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Entry: DDL_AGRFC
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ID   DDL_AGRFC               Reviewed;         308 AA.
AC   Q8UDN3;
DT   02-AUG-2002, integrated into UniProtKB/Swiss-Prot.
DT   02-AUG-2002, sequence version 2.
DT   05-DEC-2018, entry version 105.
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=Atu2089;
GN   ORFNames=AGR_C_3788;
OS   Agrobacterium fabrum (strain C58 / ATCC 33970) (Agrobacterium
OS   tumefaciens (strain C58)).
OC   Bacteria; Proteobacteria; Alphaproteobacteria; Rhizobiales;
OC   Rhizobiaceae; Rhizobium/Agrobacterium group; Agrobacterium;
OC   Agrobacterium tumefaciens complex.
OX   NCBI_TaxID=176299;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=C58 / ATCC 33970;
RX   PubMed=11743193; DOI=10.1126/science.1066804;
RA   Wood D.W., Setubal J.C., Kaul R., Monks D.E., Kitajima J.P.,
RA   Okura V.K., Zhou Y., Chen L., Wood G.E., Almeida N.F. Jr., Woo L.,
RA   Chen Y., Paulsen I.T., Eisen J.A., Karp P.D., Bovee D. Sr.,
RA   Chapman P., Clendenning J., Deatherage G., Gillet W., Grant C.,
RA   Kutyavin T., Levy R., Li M.-J., McClelland E., Palmieri A.,
RA   Raymond C., Rouse G., Saenphimmachak C., Wu Z., Romero P., Gordon D.,
RA   Zhang S., Yoo H., Tao Y., Biddle P., Jung M., Krespan W., Perry M.,
RA   Gordon-Kamm B., Liao L., Kim S., Hendrick C., Zhao Z.-Y., Dolan M.,
RA   Chumley F., Tingey S.V., Tomb J.-F., Gordon M.P., Olson M.V.,
RA   Nester E.W.;
RT   "The genome of the natural genetic engineer Agrobacterium tumefaciens
RT   C58.";
RL   Science 294:2317-2323(2001).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=C58 / ATCC 33970;
RX   PubMed=11743194; DOI=10.1126/science.1066803;
RA   Goodner B., Hinkle G., Gattung S., Miller N., Blanchard M.,
RA   Qurollo B., Goldman B.S., Cao Y., Askenazi M., Halling C., Mullin L.,
RA   Houmiel K., Gordon J., Vaudin M., Iartchouk O., Epp A., Liu F.,
RA   Wollam C., Allinger M., Doughty D., Scott C., Lappas C., Markelz B.,
RA   Flanagan C., Crowell C., Gurson J., Lomo C., Sear C., Strub G.,
RA   Cielo C., Slater S.;
RT   "Genome sequence of the plant pathogen and biotechnology agent
RT   Agrobacterium tumefaciens C58.";
RL   Science 294:2323-2328(2001).
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.
CC       {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}.
DR   EMBL; AE007869; AAK87839.2; -; Genomic_DNA.
DR   PIR; AB2833; AB2833.
DR   PIR; F97610; F97610.
DR   RefSeq; NP_355054.2; NC_003062.2.
DR   RefSeq; WP_010972048.1; NC_003062.2.
DR   ProteinModelPortal; Q8UDN3; -.
DR   SMR; Q8UDN3; -.
DR   STRING; 176299.Atu2089; -.
DR   EnsemblBacteria; AAK87839; AAK87839; Atu2089.
DR   GeneID; 1134127; -.
DR   KEGG; atu:Atu2089; -.
DR   PATRIC; fig|176299.10.peg.2102; -.
DR   eggNOG; ENOG4105CPF; Bacteria.
DR   eggNOG; COG1181; LUCA.
DR   HOGENOM; HOG000011592; -.
DR   KO; K01921; -.
DR   OMA; YETKYTE; -.
DR   BioCyc; AGRO:ATU2089-MONOMER; -.
DR   UniPathway; UPA00219; -.
DR   Proteomes; UP000000813; Chromosome circular.
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;
KW   Complete proteome; Cytoplasm; Ligase; Magnesium; Manganese;
KW   Metal-binding; Nucleotide-binding; Peptidoglycan synthesis;
KW   Reference proteome.
FT   CHAIN         1    308       D-alanine--D-alanine ligase.
FT                                /FTId=PRO_0000177777.
FT   DOMAIN      102    302       ATP-grasp. {ECO:0000255|HAMAP-
FT                                Rule:MF_00047}.
FT   NP_BIND     128    183       ATP. {ECO:0000255|HAMAP-Rule:MF_00047}.
FT   METAL       252    252       Magnesium or manganese 1.
FT                                {ECO:0000255|HAMAP-Rule:MF_00047}.
FT   METAL       269    269       Magnesium or manganese 1.
FT                                {ECO:0000255|HAMAP-Rule:MF_00047}.
FT   METAL       269    269       Magnesium or manganese 2.
FT                                {ECO:0000255|HAMAP-Rule:MF_00047}.
FT   METAL       271    271       Magnesium or manganese 2.
FT                                {ECO:0000255|HAMAP-Rule:MF_00047}.
SQ   SEQUENCE   308 AA;  33069 MW;  18A95347199404E8 CRC64;
     MGGKHVAVLL GGFSSERPVS LSSGNACALA LEGEGYKVTR VDVGRDVAAV LDELRPDVAF
     NALHGPFGED GTIQGILEYL AIPYTHSGVL ASALAMDKAQ AKKVAAAAGI PVAGERVMNR
     FDFTSEHPLQ PPYVVKPVRE GSSFGVVIVK EDQSHPPQIL TSSEWPFGNQ VMVERYIHGR
     ELTCGVLDGE ALGVTEVVPL GHNFYDYDAK YAAGGSKHVI PAGISPKIYQ KIQTLAVMAH
     QAIGCRGVSR SDFRYDDRFS EDGEVIWLEV NTQPGMTPTS LVPEMAAHAG RSFGDLVSWM
     VEDASCLR
//
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