ID A0A345YDL1_9SPHN Unreviewed; 324 AA.
AC A0A345YDL1;
DT 07-NOV-2018, integrated into UniProtKB/TrEMBL.
DT 07-NOV-2018, sequence version 1.
DT 27-MAR-2024, entry version 25.
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=DVR09_06345 {ECO:0000313|EMBL:AXK42013.1};
OS Erythrobacter aureus.
OC Bacteria; Pseudomonadota; Alphaproteobacteria; Sphingomonadales;
OC Erythrobacteraceae; Erythrobacter/Porphyrobacter group; Erythrobacter.
OX NCBI_TaxID=2182384 {ECO:0000313|EMBL:AXK42013.1, ECO:0000313|Proteomes:UP000254508};
RN [1] {ECO:0000313|Proteomes:UP000254508}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=YH-07 {ECO:0000313|Proteomes:UP000254508};
RA Tang T., Liu Q., Sun X.;
RT "Genome sequence of Erythrobacter strain YH-07, an antagonistic bacterium
RT isolated from Yellow Sea.";
RL Submitted (JUL-2018) 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; CP031357; AXK42013.1; -; Genomic_DNA.
DR AlphaFoldDB; A0A345YDL1; -.
DR KEGG; err:DVR09_06345; -.
DR OrthoDB; 9813261at2; -.
DR UniPathway; UPA00219; -.
DR Proteomes; UP000254508; 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: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:SF0; D-ALANINE-D-ALANINE LIGASE FAMILY; 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}; Reference proteome {ECO:0000313|Proteomes:UP000254508}.
FT DOMAIN 105..309
FT /note="ATP-grasp"
FT /evidence="ECO:0000259|PROSITE:PS50975"
FT BINDING 260
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000256|PIRSR:PIRSR039102-3"
FT BINDING 276
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000256|PIRSR:PIRSR039102-3"
FT BINDING 276
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000256|PIRSR:PIRSR039102-3"
FT BINDING 278
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000256|PIRSR:PIRSR039102-3"
SQ SEQUENCE 324 AA; 34923 MW; 6506EFC93538D374 CRC64;
MTDLPKLHIA VLMGGWANER PVSLMSGEGV AKALEERGHT VSRIDMDRQV AARIAEAAPD
VVFNALHGVP GEDGSVQGML DLMGIAYTHS GLATSVIAID KQLTKQALVP HGIPMPGGRI
VKSADLFERD PMPRPYVLKP VNEGSSVGVA IVTDEGNYGN PIARDAKGPW QDFAELLAEP
FIKGREMTTA VVDFEDGPRA LAVTELKPKS GFYDFDAKYT DGMTDHVCPA EIPANIEKLC
LDYALKAHRL LGCRGTSRTD FRWDEEQGEE GLFILETNTQ PGMTPLSLVP EQGRHAGIEY
GELCELVVAA ALRHHAAKSG DGDG
//
