306..312
FT                   /evidence="ECO:0007829|PDB:2PVP"
FT   STRAND          313..315
FT                   /evidence="ECO:0007829|PDB:2PVP"
FT   HELIX           316..326
FT                   /evidence="ECO:0007829|PDB:2PVP"
SQ   SEQUENCE   347 AA;  39736 MW;  5F19D9CEE4AE08CF CRC64;
     MEFCVLFGGA SFEHEISIVS AIALKGVLKD RIKYFIFLDE NHHFYLIEES NMHSKYFAQI
     KEKKLPPLIL THNGLLKNSF LGAKIIELPL VINLVHGGDG EDGKLASLLE FYRIAFIGPR
     IEASVLSYNK YLTKLYAKDL GVKTLDHVLL NEKNRANALD LMNFNFPFII KPNNAGSSLG
     VNVVKEEKEL VYALDGAFEY SKEVLIEPFI QGVKEYNLAG CKIKKDFCFS YVEEPNKQEF
     LDFKQKYLDF SRNKAPKANL SNALEEQLKE NFKKLYNDLF DGAIIRCDFF VIKNEVYLNE
     INPIPGSLAN YLFDDFKTTL ENLAQSLPKT PKIQIKNSYL LQIQKNK
//