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Vancomycin/teicoplanin A-type resistance protein VanA (EC 6.1.2.1) (D-alanine--D-lactate ligase) (VanA ligase)

 VANA_ENTFC              Reviewed;         343 AA.
P25051;
01-MAY-1992, integrated into UniProtKB/Swiss-Prot.
01-MAY-1992, sequence version 1.
05-DEC-2018, entry version 134.
RecName: Full=Vancomycin/teicoplanin A-type resistance protein VanA;
EC=6.1.2.1;
AltName: Full=D-alanine--D-lactate ligase;
AltName: Full=VanA ligase;
Name=vanA;
Enterococcus faecium (Streptococcus faecium).
Plasmid pIP816.
Bacteria; Firmicutes; Bacilli; Lactobacillales; Enterococcaceae;
Enterococcus.
NCBI_TaxID=1352;
[1]
NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND PROTEIN SEQUENCE OF 1-9.
STRAIN=BM4147;
PubMed=2266943; DOI=10.1007/BF00262430;
Dutka-Malen S., Molinas C., Arthur M., Courvalin P.;
"The VANA glycopeptide resistance protein is related to D-alanyl-D-
alanine ligase cell wall biosynthesis enzymes.";
Mol. Gen. Genet. 224:364-372(1990).
[2]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
STRAIN=BM4147;
PubMed=8380148; DOI=10.1128/jb.175.1.117-127.1993;
Arthur M., Molinas C., Depardieu F., Courvalin P.;
"Characterization of Tn1546, a Tn3-related transposon conferring
glycopeptide resistance by synthesis of depsipeptide peptidoglycan
precursors in Enterococcus faecium BM4147.";
J. Bacteriol. 175:117-127(1993).
[3]
FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, AND
BIOPHYSICOCHEMICAL PROPERTIES.
STRAIN=BM4147;
PubMed=1931965; DOI=10.1021/bi00107a007;
Bugg T.D.H., Wright G.D., Dutka-Malen S., Arthur M., Courvalin P.,
Walsh C.T.;
"Molecular basis for vancomycin resistance in Enterococcus faecium
BM4147: biosynthesis of a depsipeptide peptidoglycan precursor by
vancomycin resistance proteins VanH and VanA.";
Biochemistry 30:10408-10415(1991).
[4]
CHARACTERIZATION OF REACTION PRODUCT.
PubMed=1522072; DOI=10.1128/jb.174.18.5982-5984.1992;
Handwerger S., Pucci M.J., Volk K.J., Liu J., Lee M.S.;
"The cytoplasmic peptidoglycan precursor of vancomycin-resistant
Enterococcus faecalis terminates in lactate.";
J. Bacteriol. 174:5982-5984(1992).
[5]
X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) IN COMPLEX WITH MAGNESIUM; ADP
AND INHIBITOR.
PubMed=10908650; DOI=10.1073/pnas.150116497;
Roper D.I., Huyton T., Vagin A., Dodson G.;
"The molecular basis of vancomycin resistance in clinically relevant
Enterococci: crystal structure of D-alanyl-D-lactate ligase (VanA).";
Proc. Natl. Acad. Sci. U.S.A. 97:8921-8925(2000).
-!- FUNCTION: Required for high-level resistance to glycopeptide
antibiotics. D-Ala--D-Ala ligase of altered specificity which
catalyzes ester bond formation between D-Ala and various D-hydroxy
acids; produces a peptidoglycan which does not terminate in D-
alanine but in D-lactate, thus preventing vancomycin or
teicoplanin binding. {ECO:0000269|PubMed:1931965}.
-!- CATALYTIC ACTIVITY:
Reaction=(R)-lactate + ATP + D-alanine = ADP + D-alanyl-(R)-
lactate + phosphate; Xref=Rhea:RHEA:37347, ChEBI:CHEBI:16004,
ChEBI:CHEBI:30616, ChEBI:CHEBI:43474, ChEBI:CHEBI:57416,
ChEBI:CHEBI:61166, ChEBI:CHEBI:456216; EC=6.1.2.1;
Evidence={ECO:0000269|PubMed:1931965};
-!- COFACTOR:
Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Evidence={ECO:0000250};
Name=Mn(2+); Xref=ChEBI:CHEBI:29035; Evidence={ECO:0000250};
Note=Binds 2 magnesium or manganese ions per subunit.
{ECO:0000250};
-!- BIOPHYSICOCHEMICAL PROPERTIES:
Kinetic parameters:
KM=7.1 mM for D-lactate {ECO:0000269|PubMed:1931965};
KM=3.8 mM for D-alanine {ECO:0000269|PubMed:1931965};
KM=0.6 mM for 2-hydroxybutyrate {ECO:0000269|PubMed:1931965};
KM=3.2 mM for 2-hydroxyvalerate {ECO:0000269|PubMed:1931965};
KM=11 mM for 2-hydroxycaproate {ECO:0000269|PubMed:1931965};
-!- SUBCELLULAR LOCATION: Cell membrane; Peripheral membrane protein;
Cytoplasmic side.
-!- INDUCTION: By vancomycin, mediated by VanS/VanR.
-!- SIMILARITY: Belongs to the D-alanine--D-alanine ligase family.
{ECO:0000305}.
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EMBL; X56895; CAA40215.1; -; Genomic_DNA.
EMBL; M97297; AAA65956.1; -; Genomic_DNA.
PIR; S12254; CESOVM.
RefSeq; WP_001079845.1; NZ_UFYT01000005.1.
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.
PDB; 1E4E; X-ray; 2.50 A; A/B=1-343.
PDBsum; 1E4E; -.
ProteinModelPortal; P25051; -.
SMR; P25051; -.
BindingDB; P25051; -.
ChEMBL; CHEMBL6037; -.
PRIDE; P25051; -.
GeneID; 4670249; -.
GeneID; 4783144; -.
GeneID; 6385877; -.
GeneID; 6779647; -.
KEGG; ag:CAA40215; -.
KO; K15739; -.
BioCyc; MetaCyc:MONOMER-15466; -.
BRENDA; 6.1.2.1; 2096.
SABIO-RK; P25051; -.
EvolutionaryTrace; P25051; -.
PRO; PR:P25051; -.
GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-UniRule.
GO; GO:0005886; C:plasma membrane; IEA:UniProtKB-SubCell.
GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
GO; GO:0008716; F:D-alanine-D-alanine ligase activity; IDA:CACAO.
GO; GO:0046872; F:metal ion binding; 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.
GO; GO:0046677; P:response to antibiotic; 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.
1: Evidence at protein level;
3D-structure; Antibiotic resistance; ATP-binding; Cell membrane;
Cell shape; Cell wall biogenesis/degradation;
Direct protein sequencing; Ligase; Magnesium; Manganese; Membrane;
Metal-binding; Nucleotide-binding; Peptidoglycan synthesis; Plasmid.
CHAIN 1 343 Vancomycin/teicoplanin A-type resistance
protein VanA.
/FTId=PRO_0000177917.
DOMAIN 137 338 ATP-grasp.
NP_BIND 169 171 ATP.
NP_BIND 177 178 ATP.
NP_BIND 207 214 ATP.
NP_BIND 304 305 ATP.
METAL 305 305 Magnesium 1.
{ECO:0000269|PubMed:10908650}.
METAL 305 305 Magnesium 2.
{ECO:0000269|PubMed:10908650}.
METAL 307 307 Magnesium 2.
{ECO:0000269|PubMed:10908650}.
BINDING 133 133 ATP.
BINDING 241 241 ATP; via amide nitrogen.
BINDING 244 244 Substrate.
STRAND 4 11 {ECO:0000244|PDB:1E4E}.
HELIX 17 30 {ECO:0000244|PDB:1E4E}.
TURN 33 35 {ECO:0000244|PDB:1E4E}.
STRAND 36 43 {ECO:0000244|PDB:1E4E}.
STRAND 49 53 {ECO:0000244|PDB:1E4E}.
STRAND 65 69 {ECO:0000244|PDB:1E4E}.
TURN 73 75 {ECO:0000244|PDB:1E4E}.
STRAND 77 82 {ECO:0000244|PDB:1E4E}.
STRAND 85 90 {ECO:0000244|PDB:1E4E}.
STRAND 92 96 {ECO:0000244|PDB:1E4E}.
TURN 101 103 {ECO:0000244|PDB:1E4E}.
STRAND 104 106 {ECO:0000244|PDB:1E4E}.
HELIX 107 115 {ECO:0000244|PDB:1E4E}.
STRAND 119 121 {ECO:0000244|PDB:1E4E}.
HELIX 124 131 {ECO:0000244|PDB:1E4E}.
HELIX 133 142 {ECO:0000244|PDB:1E4E}.
STRAND 150 153 {ECO:0000244|PDB:1E4E}.
HELIX 161 163 {ECO:0000244|PDB:1E4E}.
STRAND 168 174 {ECO:0000244|PDB:1E4E}.
TURN 177 180 {ECO:0000244|PDB:1E4E}.
STRAND 182 184 {ECO:0000244|PDB:1E4E}.
HELIX 187 189 {ECO:0000244|PDB:1E4E}.
HELIX 190 197 {ECO:0000244|PDB:1E4E}.
TURN 198 200 {ECO:0000244|PDB:1E4E}.
STRAND 202 208 {ECO:0000244|PDB:1E4E}.
STRAND 212 222 {ECO:0000244|PDB:1E4E}.
STRAND 232 239 {ECO:0000244|PDB:1E4E}.
HELIX 243 245 {ECO:0000244|PDB:1E4E}.
STRAND 246 248 {ECO:0000244|PDB:1E4E}.
HELIX 249 251 {ECO:0000244|PDB:1E4E}.
STRAND 254 258 {ECO:0000244|PDB:1E4E}.
HELIX 266 282 {ECO:0000244|PDB:1E4E}.
STRAND 286 295 {ECO:0000244|PDB:1E4E}.
STRAND 301 309 {ECO:0000244|PDB:1E4E}.
HELIX 317 324 {ECO:0000244|PDB:1E4E}.
HELIX 329 341 {ECO:0000244|PDB:1E4E}.
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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