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D-alanyl-D-alanine dipeptidase (D-Ala-D-Ala dipeptidase) (EC 3.4.13.22) (Vancomycin B-type resistance protein VanX)

 VANX_ENTFC              Reviewed;         202 AA.
Q06241;
01-OCT-1994, integrated into UniProtKB/Swiss-Prot.
01-OCT-1994, sequence version 1.
23-MAY-2018, entry version 110.
RecName: Full=D-alanyl-D-alanine dipeptidase {ECO:0000255|HAMAP-Rule:MF_01924};
Short=D-Ala-D-Ala dipeptidase {ECO:0000255|HAMAP-Rule:MF_01924};
EC=3.4.13.22 {ECO:0000255|HAMAP-Rule:MF_01924};
AltName: Full=Vancomycin B-type resistance protein VanX;
Name=vanX;
Enterococcus faecium (Streptococcus faecium).
Plasmid pIP816.
Bacteria; Firmicutes; Bacilli; Lactobacillales; Enterococcaceae;
Enterococcus.
NCBI_TaxID=1352;
[1]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
STRAIN=BM4147; TRANSPOSON=Tn1546;
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).
[2]
PROTEIN SEQUENCE OF 1-10, FUNCTION, CATALYTIC ACTIVITY, COFACTOR,
SUBUNIT, ENZYME REGULATION, AND BIOPHYSICOCHEMICAL PROPERTIES.
PubMed=7873524; DOI=10.1021/bi00008a008;
Wu Z., Wright G.D., Walsh C.T.;
"Overexpression, purification, and characterization of VanX, a D-, D-
dipeptidase which is essential for vancomycin resistance in
Enterococcus faecium BM4147.";
Biochemistry 34:2455-2463(1995).
[3]
INDUCTION.
STRAIN=BM4147;
PubMed=1556077; DOI=10.1128/jb.174.8.2582-2591.1992;
Arthur M., Molinas C., Courvalin P.;
"The VanS-VanR two-component regulatory system controls synthesis of
depsipeptide peptidoglycan precursors in Enterococcus faecium
BM4147.";
J. Bacteriol. 174:2582-2591(1992).
[4]
FUNCTION, AND CATALYTIC ACTIVITY.
PubMed=7854121; DOI=10.1111/j.1365-2958.1994.tb00497.x;
Reynolds P.E., Depardieu F., Dutka-Malen S., Arthur M., Courvalin P.;
"Glycopeptide resistance mediated by enterococcal transposon Tn1546
requires production of VanX for hydrolysis of D-alanyl-D-alanine.";
Mol. Microbiol. 13:1065-1070(1994).
[5]
X-RAY CRYSTALLOGRAPHY (2.25 ANGSTROMS) IN COMPLEX WITH ZINC, COFACTOR,
SUBUNIT, AND ACTIVE SITE.
PubMed=9702193; DOI=10.1016/S1097-2765(00)80115-X;
Bussiere D.E., Pratt S.D., Katz L., Severin J.M., Holzman T.,
Park C.H.;
"The structure of VanX reveals a novel amino-dipeptidase involved in
mediating transposon-based vancomycin resistance.";
Mol. Cell 2:75-84(1998).
-!- FUNCTION: Catalyzes hydrolysis of the D-alanyl-D-alanine
dipeptide. {ECO:0000255|HAMAP-Rule:MF_01924,
ECO:0000269|PubMed:7854121, ECO:0000269|PubMed:7873524}.
-!- CATALYTIC ACTIVITY: D-Ala-D-Ala + H(2)O = 2 D-Ala.
{ECO:0000255|HAMAP-Rule:MF_01924, ECO:0000269|PubMed:7854121,
ECO:0000269|PubMed:7873524}.
-!- COFACTOR:
Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
Evidence={ECO:0000255|HAMAP-Rule:MF_01924,
ECO:0000269|PubMed:7873524, ECO:0000269|PubMed:9702193};
Name=Fe(2+); Xref=ChEBI:CHEBI:29033;
Evidence={ECO:0000255|HAMAP-Rule:MF_01924,
ECO:0000269|PubMed:7873524, ECO:0000269|PubMed:9702193};
Name=Co(2+); Xref=ChEBI:CHEBI:48828;
Evidence={ECO:0000255|HAMAP-Rule:MF_01924,
ECO:0000269|PubMed:7873524, ECO:0000269|PubMed:9702193};
Name=Ni(2+); Xref=ChEBI:CHEBI:49786;
Evidence={ECO:0000255|HAMAP-Rule:MF_01924,
ECO:0000269|PubMed:7873524, ECO:0000269|PubMed:9702193};
Note=Binds 1 zinc ion per subunit. Can also be activated by other
divalent cations such as iron, cobalt, or nickel.
{ECO:0000255|HAMAP-Rule:MF_01924, ECO:0000269|PubMed:7873524,
ECO:0000269|PubMed:9702193};
-!- ENZYME REGULATION: Inhibited by aminoalkyl phosphinate analogs.
{ECO:0000269|PubMed:7873524}.
-!- BIOPHYSICOCHEMICAL PROPERTIES:
Kinetic parameters:
KM=1 mM for D-Ala-D-Ala (in the absence of divalent cations)
{ECO:0000269|PubMed:7873524};
KM=2.8 mM for D-Ala-D-Ser KM=1.7 mM for D-Ser-D-Ala Vmax=12.3
nmol/min/ug enzyme with D-Ala-D-Ala as substrate
{ECO:0000269|PubMed:7873524};
Vmax=4.7 nmol/min/ug enzyme with D-Ala-D-Ser as substrate
{ECO:0000269|PubMed:7873524};
Vmax=1.3 nmol/min/ug enzyme with D-Ser-D-Ala as substrate
{ECO:0000269|PubMed:7873524};
Note=Kcat is 4.7 sec(-1) with D-Ala-D-Ala. Kcat is 1.8 sec(-1)
with D-Ala-D-Ser. Kcat is 0.35 sec(-1) with D-Ser-D-Ala. Kcat is
0.005 sec(-1) with D-Ala-D-lactate.;
pH dependence:
Optimum pH is 7-9. {ECO:0000269|PubMed:7873524};
-!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:7873524,
ECO:0000269|PubMed:9702193}.
-!- INDUCTION: By vancomycin, mediated by VanS/VanR.
{ECO:0000269|PubMed:1556077}.
-!- MISCELLANEOUS: Does not hydrolyze D-Ala-D-lactate, which remains
intact for subsequent incorporation into peptidoglycan precursors.
Production of precursors ending in D-Ala-D-lactate instead of D-
Ala-D-Ala decreases affinity of vancomycin for the peptidoglycan
chain and leads to vancomycin resistance (PubMed:7873524).
{ECO:0000305|PubMed:7873524}.
-!- SIMILARITY: Belongs to the peptidase M15D family.
{ECO:0000255|HAMAP-Rule:MF_01924}.
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EMBL; M97297; AAA65957.1; -; Genomic_DNA.
PIR; S72342; S72342.
RefSeq; WP_000402347.1; NZ_PJZU01000110.1.
RefSeq; YP_001019034.1; NC_008821.1.
RefSeq; YP_001974795.1; NC_010980.1.
RefSeq; YP_002128400.1; NC_011140.1.
RefSeq; YP_976076.1; NC_008768.1.
PDB; 1R44; X-ray; 2.25 A; A/B/C/D/E/F=1-202.
PDBsum; 1R44; -.
ProteinModelPortal; Q06241; -.
SMR; Q06241; -.
BindingDB; Q06241; -.
ChEMBL; CHEMBL1681622; -.
DrugBank; DB00512; Vancomycin.
MEROPS; M15.011; -.
GeneID; 4670250; -.
GeneID; 4783136; -.
GeneID; 6385878; -.
GeneID; 6779646; -.
KEGG; ag:AAA65957; -.
KO; K08641; -.
BioCyc; MetaCyc:MONOMER-15475; -.
BRENDA; 3.4.13.22; 2096.
SABIO-RK; Q06241; -.
EvolutionaryTrace; Q06241; -.
GO; GO:0005618; C:cell wall; IEA:InterPro.
GO; GO:0016805; F:dipeptidase activity; IEA:UniProtKB-KW.
GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
GO; GO:0008237; F:metallopeptidase activity; IEA:UniProtKB-KW.
GO; GO:0071555; P:cell wall organization; IEA:UniProtKB-KW.
GO; GO:0046677; P:response to antibiotic; IEA:UniProtKB-KW.
Gene3D; 3.30.1380.10; -; 1.
HAMAP; MF_01924; A_A_dipeptidase; 1.
InterPro; IPR000755; A_A_dipeptidase.
InterPro; IPR009045; Hedgehog_sig/DD-Pept_Zn-bd_sf.
Pfam; PF01427; Peptidase_M15; 1.
PIRSF; PIRSF026671; AA_dipeptidase; 1.
SUPFAM; SSF55166; SSF55166; 1.
1: Evidence at protein level;
3D-structure; Antibiotic resistance; Cell wall biogenesis/degradation;
Dipeptidase; Direct protein sequencing; Hydrolase; Metal-binding;
Metalloprotease; Plasmid; Protease; Zinc.
CHAIN 1 202 D-alanyl-D-alanine dipeptidase.
/FTId=PRO_0000217840.
ACT_SITE 181 181 Proton donor/acceptor.
{ECO:0000305|PubMed:9702193}.
METAL 116 116 Zinc; via tele nitrogen; catalytic.
{ECO:0000255|HAMAP-Rule:MF_01924,
ECO:0000269|PubMed:9702193}.
METAL 123 123 Zinc; catalytic. {ECO:0000255|HAMAP-
Rule:MF_01924,
ECO:0000269|PubMed:9702193}.
METAL 184 184 Zinc; via pros nitrogen; catalytic.
{ECO:0000255|HAMAP-Rule:MF_01924,
ECO:0000269|PubMed:9702193}.
SITE 71 71 Transition state stabilizer.
{ECO:0000305}.
STRAND 5 7 {ECO:0000244|PDB:1R44}.
HELIX 8 10 {ECO:0000244|PDB:1R44}.
HELIX 20 22 {ECO:0000244|PDB:1R44}.
STRAND 37 39 {ECO:0000244|PDB:1R44}.
STRAND 41 43 {ECO:0000244|PDB:1R44}.
HELIX 44 56 {ECO:0000244|PDB:1R44}.
STRAND 59 68 {ECO:0000244|PDB:1R44}.
HELIX 73 83 {ECO:0000244|PDB:1R44}.
HELIX 92 95 {ECO:0000244|PDB:1R44}.
STRAND 97 99 {ECO:0000244|PDB:1R44}.
HELIX 103 106 {ECO:0000244|PDB:1R44}.
STRAND 108 110 {ECO:0000244|PDB:1R44}.
HELIX 115 118 {ECO:0000244|PDB:1R44}.
STRAND 121 128 {ECO:0000244|PDB:1R44}.
TURN 129 131 {ECO:0000244|PDB:1R44}.
HELIX 146 148 {ECO:0000244|PDB:1R44}.
STRAND 153 155 {ECO:0000244|PDB:1R44}.
HELIX 157 171 {ECO:0000244|PDB:1R44}.
TURN 172 174 {ECO:0000244|PDB:1R44}.
STRAND 175 177 {ECO:0000244|PDB:1R44}.
STRAND 184 189 {ECO:0000244|PDB:1R44}.
SEQUENCE 202 AA; 23380 MW; 649C00927D08669C CRC64;
MEIGFTFLDE IVHGVRWDAK YATWDNFTGK PVDGYEVNRI VGTYELAESL LKAKELAATQ
GYGLLLWDGY RPKRAVNCFM QWAAQPENNL TKESYYPNID RTEMISKGYV ASKSSHSRGS
AIDLTLYRLD TGELVPMGSR FDFMDERSHH AANGISCNEA QNRRRLRSIM ENSGFEAYSL
EWWHYVLRDE PYPNSYFDFP VK


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