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Database: UniProt
Entry: J2L261_9SPHN
LinkDB: J2L261_9SPHN
Original site: J2L261_9SPHN 
ID   J2L261_9SPHN            Unreviewed;       313 AA.
AC   J2L261;
DT   03-OCT-2012, integrated into UniProtKB/TrEMBL.
DT   03-OCT-2012, sequence version 1.
DT   24-JAN-2024, entry version 60.
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   ORFNames=PMI04_02955 {ECO:0000313|EMBL:EJK81451.1};
OS   Sphingobium sp. AP49.
OC   Bacteria; Pseudomonadota; Alphaproteobacteria; Sphingomonadales;
OC   Sphingomonadaceae; Sphingobium.
OX   NCBI_TaxID=1144307 {ECO:0000313|EMBL:EJK81451.1, ECO:0000313|Proteomes:UP000006480};
RN   [1] {ECO:0000313|EMBL:EJK81451.1, ECO:0000313|Proteomes:UP000006480}
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=AP49 {ECO:0000313|EMBL:EJK81451.1,
RC   ECO:0000313|Proteomes:UP000006480};
RX   PubMed=23045501; DOI=10.1128/JB.01243-12;
RA   Brown S.D., Utturkar S.M., Klingeman D.M., Johnson C.M., Martin S.L.,
RA   Land M.L., Lu T.Y., Schadt C.W., Doktycz M.J., Pelletier D.A.;
RT   "Twenty-one genome sequences from Pseudomonas species and 19 genome
RT   sequences from diverse bacteria isolated from the rhizosphere and
RT   endosphere of Populus deltoides.";
RL   J. Bacteriol. 194:5991-5993(2012).
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|ARBA:ARBA00004496,
CC       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}.
CC   -!- CAUTION: The sequence shown here is derived from an EMBL/GenBank/DDBJ
CC       whole genome shotgun (WGS) entry which is preliminary data.
CC       {ECO:0000313|EMBL:EJK81451.1}.
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DR   EMBL; AJVL01000062; EJK81451.1; -; Genomic_DNA.
DR   RefSeq; WP_007711637.1; NZ_CP124576.1.
DR   AlphaFoldDB; J2L261; -.
DR   STRING; 1144307.PMI04_02955; -.
DR   PATRIC; fig|1144307.3.peg.2717; -.
DR   eggNOG; COG1181; Bacteria.
DR   OrthoDB; 9813261at2; -.
DR   UniPathway; UPA00219; -.
DR   Proteomes; UP000006480; 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|ARBA:ARBA00022490, 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          104..304
FT                   /note="ATP-grasp"
FT                   /evidence="ECO:0000259|PROSITE:PS50975"
FT   BINDING         255
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000256|PIRSR:PIRSR039102-3"
FT   BINDING         271
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000256|PIRSR:PIRSR039102-3"
FT   BINDING         271
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000256|PIRSR:PIRSR039102-3"
FT   BINDING         273
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;  33570 MW;  598F70BE6A53C239 CRC64;
     MSRGPWHVAV LMGGWSAERP VSLSSGEGVA KALESRGHRV TRIDMDRDVA ARLAETKADV
     VFNALHGVPG EDGTVQGMMD LMGLTYTHSG LATSVIAIDK QLTKQALVPH GIPMPGGHIV
     TSESLYAGDP LPRPYVLKPV NEGSSVGVAI VTAEGNYGNP IARDSVGPWQ EFPELLAEPY
     IRGRELTTAV LGDEALLVTE LRPKSGFYDF DAKYTDGMTE HVCPAEIPDE ITQACKAIAL
     QAHQLLGCKG ASRSDFRWDD SQGIEGLFLL EVNTQPGMTP LSLVPEQAKK LGIDYAELVE
     RIVEDALKGA NDG
//
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