DDL_NATTJ
ID DDL_NATTJ Reviewed; 365 AA.
AC B2A2Z6;
DT 24-MAR-2009, integrated into UniProtKB/Swiss-Prot.
DT 20-MAY-2008, sequence version 1.
DT 03-AUG-2022, entry version 79.
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=Nther_0011;
OS Natranaerobius thermophilus (strain ATCC BAA-1301 / DSM 18059 /
OS JW/NM-WN-LF).
OC Bacteria; Firmicutes; Clostridia; Natranaerobiales; Natranaerobiaceae;
OC Natranaerobius.
OX NCBI_TaxID=457570;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC BAA-1301 / DSM 18059 / JW/NM-WN-LF;
RG US DOE Joint Genome Institute;
RA Copeland A., Lucas S., Lapidus A., Glavina del Rio T., Dalin E., Tice H.,
RA Bruce D., Goodwin L., Pitluck S., Chertkov O., Brettin T., Detter J.C.,
RA Han C., Kuske C.R., Schmutz J., Larimer F., Land M., Hauser L.,
RA Kyrpides N., Lykidis A., Mesbah N.M., Wiegel J.;
RT "Complete sequence of chromosome of Natranaerobius thermophilus JW/NM-WN-
RT LF.";
RL Submitted (APR-2008) to the EMBL/GenBank/DDBJ databases.
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; CP001034; ACB83610.1; -; Genomic_DNA.
DR RefSeq; WP_012446501.1; NC_010718.1.
DR AlphaFoldDB; B2A2Z6; -.
DR SMR; B2A2Z6; -.
DR STRING; 457570.Nther_0011; -.
DR PRIDE; B2A2Z6; -.
DR EnsemblBacteria; ACB83610; ACB83610; Nther_0011.
DR KEGG; nth:Nther_0011; -.
DR eggNOG; COG1181; Bacteria.
DR HOGENOM; CLU_039268_0_0_9; -.
DR OMA; NTTPGMT; -.
DR OrthoDB; 764798at2; -.
DR UniPathway; UPA00219; -.
DR Proteomes; UP000001683; 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; Reference proteome.
FT CHAIN 1..365
FT /note="D-alanine--D-alanine ligase"
FT /id="PRO_1000091196"
FT DOMAIN 140..346
FT /note="ATP-grasp"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT BINDING 173..228
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT BINDING 299
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT BINDING 313
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT BINDING 313
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT BINDING 315
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
SQ SEQUENCE 365 AA; 41090 MW; 9BB79AE18B548A86 CRC64;
MKKLRVGVLF GGRSGEHEVS LKSANSILNA LDRELFEVIP IGIRKNGEWI SGEAPLEELE
TGIKNQGNYA VSILPDPSKK VLWKLDPFEK ISEIDLIFPV LHGTFGEDGT VQGFLDLCGI
PYVGSGVLGS SLAMDKVMMK KILRRHGLQV ANYYSFKRSE WEQDRDEIIF SIEKQLSYPI
FVKPANLGSS VGISKVKNRE ELIQGIDLAV KYDMKCLAEE FIPGKEIELS ILGNDNPKTS
VPGEIIPANE FYDYNAKYIN NKSKLVIPAP LSETLKTKIE DMGVEAFRVL DCYGLSRVDY
FVLEDQEEVY INEINTMPGF TEISMYPKLW TESGLSYSQL LTDLIYLALA RQQEKDRNST
DFSES
