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D-alanine--D-alanine ligase (EC 6.3.2.4) (D-Ala-D-Ala ligase) (D-alanylalanine synthetase)

 Q7B608_ENTFC            Unreviewed;       343 AA.
Q7B608;
10-MAY-2005, integrated into UniProtKB/TrEMBL.
10-MAY-2005, sequence version 1.
10-OCT-2018, entry version 118.
RecName: Full=D-alanine--D-alanine ligase {ECO:0000256|HAMAP-Rule:MF_00047, ECO:0000256|SAAS:SAAS00910572};
EC=6.3.2.4 {ECO:0000256|HAMAP-Rule:MF_00047, ECO:0000256|SAAS:SAAS00910572};
AltName: Full=D-Ala-D-Ala ligase {ECO:0000256|HAMAP-Rule:MF_00047};
AltName: Full=D-alanylalanine synthetase {ECO:0000256|HAMAP-Rule:MF_00047};
Name=vanA {ECO:0000313|EMBL:AAM77885.1};
Synonyms=ddl {ECO:0000256|HAMAP-Rule:MF_00047};
ORFNames=B4W81_17380 {ECO:0000313|EMBL:AQY33699.1},
DKP91_13550 {ECO:0000313|EMBL:PZM53774.1};
Enterococcus faecium (Streptococcus faecium).
Plasmid p268-3 {ECO:0000313|EMBL:AQY33699.1},
Plasmid p268-3 sequence {ECO:0000313|Proteomes:UP000190755},
Plasmid pIP816 {ECO:0000313|EMBL:CAP70014.1},
Plasmid pUW786 {ECO:0000313|EMBL:AAM77885.1},
Plasmid pVEF1 {ECO:0000313|EMBL:CAL36534.1},
Plasmid pVEF2 {ECO:0000313|EMBL:CAL90940.1},
Plasmid pVEF3 {ECO:0000313|EMBL:CAP62631.1},
Plasmid pVEF4 {ECO:0000313|EMBL:CAZ67071.1}, and
Plasmid unnamed {ECO:0000313|EMBL:AFC95874.1}.
Bacteria; Firmicutes; Bacilli; Lactobacillales; Enterococcaceae;
Enterococcus.
NCBI_TaxID=1352 {ECO:0000313|EMBL:AAM77885.1};
[1] {ECO:0000313|EMBL:AAM77885.1}
NUCLEOTIDE SEQUENCE.
STRAIN=UW786 {ECO:0000313|EMBL:AAM77885.1};
PLASMID=pUW786 {ECO:0000313|EMBL:AAM77885.1};
Werner G., Klare I., Witte W.;
"Multi-resistance gene cluster on a plasmid in a clinical isolate of
Enterococcus faecium.";
Submitted (MAY-2002) to the EMBL/GenBank/DDBJ databases.
[2] {ECO:0000313|EMBL:CAL36534.1}
NUCLEOTIDE SEQUENCE.
STRAIN=399/F99/A9 {ECO:0000313|EMBL:CAL90940.1}, and
399/F99/H8 {ECO:0000313|EMBL:CAL36534.1};
PLASMID=pVEF1 {ECO:0000313|EMBL:CAL36534.1}, and
pVEF2 {ECO:0000313|EMBL:CAL90940.1};
PubMed=17116680; DOI=10.1128/AAC.00557-06;
Sletvold H., Johnsen P.J., Simonsen G.S., Aasnaes B., Sundsfjord A.,
Nielsen K.M.;
"Comparative DNA analysis of two vanA plasmids from Enterococcus
faecium strains isolated from poultry and a poultry farmer in
Norway.";
Antimicrob. Agents Chemother. 51:736-739(2007).
[3] {ECO:0000313|EMBL:ACC93633.1}
NUCLEOTIDE SEQUENCE.
STRAIN=ZP2298 {ECO:0000313|EMBL:ACC93633.1};
PubMed=17951264; DOI=10.1093/jac/dkm399;
Qu T.T., Chen Y.G., Yu Y.S., Lv H.X., Dong X.Q., Xiao Z., Gu H.Q.,
Li L.J.;
"Molecular characterization of vancomycin-resistant enterococci in
Hangzhou, China.";
J. Antimicrob. Chemother. 60:1403-1405(2007).
[4] {ECO:0000313|EMBL:CAP62631.1}
NUCLEOTIDE SEQUENCE.
STRAIN=399/S99/A7 {ECO:0000313|EMBL:CAP62631.1};
PLASMID=pVEF3 {ECO:0000313|EMBL:CAP62631.1};
PubMed=18511120; DOI=10.1016/j.plasmid.2008.04.002;
Sletvold H., Johnsen P.J., Simonsen G.S., Sundsfjord A., Nielsen K.M.;
"The toxin-antitoxin system w-e-z ensures stable maintenance of vanA
plasmids in an antibiotic-free environment.";
Plasmid 60:75-85(2008).
[5] {ECO:0000313|EMBL:ACC93633.1}
NUCLEOTIDE SEQUENCE.
STRAIN=ZP2298 {ECO:0000313|EMBL:ACC93633.1};
PubMed=19846656; DOI=10.1128/JCM.01802-09;
Qu T.T., Zhang J.L., Zhou Z.H., Wei Z.Q., Yu Y.S., Chen Y.G., Li L.J.;
"Heteroresistance to teicoplanin in Enterococcus faecium harboring the
vanA gene.";
J. Clin. Microbiol. 47:4194-4196(2009).
[6] {ECO:0000313|EMBL:CAP70014.1}
NUCLEOTIDE SEQUENCE.
STRAIN=399/F98/A4 {ECO:0000313|EMBL:CAZ67071.1}, and
BM4147 {ECO:0000313|EMBL:CAP70014.1};
PLASMID=pIP816 {ECO:0000313|EMBL:CAP70014.1}, and
pVEF4 {ECO:0000313|EMBL:CAZ67071.1};
Sletvold H., Johnsen P.J., Wikmark O.G., Simonsen G.S., Sundsfjord A.,
Nielsen K.M.;
"Tn1546 is part of a larger plasmid-encoded genetic unit horizontally
disseminated among clonal Enterococcus faecium lineages.";
J. Antimicrob. Chemother. 65:1894-1906(2010).
[7] {ECO:0000313|EMBL:AFC95874.1}
NUCLEOTIDE SEQUENCE.
STRAIN=A94 {ECO:0000313|EMBL:AFC95874.1};
PLASMID=unnamed {ECO:0000313|EMBL:AFC95874.1};
Qu T.-T., Yang Q., Shen P., Wei Z.-Q., Yu Y.-S.;
"Novel vancomycin resistance transposon, plasmid replicon types and
virulence factors of vancomycin-resistant Enterococci in Zhejiang,
China.";
Submitted (OCT-2011) to the EMBL/GenBank/DDBJ databases.
[8] {ECO:0000313|EMBL:AFC95874.1}
NUCLEOTIDE SEQUENCE.
STRAIN=A94 {ECO:0000313|EMBL:AFC95874.1};
PLASMID=unnamed {ECO:0000313|EMBL:AFC95874.1};
PubMed=22867881; DOI=10.1016/j.ijantimicag.2012.06.010;
Wang R., Lou J., Liu J., Zhang L., Li J., Kan B.;
"Antibiotic resistance of Vibrio cholerae O1 El Tor strains from the
seventh pandemic in China, 1961-2010.";
Int. J. Antimicrob. Agents 40:361-364(2012).
[9] {ECO:0000313|EMBL:AQY33699.1, ECO:0000313|Proteomes:UP000190755}
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=2014-VREF-268 {ECO:0000313|EMBL:AQY33699.1};
PLASMID=p268-3 {ECO:0000313|EMBL:AQY33699.1};
Kim H.M.;
"Non-typeable vancomycin-resistant E. faecium.";
Submitted (MAR-2017) to the EMBL/GenBank/DDBJ databases.
[10] {ECO:0000313|EMBL:PZM53774.1, ECO:0000313|Proteomes:UP000249070}
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=20 {ECO:0000313|EMBL:PZM53774.1,
ECO:0000313|Proteomes:UP000249070};
Gostev V., Goncharov A., Kolodzhieva V., Suvorov A., Sidorenko S.,
Zueva L.;
"Vancomycin-resistant Enterococcus faecium strain from Chelyabinsk,
Russia.";
Submitted (MAY-2018) to the EMBL/GenBank/DDBJ databases.
-!- FUNCTION: Cell wall formation. {ECO:0000256|HAMAP-Rule:MF_00047,
ECO:0000256|SAAS:SAAS00910576}.
-!- CATALYTIC ACTIVITY: ATP + 2 D-alanine = ADP + phosphate + D-
alanyl-D-alanine. {ECO:0000256|HAMAP-Rule:MF_00047,
ECO:0000256|SAAS:SAAS00910566}.
-!- COFACTOR:
Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
Evidence={ECO:0000256|PIRSR:PIRSR039102-3};
Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
Evidence={ECO:0000256|PIRSR:PIRSR039102-3};
Note=Binds 2 magnesium or manganese ions per subunit.
{ECO:0000256|PIRSR:PIRSR039102-3};
-!- COFACTOR:
Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
Evidence={ECO:0000256|SAAS:SAAS00910564};
-!- PATHWAY: Cell wall biogenesis; peptidoglycan biosynthesis.
{ECO:0000256|HAMAP-Rule:MF_00047, ECO:0000256|SAAS:SAAS00910582}.
-!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000256|HAMAP-Rule:MF_00047,
ECO:0000256|SAAS:SAAS00644680}.
-!- SIMILARITY: Belongs to the D-alanine--D-alanine ligase family.
{ECO:0000256|HAMAP-Rule:MF_00047, ECO:0000256|SAAS:SAAS00910642}.
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EMBL; AF516335; AAM77885.1; -; Genomic_DNA.
EMBL; EU599211; ACC93633.1; -; Genomic_DNA.
EMBL; JN982328; AFC95874.1; -; Genomic_DNA.
EMBL; CP019995; AQY33699.1; -; Genomic_DNA.
EMBL; AM296544; CAL36534.1; -; Genomic_DNA.
EMBL; AM410096; CAL90940.1; -; Genomic_DNA.
EMBL; AM931300; CAP62631.1; -; Genomic_DNA.
EMBL; AM932524; CAP70014.1; -; Genomic_DNA.
EMBL; FN424376; CAZ67071.1; -; Genomic_DNA.
EMBL; QHGU01000106; PZM53774.1; -; Genomic_DNA.
RefSeq; WP_001079845.1; NZ_QHGU01000106.1.
RefSeq; YP_001019035.1; NC_008821.1.
RefSeq; YP_001974796.1; NC_010980.1.
RefSeq; YP_002128399.1; NC_011140.1.
RefSeq; YP_976077.1; NC_008768.1.
EnsemblBacteria; KWY81474; KWY81474; AS252_02495.
GeneID; 4670249; -.
GeneID; 4783144; -.
GeneID; 6385877; -.
GeneID; 6779647; -.
PATRIC; fig|1352.1358.peg.3010; -.
UniPathway; UPA00219; -.
Proteomes; UP000190755; Plasmid p268-3 sequence.
Proteomes; UP000249070; Unassembled WGS sequence.
GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
GO; GO:0005524; F:ATP binding; IEA:UniProtKB-UniRule.
GO; GO:0008716; F:D-alanine-D-alanine ligase activity; IEA:UniProtKB-UniRule.
GO; GO:0003887; F:DNA-directed DNA polymerase activity; IEA:UniProtKB-KW.
GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
GO; GO:0003964; F:RNA-directed DNA polymerase activity; IEA:UniProtKB-KW.
GO; GO:0071555; P:cell wall organization; IEA:UniProtKB-KW.
GO; GO:0009252; P:peptidoglycan biosynthetic process; IEA:UniProtKB-UniRule.
GO; GO:0008360; P:regulation of cell shape; IEA:UniProtKB-KW.
Gene3D; 3.30.1490.20; -; 1.
HAMAP; MF_00047; Dala_Dala_lig; 1.
InterPro; IPR011761; ATP-grasp.
InterPro; IPR013815; ATP_grasp_subdomain_1.
InterPro; IPR000291; D-Ala_lig_Van_CS.
InterPro; IPR005905; D_ala_D_ala.
InterPro; IPR011095; Dala_Dala_lig_C.
InterPro; IPR011127; Dala_Dala_lig_N.
InterPro; IPR016185; PreATP-grasp_dom_sf.
Pfam; PF07478; Dala_Dala_lig_C; 1.
Pfam; PF01820; Dala_Dala_lig_N; 1.
PIRSF; PIRSF039102; Ddl/VanB; 1.
SUPFAM; SSF52440; SSF52440; 1.
TIGRFAMs; TIGR01205; D_ala_D_alaTIGR; 1.
PROSITE; PS50975; ATP_GRASP; 1.
PROSITE; PS00843; DALA_DALA_LIGASE_1; 1.
PROSITE; PS00844; DALA_DALA_LIGASE_2; 1.
3: Inferred from homology;
ATP-binding {ECO:0000256|PROSITE-ProRule:PRU00409,
ECO:0000256|SAAS:SAAS00644673};
Cell shape {ECO:0000256|HAMAP-Rule:MF_00047,
ECO:0000256|SAAS:SAAS00644714};
Cell wall biogenesis/degradation {ECO:0000256|HAMAP-Rule:MF_00047,
ECO:0000256|SAAS:SAAS00644792};
Complete proteome {ECO:0000313|Proteomes:UP000190755,
ECO:0000313|Proteomes:UP000249070};
Cytoplasm {ECO:0000256|HAMAP-Rule:MF_00047,
ECO:0000256|SAAS:SAAS00910562};
DNA-directed DNA polymerase {ECO:0000313|EMBL:CAP62631.1};
Ligase {ECO:0000256|HAMAP-Rule:MF_00047,
ECO:0000256|SAAS:SAAS00644741, ECO:0000313|EMBL:AAM77885.1};
Magnesium {ECO:0000256|PIRSR:PIRSR039102-3,
ECO:0000256|SAAS:SAAS00910568};
Manganese {ECO:0000256|PIRSR:PIRSR039102-3,
ECO:0000256|SAAS:SAAS00910578};
Metal-binding {ECO:0000256|PIRSR:PIRSR039102-3,
ECO:0000256|SAAS:SAAS00910590};
Nucleotide-binding {ECO:0000256|PROSITE-ProRule:PRU00409,
ECO:0000256|SAAS:SAAS00644673};
Nucleotidyltransferase {ECO:0000313|EMBL:CAP62631.1};
Peptidoglycan synthesis {ECO:0000256|HAMAP-Rule:MF_00047,
ECO:0000256|SAAS:SAAS00644714}; Plasmid {ECO:0000313|EMBL:AAM77885.1};
RNA-directed DNA polymerase {ECO:0000313|EMBL:CAP62631.1};
Transferase {ECO:0000313|EMBL:CAP62631.1}.
DOMAIN 137 338 ATP-grasp. {ECO:0000259|PROSITE:PS50975}.
METAL 292 292 Magnesium or manganese 1.
{ECO:0000256|PIRSR:PIRSR039102-3}.
METAL 305 305 Magnesium or manganese 1.
{ECO:0000256|PIRSR:PIRSR039102-3}.
METAL 305 305 Magnesium or manganese 2.
{ECO:0000256|PIRSR:PIRSR039102-3}.
METAL 307 307 Magnesium or manganese 2.
{ECO:0000256|PIRSR:PIRSR039102-3}.
SEQUENCE 343 AA; 37443 MW; AAA48E3B2AD48E03 CRC64;
MNRIKVAILF GGCSEEHDVS VKSAIEIAAN INKEKYEPLY IGITKSGVWK MCEKPCAEWE
NDNCYSAVLS PDKKMHGLLV KKNHEYEINH VDVAFSALHG KSGEDGSIQG LFELSGIPFV
GCDIQSSAIC MDKSLTYIVA KNAGIATPAF WVINKDDRPV AATFTYPVFV KPARSGSSFG
VKKVNSADEL DYAIESARQY DSKILIEQAV SGCEVGCAVL GNSAALVVGE VDQIRLQYGI
FRIHQEVEPE KGSENAVITV PADLSAEERG RIQETAKKIY KALGCRGLAR VDMFLQDNGR
IVLNEVNTLP GFTSYSRYPR MMAAAGIALP ELIDRLIVLA LKG


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