ID   Q39JW8_BURL3            Unreviewed;       313 AA.
AC   Q39JW8;
DT   22-NOV-2005, integrated into UniProtKB/TrEMBL.
DT   22-NOV-2005, sequence version 1.
DT   27-MAR-2024, entry version 124.
DE   RecName: Full=D-alanine--D-alanine ligase {ECO:0000256|ARBA:ARBA00012216, ECO:0000256|HAMAP-Rule:MF_00047};
DE            EC=6.3.2.4 {ECO:0000256|ARBA:ARBA00012216, 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   OrderedLocusNames=Bcep18194_A3647 {ECO:0000313|EMBL:ABB07248.1};
GN   ORFNames=BLA14095_04102 {ECO:0000313|EMBL:VWB88139.1}, BLA15816_04484
GN   {ECO:0000313|EMBL:VWB93092.1}, BLA15945_05987
GN   {ECO:0000313|EMBL:VWC22523.1}, BLA18109_06531
GN   {ECO:0000313|EMBL:VWD29308.1}, BLA18110_07898
GN   {ECO:0000313|EMBL:VWD53956.1}, BLA18112_05628
GN   {ECO:0000313|EMBL:VWD24921.1}, BLA50215_04552
GN   {ECO:0000313|EMBL:VWD29526.1}, BLA6860_02429
GN   {ECO:0000313|EMBL:VWB52895.1}, BLA6992_03825
GN   {ECO:0000313|EMBL:VWM10123.1};
OS   Burkholderia lata (strain ATCC 17760 / DSM 23089 / LMG 22485 / NCIMB 9086 /
OS   R18194 / 383).
OC   Bacteria; Pseudomonadota; Betaproteobacteria; Burkholderiales;
OC   Burkholderiaceae; Burkholderia; Burkholderia cepacia complex.
OX   NCBI_TaxID=482957 {ECO:0000313|EMBL:ABB07248.1, ECO:0000313|Proteomes:UP000002705};
RN   [1] {ECO:0000313|Proteomes:UP000002705}
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC 17760 / DSM 23089 / LMG 22485 / NCIMB 9086 / R18194 / 383
RC   {ECO:0000313|Proteomes:UP000002705};
RG   US DOE Joint Genome Institute;
RA   Copeland A., Lucas S., Lapidus A., Barry K., Detter J.C., Glavina T.,
RA   Hammon N., Israni S., Pitluck S., Chain P., Malfatti S., Shin M.,
RA   Vergez L., Schmutz J., Larimer F., Land M., Kyrpides N., Lykidis A.,
RA   Richardson P.;
RT   "Complete sequence of chromosome 1 of Burkholderia sp. 383.";
RL   Submitted (OCT-2005) to the EMBL/GenBank/DDBJ databases.
RN   [2] {ECO:0000313|EMBL:ABB07248.1}
RP   NUCLEOTIDE SEQUENCE.
RC   STRAIN=383 {ECO:0000313|EMBL:ABB07248.1};
RG   US DOE Joint Genome Institute;
RA   Copeland A., Lucas S., Lapidus A., Barry K., Detter J.C., Glavina T.,
RA   Hammon N., Israni S., Pitluck S., Chain P., Malfatti S., Shin M.,
RA   Vergez L., Schmutz J., Larimer F., Land M., Kyrpides N., Lykidis A.,
RA   Richardson P.;
RT   "Complete sequence of chromosome 1 of Burkholderia sp. 383.";
RL   Submitted (JAN-2009) to the EMBL/GenBank/DDBJ databases.
RN   [3] {ECO:0000313|Proteomes:UP000494126, ECO:0000313|Proteomes:UP000494129}
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=LMG 14095 {ECO:0000313|EMBL:VWB88139.1}, LMG 6860t1
RC   {ECO:0000313|EMBL:VWB52895.1}, LMG 6992 {ECO:0000313|EMBL:VWM10123.1,
RC   ECO:0000313|Proteomes:UP000494177}, R-15816
RC   {ECO:0000313|EMBL:VWB93092.1}, R-15945 {ECO:0000313|EMBL:VWC22523.1},
RC   R-18109 {ECO:0000313|EMBL:VWD29308.1}, R-18110
RC   {ECO:0000313|EMBL:VWD53956.1}, R-18112 {ECO:0000313|EMBL:VWD24921.1},
RC   and R-50215 {ECO:0000313|EMBL:VWD29526.1};
RA   Depoorter E.;
RL   Submitted (SEP-2019) to the EMBL/GenBank/DDBJ databases.
CC   -!- FUNCTION: Cell wall formation. {ECO:0000256|ARBA:ARBA00003921,
CC       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|ARBA:ARBA00000236, ECO:0000256|HAMAP-
CC         Rule:MF_00047};
CC   -!- COFACTOR:
CC       Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC         Evidence={ECO:0000256|PIRSR:PIRSR039102-3};
CC       Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC         Evidence={ECO:0000256|PIRSR:PIRSR039102-3};
CC       Note=Binds 2 magnesium or manganese ions per subunit.
CC       {ECO:0000256|PIRSR:PIRSR039102-3};
CC   -!- COFACTOR:
CC       Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC         Evidence={ECO:0000256|ARBA:ARBA00001936};
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; CP000151; ABB07248.1; -; Genomic_DNA.
DR   EMBL; CABVPZ010000012; VWB52895.1; -; Genomic_DNA.
DR   EMBL; CABVQE010000023; VWB88139.1; -; Genomic_DNA.
DR   EMBL; CABVPS010000017; VWB93092.1; -; Genomic_DNA.
DR   EMBL; CABVPU010000029; VWC22523.1; -; Genomic_DNA.
DR   EMBL; CABVQI010000021; VWD24921.1; -; Genomic_DNA.
DR   EMBL; CABVQH010000031; VWD29308.1; -; Genomic_DNA.
DR   EMBL; CABVQP010000017; VWD29526.1; -; Genomic_DNA.
DR   EMBL; CABVQK010000029; VWD53956.1; -; Genomic_DNA.
DR   EMBL; CABWIJ010000008; VWM10123.1; -; Genomic_DNA.
DR   RefSeq; WP_011350841.1; NZ_CADFCT010000005.1.
DR   AlphaFoldDB; Q39JW8; -.
DR   GeneID; 45093561; -.
DR   KEGG; bur:Bcep18194_A3647; -.
DR   PATRIC; fig|482957.22.peg.501; -.
DR   HOGENOM; CLU_039268_1_2_4; -.
DR   UniPathway; UPA00219; -.
DR   Proteomes; UP000002705; Chromosome 1.
DR   Proteomes; UP000494126; Unassembled WGS sequence.
DR   Proteomes; UP000494129; Unassembled WGS sequence.
DR   Proteomes; UP000494169; Unassembled WGS sequence.
DR   Proteomes; UP000494174; Unassembled WGS sequence.
DR   Proteomes; UP000494177; Unassembled WGS sequence.
DR   Proteomes; UP000494247; Unassembled WGS sequence.
DR   Proteomes; UP000494250; Unassembled WGS sequence.
DR   Proteomes; UP000494260; Unassembled WGS sequence.
DR   Proteomes; UP000494274; Unassembled WGS sequence.
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: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: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   PIRSF; PIRSF039102; Ddl/VanB; 2.
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 {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   Magnesium {ECO:0000256|PIRSR:PIRSR039102-3};
KW   Manganese {ECO:0000256|PIRSR:PIRSR039102-3};
KW   Metal-binding {ECO:0000256|PIRSR:PIRSR039102-3};
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          108..308
FT                   /note="ATP-grasp"
FT                   /evidence="ECO:0000259|PROSITE:PS50975"
FT   BINDING         262
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000256|PIRSR:PIRSR039102-3"
FT   BINDING         275
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000256|PIRSR:PIRSR039102-3"
FT   BINDING         275
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000256|PIRSR:PIRSR039102-3"
FT   BINDING         277
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000256|PIRSR:PIRSR039102-3"
SQ   SEQUENCE   313 AA;  33237 MW;  53A8BEC7856A9967 CRC64;
     MSGIDPKRFG KVAVLFGGES SEREVSLTSG KLVLQGLRDA GIDAHPFDPA ERPLAALKDE
     GFVRAFNALH GGYGENGQIQ GALDFYGIRY TGSGVLGSAL GLDKFRTKLV WQQTGVPTPP
     FETVLRGDDL AARATDIVAK LGLPLFVKPA SEGSSVAVLK VKTADALPAA LAEAATHDPI
     VIVEKSIEGG GEYTACIAGD LDLPVIKIVP AGEFYDYHAK YIADDTQYLI PCGLPADKEA
     ELKRVARRAF DVLGCTDWGR ADFMLDADGN AYFLEVNTAP GMTDHSLPPK AARAVGISYS
     ELVVKVLSLT LND
//