DDL_BIFLD
ID DDL_BIFLD Reviewed; 395 AA.
AC B3DTT9;
DT 22-SEP-2009, integrated into UniProtKB/Swiss-Prot.
DT 22-JUL-2008, sequence version 1.
DT 03-AUG-2022, entry version 75.
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}; OrderedLocusNames=BLD_1112;
OS Bifidobacterium longum (strain DJO10A).
OC Bacteria; Actinobacteria; Bifidobacteriales; Bifidobacteriaceae;
OC Bifidobacterium.
OX NCBI_TaxID=205913;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=DJO10A;
RX PubMed=18505588; DOI=10.1186/1471-2164-9-247;
RA Lee J.H., Karamychev V.N., Kozyavkin S.A., Mills D., Pavlov A.R.,
RA Pavlova N.V., Polouchine N.N., Richardson P.M., Shakhova V.V.,
RA Slesarev A.I., Weimer B., O'Sullivan D.J.;
RT "Comparative genomic analysis of the gut bacterium Bifidobacterium longum
RT reveals loci susceptible to deletion during pure culture growth.";
RL BMC Genomics 9:247-247(2008).
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; CP000605; ACD98558.1; -; Genomic_DNA.
DR RefSeq; WP_010081636.1; NC_010816.1.
DR AlphaFoldDB; B3DTT9; -.
DR SMR; B3DTT9; -.
DR EnsemblBacteria; ACD98558; ACD98558; BLD_1112.
DR KEGG; blj:BLD_1112; -.
DR HOGENOM; CLU_039268_0_1_11; -.
DR OMA; NTTPGMT; -.
DR UniPathway; UPA00219; -.
DR Proteomes; UP000002419; 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; 3.30.1490.20; -; 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 Pfam; PF07478; Dala_Dala_lig_C; 1.
DR Pfam; PF01820; Dala_Dala_lig_N; 1.
DR PIRSF; PIRSF039102; Ddl/VanB; 1.
DR SUPFAM; SSF52440; SSF52440; 1.
DR TIGRFAMs; TIGR01205; D_ala_D_alaTIGR; 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.
FT CHAIN 1..395
FT /note="D-alanine--D-alanine ligase"
FT /id="PRO_1000202194"
FT DOMAIN 172..391
FT /note="ATP-grasp"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT BINDING 204..266
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT BINDING 345
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT BINDING 358
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT BINDING 358
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT BINDING 360
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
SQ SEQUENCE 395 AA; 42397 MW; D062392B3C4665CF CRC64;
MAKKRVVVLY GGRADEHSIS CISTAGVLGA MDTERFEPIP VGITKDGKWI INGEDPRGWN
LDGGELPTVK ITPESRPVML DPSRGQDGFF IGEPSHINSA DSGFGTSFVS MSDPEMHHVL
TSLGHVDAVL PVLHGPYGED GTVQGLLEMM GVPYVGCGVF ASAACMDKHY TKVVLDAAGI
PTAPGVTVDA RNFTAADVLA EIEDAGLTYP LFVKPSRAGS SFGVTKVEKA DDRETQQDRL
AAAIATAGEH DWKVLVEQGI DGREIECAVL CPKAGDEPEA SWPGEIVLDH QNDDQFYDFD
SKYMDASASH VEVPANLPVS VLEDVRDVAR RAFKAVDGVG LSRVDTFVTP DGTVMVNEIN
TMPGFTPISM YPKAWDATGV SYTELITRLI EGVLR
