ID   DDL_ENTHA               Reviewed;         358 AA.
AC   Q47827; I6SB04;
DT   01-NOV-1997, integrated into UniProtKB/Swiss-Prot.
DT   09-JAN-2013, sequence version 2.
DT   24-JAN-2024, entry version 123.
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=EHR_03915;
OS   Enterococcus hirae (strain ATCC 9790 / DSM 20160 / JCM 8729 / LMG 6399 /
OS   NBRC 3181 / NCIMB 6459 / NCDO 1258 / NCTC 12367 / WDCM 00089 / R).
OC   Bacteria; Bacillota; Bacilli; Lactobacillales; Enterococcaceae;
OC   Enterococcus.
OX   NCBI_TaxID=768486;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC   STRAIN=ATCC 9790 / DSM 20160 / JCM 8729 / LMG 6399 / NBRC 3181 / NCIMB
RC   6459 / NCDO 1258 / NCTC 12367 / WDCM 00089 / R;
RX   PubMed=8662022; DOI=10.1007/bf02338803;
RA   Evers S., Casadewall B., Charles M., Dutka-Malen S., Galimand M.,
RA   Courvalin P.;
RT   "Evolution of structure and substrate specificity in D-alanine:D-alanine
RT   ligases and related enzymes.";
RL   J. Mol. Evol. 42:706-712(1996).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC 9790 / DSM 20160 / JCM 8729 / LMG 6399 / NBRC 3181 / NCIMB
RC   6459 / NCDO 1258 / NCTC 12367 / WDCM 00089 / R;
RX   PubMed=22933757; DOI=10.1128/jb.01075-12;
RA   Gaechter T., Wunderlin C., Schmidheini T., Solioz M.;
RT   "Genome sequence of Enterococcus hirae (Streptococcus faecalis) ATCC 9790,
RT   a model organism for the study of ion transport, bioenergetics, and copper
RT   homeostasis.";
RL   J. Bacteriol. 194:5126-5127(2012).
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; U39788; AAB17904.1; -; Genomic_DNA.
DR   EMBL; CP003504; AFM69753.1; -; Genomic_DNA.
DR   RefSeq; WP_010736859.1; NZ_KB946222.1.
DR   AlphaFoldDB; Q47827; -.
DR   SMR; Q47827; -.
DR   KEGG; ehr:EHR_03915; -.
DR   eggNOG; COG1181; Bacteria.
DR   HOGENOM; CLU_039268_0_0_9; -.
DR   OrthoDB; 9813261at2; -.
DR   UniPathway; UPA00219; -.
DR   Proteomes; UP000002895; 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; 3.40.50.20; -; 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: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..358
FT                   /note="D-alanine--D-alanine ligase"
FT                   /id="PRO_0000177823"
FT   DOMAIN          136..341
FT                   /note="ATP-grasp"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT   BINDING         169..224
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT   BINDING         295
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT   BINDING         308
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT   BINDING         308
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT   BINDING         310
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT   CONFLICT        355
FT                   /note="E -> N (in Ref. 1; AAB17904)"
FT                   /evidence="ECO:0000305"
SQ   SEQUENCE   358 AA;  40143 MW;  225CF997F0A979F1 CRC64;
     MKITLLYGGR SAEHDVSVLS AFSVLNAIYY TYYQVQLIFI SKEGQWVKGP LLTEKPTSKE
     DLHLTWDPSG KVTDGFTGRV INPGEIKEEG TIVFPVLHGP NGEDGTIQGF LETLNLPYVG
     AGVLTSACAM DKIMTKYILQ AAGVPQVPYV PVLKNQWKEN PKKIFDQCEG SLLYPMFVKP
     ANMGSSVGIS KAENREELQN ALALAYQYDS RAIVEQGIEA REIEVAVLGN EDVRTTLPGE
     VVKDVAFYDY DAKYINNKIE MQIPAEVPEE VYQKAQEYAK IAYTMLGGSG LSRCDFFLTN
     KNELFLNELN TMPGFTQFSM YPLLWENMGL KYGDLIEELI QLGINRFNQR QGFFEANE
//