ID A0A2N5EM86_9GAMM Unreviewed; 365 AA.
AC A0A2N5EM86;
DT 25-APR-2018, integrated into UniProtKB/TrEMBL.
DT 25-APR-2018, sequence version 1.
DT 28-JAN-2026, entry version 33.
DE RecName: Full=D-alanine--D-alanine ligase {ECO:0000256|HAMAP-Rule:MF_00047};
DE EC=6.3.2.4 {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=CYR34_12265 {ECO:0000313|EMBL:PLR48910.1};
OS Chimaeribacter arupi.
OC Bacteria; Pseudomonadati; Pseudomonadota; Gammaproteobacteria;
OC Enterobacterales; Yersiniaceae; Chimaeribacter.
OX NCBI_TaxID=2060066 {ECO:0000313|EMBL:PLR48910.1, ECO:0000313|Proteomes:UP000234626};
RN [1] {ECO:0000313|EMBL:PLR48910.1, ECO:0000313|Proteomes:UP000234626}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=2016Iso1 {ECO:0000313|EMBL:PLR48910.1,
RC ECO:0000313|Proteomes:UP000234626};
RA Rossi A., Fisher M.;
RT "Characterization of six clinical isolates of Enterochimera gen. nov., a
RT novel genus of the Yersiniaciae family and the three species Enterochimera
RT arupensis sp. nov., Enterochimera coloradensis sp. nov, and Enterochimera
RT californica sp. nov.";
RL Submitted (DEC-2017) 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=2 D-alanine + ATP = D-alanyl-D-alanine + ADP + phosphate +
CC H(+); Xref=Rhea:RHEA:11224, ChEBI:CHEBI:15378, ChEBI:CHEBI:30616,
CC ChEBI:CHEBI:43474, ChEBI:CHEBI:57416, ChEBI:CHEBI:57822,
CC ChEBI:CHEBI:456216; EC=6.3.2.4;
CC Evidence={ECO:0000256|ARBA:ARBA00047614, 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|ARBA:ARBA00004752, ECO:0000256|HAMAP-Rule:MF_00047}.
CC -!- PATHWAY: Glycan biosynthesis. {ECO:0000256|ARBA:ARBA00060592}.
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:PLR48910.1}.
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DR EMBL; PJZK01000011; PLR48910.1; -; Genomic_DNA.
DR RefSeq; WP_072926112.1; NZ_JAWJZE010000021.1.
DR AlphaFoldDB; A0A2N5EM86; -.
DR OrthoDB; 9813261at2; -.
DR UniPathway; UPA00219; -.
DR Proteomes; UP000234626; Unassembled WGS sequence.
DR GO; GO:0005829; C:cytosol; IEA:TreeGrafter.
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 FunFam; 3.30.1490.20:FF:000007; D-alanine--D-alanine ligase; 1.
DR FunFam; 3.30.470.20:FF:000008; D-alanine--D-alanine ligase; 1.
DR FunFam; 3.40.50.20:FF:000015; D-alanine--D-alanine ligase; 1.
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 NCBIfam; NF002378; PRK01372.1; 1.
DR NCBIfam; NF002525; PRK01966.1-1; 1.
DR NCBIfam; NF002528; PRK01966.1-4; 1.
DR PANTHER; PTHR23132; D-ALANINE--D-ALANINE LIGASE; 1.
DR PANTHER; PTHR23132:SF25; D-ALANINE--D-ALANINE LIGASE A; 1.
DR Pfam; PF07478; Dala_Dala_lig_C; 1.
DR Pfam; PF01820; Dala_Dala_lig_N; 1.
DR PIRSF; PIRSF039102; Ddl/VanB; 1.
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|ARBA:ARBA00022842, ECO:0000256|PIRSR:PIRSR039102-3};
KW Manganese {ECO:0000256|ARBA:ARBA00023211, ECO:0000256|PIRSR:PIRSR039102-3};
KW Metal-binding {ECO:0000256|ARBA:ARBA00022723,
KW ECO:0000256|PIRSR:PIRSR039102-3};
KW Nucleotide-binding {ECO:0000256|ARBA:ARBA00022741,
KW ECO:0000256|PIRSR:PIRSR039102-2};
KW Peptidoglycan synthesis {ECO:0000256|ARBA:ARBA00022984, ECO:0000256|HAMAP-
KW Rule:MF_00047}; Reference proteome {ECO:0000313|Proteomes:UP000234626}.
FT DOMAIN 145..348
FT /note="ATP-grasp"
FT /evidence="ECO:0000259|PROSITE:PS50975"
FT ACT_SITE 16
FT /evidence="ECO:0000256|PIRSR:PIRSR039102-1"
FT ACT_SITE 191
FT /evidence="ECO:0000256|PIRSR:PIRSR039102-1"
FT ACT_SITE 326
FT /evidence="ECO:0000256|PIRSR:PIRSR039102-1"
FT BINDING 141
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000256|PIRSR:PIRSR039102-2"
FT BINDING 183..185
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000256|PIRSR:PIRSR039102-2"
FT BINDING 191..192
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000256|PIRSR:PIRSR039102-2"
FT BINDING 221..228
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000256|PIRSR:PIRSR039102-2"
FT BINDING 302
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000256|PIRSR:PIRSR039102-3"
FT BINDING 314..315
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000256|PIRSR:PIRSR039102-2"
FT BINDING 315
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000256|PIRSR:PIRSR039102-3"
FT BINDING 315
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000256|PIRSR:PIRSR039102-3"
FT BINDING 317
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000256|PIRSR:PIRSR039102-3"
SQ SEQUENCE 365 AA; 39782 MW; 5DB8AAA678E004B1 CRC64;
MAKIRVGVIF GGKSAEHEVS LQSAKNIVDA MDKERFEVTL LGIDKQGQWH VSDAAHYLQH
ADDPARIALN PSQRNVALIP GQQQHQLIES RDASALAQLD VIFPIVHGTL GEDGSLQGLL
RMANIPFVGA GVLGSALSMD KDVTKRLLRD AGLAVAPFVT LTRRNAAQHD FARVSEKLGL
PLFIKPANQG SSVGVSKVRS AQEYDTALAL AFRYDHKVLV ESAIAGREIE CAVLGNDHPQ
ASVCGEVILQ DEFYAYDTKY INAQGATVAI PADLPPDVND RIRAIAVRAF QVLECSGMAR
VDVFLTNDGE VIINEINTLP GFTNISMYPK LWEASGLAYR DLITQLIELA LERHQADNRL
QSSVR
//
