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
//