ID   Q2N4T5_HELPX            Unreviewed;       347 AA.
AC   Q2N4T5;
DT   07-FEB-2006, integrated into UniProtKB/TrEMBL.
DT   07-FEB-2006, sequence version 1.
DT   27-MAR-2024, entry version 107.
DE   RecName: Full=D-alanine--D-alanine ligase {ECO:0000256|HAMAP-Rule:MF_00047};
DE            EC=6.3.2.4 {ECO:0000256|HAMAP-Rule:MF_00047};
DE   AltName: Full=D-Ala-D-Ala ligase {ECO:0000256|HAMAP-Rule:MF_00047};
DE   AltName: Full=D-alanylalanine synthetase {ECO:0000256|HAMAP-Rule:MF_00047};
GN   Name=ddl {ECO:0000256|HAMAP-Rule:MF_00047,
GN   ECO:0000313|EMBL:BBI24377.1};
GN   ORFNames=HPPMSS1_c00834 {ECO:0000313|EMBL:BBI24377.1};
OS   Helicobacter pylori (Campylobacter pylori).
OC   Bacteria; Campylobacterota; Epsilonproteobacteria; Campylobacterales;
OC   Helicobacteraceae; Helicobacter.
OX   NCBI_TaxID=210 {ECO:0000313|EMBL:AAY56773.1};
RN   [1] {ECO:0000313|EMBL:AAY56773.1}
RP   NUCLEOTIDE SEQUENCE.
RC   STRAIN=SS1 {ECO:0000313|EMBL:AAY56773.1};
RA   Wu D., Han C., Jiang H., Shen X.;
RL   Submitted (APR-2005) to the EMBL/GenBank/DDBJ databases.
RN   [2] {ECO:0007829|PDB:2PVP}
RP   X-RAY CRYSTALLOGRAPHY (2.40 ANGSTROMS).
RX   PubMed=18320587; DOI=10.1002/prot.22009;
RA   Wu D., Zhang L., Kong Y., Du J., Chen S., Chen J., Ding J., Jiang H.,
RA   Shen X.;
RT   "Enzymatic characterization and crystal structure analysis of the D-
RT   alanine-D-alanine ligase from Helicobacter pylori.";
RL   Proteins 72:1148-1160(2008).
RN   [3] {ECO:0000313|EMBL:BBI24377.1, ECO:0000313|Proteomes:UP000289502}
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=PMSS1 {ECO:0000313|EMBL:BBI24377.1,
RC   ECO:0000313|Proteomes:UP000289502};
RA   Mimuro H., Ogura Y., Katsura K., Hayashi T.;
RT   "Whole genome shotgun sequence of Helicobacter pylori strain PMSS1.";
RL   Submitted (AUG-2016) to the EMBL/GenBank/DDBJ databases.
CC   -!- FUNCTION: Cell wall formation. {ECO:0000256|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:0000256|HAMAP-Rule:MF_00047};
CC   -!- PATHWAY: Cell wall biogenesis; peptidoglycan biosynthesis.
CC       {ECO:0000256|HAMAP-Rule:MF_00047}.
CC   -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000256|HAMAP-Rule:MF_00047}.
CC   -!- SIMILARITY: Belongs to the D-alanine--D-alanine ligase family.
CC       {ECO:0000256|ARBA:ARBA00010871, ECO:0000256|HAMAP-Rule:MF_00047}.
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DR   EMBL; DQ009011; AAY56773.1; -; Genomic_DNA.
DR   EMBL; AP017633; BBI24377.1; -; Genomic_DNA.
DR   RefSeq; WP_077232636.1; NZ_CP109885.1.
DR   PDB; 2PVP; X-ray; 2.40 A; A/B=1-347.
DR   PDBsum; 2PVP; -.
DR   AlphaFoldDB; Q2N4T5; -.
DR   SMR; Q2N4T5; -.
DR   BRENDA; 6.3.2.4; 2604.
DR   UniPathway; UPA00219; -.
DR   EvolutionaryTrace; Q2N4T5; -.
DR   Proteomes; UP000289502; Chromosome.
DR   GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR   GO; GO:0005524; F:ATP binding; IEA:UniProtKB-UniRule.
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: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; 3.40.50.20; -; 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   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 {ECO:0007829|PDB:2PVP};
KW   ATP-binding {ECO:0000256|ARBA:ARBA00022840, ECO:0000256|PROSITE-
KW   ProRule:PRU00409};
KW   Cell shape {ECO:0000256|ARBA:ARBA00022960, ECO:0000256|HAMAP-
KW   Rule:MF_00047};
KW   Cell wall biogenesis/degradation {ECO:0000256|ARBA:ARBA00023316,
KW   ECO:0000256|HAMAP-Rule:MF_00047};
KW   Cytoplasm {ECO:0000256|HAMAP-Rule:MF_00047};
KW   Ligase {ECO:0000256|ARBA:ARBA00022598, ECO:0000256|HAMAP-Rule:MF_00047};
KW   Nucleotide-binding {ECO:0000256|ARBA:ARBA00022741, ECO:0000256|PROSITE-
KW   ProRule:PRU00409};
KW   Peptidoglycan synthesis {ECO:0000256|ARBA:ARBA00022984, ECO:0000256|HAMAP-
KW   Rule:MF_00047}.
FT   DOMAIN          134..332
FT                   /note="ATP-grasp"
FT                   /evidence="ECO:0000259|PROSITE:PS50975"
SQ   SEQUENCE   347 AA;  39740 MW;  76FF9FF841429903 CRC64;
     MEFCVLFGGA SFEHEISIVS AIALKGVLKD RIKYFIFLDE NHHFYLIEES NMHSKYFAQI
     KEKKLPPLIL THNGLLKNSF LGAKIIELPL VINLVHGGDG EDGKLASLLE FYRIAFIGPR
     IEASVLSYNK YLTKLYAKDL GIKTLDYVLL NEKNRANALD LMNFNFPFIV KPSNAGSSLG
     VNVVKEEKEL IYALDSAFEY SKEVLIEPFI QGVKEYNLAG CKIKKDFCFS YIEEPNKQEF
     LDFKQKYLDF SRNKAPKASL SNALEEQLKE NFKKLYSDLF DGAIIRCDFF VIENEVYLNE
     INPIPGSLAN YLFDDFKTTL ENLAQSLPKT PKIQIKNSYL LQIQKNK
//