VANX_ENTFC
ID VANX_ENTFC Reviewed; 202 AA.
AC Q06241;
DT 01-OCT-1994, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-1994, sequence version 1.
DT 03-AUG-2022, entry version 130.
DE RecName: Full=D-alanyl-D-alanine dipeptidase {ECO:0000255|HAMAP-Rule:MF_01924};
DE Short=D-Ala-D-Ala dipeptidase {ECO:0000255|HAMAP-Rule:MF_01924};
DE EC=3.4.13.22 {ECO:0000255|HAMAP-Rule:MF_01924};
DE AltName: Full=Vancomycin B-type resistance protein VanX;
GN Name=vanX;
OS Enterococcus faecium (Streptococcus faecium).
OG Plasmid pIP816.
OC Bacteria; Firmicutes; Bacilli; Lactobacillales; Enterococcaceae;
OC Enterococcus.
OX NCBI_TaxID=1352;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=BM4147; TRANSPOSON=Tn1546;
RX PubMed=8380148; DOI=10.1128/jb.175.1.117-127.1993;
RA Arthur M., Molinas C., Depardieu F., Courvalin P.;
RT "Characterization of Tn1546, a Tn3-related transposon conferring
RT glycopeptide resistance by synthesis of depsipeptide peptidoglycan
RT precursors in Enterococcus faecium BM4147.";
RL J. Bacteriol. 175:117-127(1993).
RN [2]
RP PROTEIN SEQUENCE OF 1-10, FUNCTION, CATALYTIC ACTIVITY, COFACTOR, SUBUNIT,
RP ACTIVITY REGULATION, AND BIOPHYSICOCHEMICAL PROPERTIES.
RX PubMed=7873524; DOI=10.1021/bi00008a008;
RA Wu Z., Wright G.D., Walsh C.T.;
RT "Overexpression, purification, and characterization of VanX, a D-, D-
RT dipeptidase which is essential for vancomycin resistance in Enterococcus
RT faecium BM4147.";
RL Biochemistry 34:2455-2463(1995).
RN [3]
RP INDUCTION.
RC STRAIN=BM4147;
RX PubMed=1556077; DOI=10.1128/jb.174.8.2582-2591.1992;
RA Arthur M., Molinas C., Courvalin P.;
RT "The VanS-VanR two-component regulatory system controls synthesis of
RT depsipeptide peptidoglycan precursors in Enterococcus faecium BM4147.";
RL J. Bacteriol. 174:2582-2591(1992).
RN [4]
RP FUNCTION, AND CATALYTIC ACTIVITY.
RX PubMed=7854121; DOI=10.1111/j.1365-2958.1994.tb00497.x;
RA Reynolds P.E., Depardieu F., Dutka-Malen S., Arthur M., Courvalin P.;
RT "Glycopeptide resistance mediated by enterococcal transposon Tn1546
RT requires production of VanX for hydrolysis of D-alanyl-D-alanine.";
RL Mol. Microbiol. 13:1065-1070(1994).
RN [5]
RP X-RAY CRYSTALLOGRAPHY (2.25 ANGSTROMS) IN COMPLEX WITH ZINC, COFACTOR,
RP SUBUNIT, AND ACTIVE SITE.
RX PubMed=9702193; DOI=10.1016/s1097-2765(00)80115-x;
RA Bussiere D.E., Pratt S.D., Katz L., Severin J.M., Holzman T., Park C.H.;
RT "The structure of VanX reveals a novel amino-dipeptidase involved in
RT mediating transposon-based vancomycin resistance.";
RL Mol. Cell 2:75-84(1998).
CC -!- FUNCTION: Catalyzes hydrolysis of the D-alanyl-D-alanine dipeptide.
CC {ECO:0000255|HAMAP-Rule:MF_01924, ECO:0000269|PubMed:7854121,
CC ECO:0000269|PubMed:7873524}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=D-alanyl-D-alanine + H2O = 2 D-alanine; Xref=Rhea:RHEA:20661,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:57416, ChEBI:CHEBI:57822;
CC EC=3.4.13.22; Evidence={ECO:0000255|HAMAP-Rule:MF_01924,
CC ECO:0000269|PubMed:7854121, ECO:0000269|PubMed:7873524};
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01924,
CC ECO:0000269|PubMed:7873524, ECO:0000269|PubMed:9702193};
CC Name=Fe(2+); Xref=ChEBI:CHEBI:29033;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01924,
CC ECO:0000269|PubMed:7873524, ECO:0000269|PubMed:9702193};
CC Name=Co(2+); Xref=ChEBI:CHEBI:48828;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01924,
CC ECO:0000269|PubMed:7873524, ECO:0000269|PubMed:9702193};
CC Name=Ni(2+); Xref=ChEBI:CHEBI:49786;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01924,
CC ECO:0000269|PubMed:7873524, ECO:0000269|PubMed:9702193};
CC Note=Binds 1 zinc ion per subunit. Can also be activated by other
CC divalent cations such as iron, cobalt, or nickel. {ECO:0000255|HAMAP-
CC Rule:MF_01924, ECO:0000269|PubMed:7873524, ECO:0000269|PubMed:9702193};
CC -!- ACTIVITY REGULATION: Inhibited by aminoalkyl phosphinate analogs.
CC {ECO:0000269|PubMed:7873524}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=1 mM for D-Ala-D-Ala (in the absence of divalent cations)
CC {ECO:0000269|PubMed:7873524};
CC KM=2.8 mM for D-Ala-D-Ser {ECO:0000269|PubMed:7873524};
CC KM=1.7 mM for D-Ser-D-Ala {ECO:0000269|PubMed:7873524};
CC Vmax=12.3 nmol/min/ug enzyme with D-Ala-D-Ala as substrate
CC {ECO:0000269|PubMed:7873524};
CC Vmax=4.7 nmol/min/ug enzyme with D-Ala-D-Ser as substrate
CC {ECO:0000269|PubMed:7873524};
CC Vmax=1.3 nmol/min/ug enzyme with D-Ser-D-Ala as substrate
CC {ECO:0000269|PubMed:7873524};
CC Note=kcat is 4.7 sec(-1) with D-Ala-D-Ala. kcat is 1.8 sec(-1) with
CC D-Ala-D-Ser. kcat is 0.35 sec(-1) with D-Ser-D-Ala. kcat is 0.005
CC sec(-1) with D-Ala-D-lactate.;
CC pH dependence:
CC Optimum pH is 7-9. {ECO:0000269|PubMed:7873524};
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:7873524,
CC ECO:0000269|PubMed:9702193}.
CC -!- INDUCTION: By vancomycin, mediated by VanS/VanR.
CC {ECO:0000269|PubMed:1556077}.
CC -!- MISCELLANEOUS: Does not hydrolyze D-Ala-D-lactate, which remains intact
CC for subsequent incorporation into peptidoglycan precursors. Production
CC of precursors ending in D-Ala-D-lactate instead of D-Ala-D-Ala
CC decreases affinity of vancomycin for the peptidoglycan chain and leads
CC to vancomycin resistance (PubMed:7873524).
CC {ECO:0000305|PubMed:7873524}.
CC -!- SIMILARITY: Belongs to the peptidase M15D family. {ECO:0000255|HAMAP-
CC Rule:MF_01924}.
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DR EMBL; M97297; AAA65957.1; -; Genomic_DNA.
DR PIR; S72342; S72342.
DR RefSeq; WP_000402347.1; NZ_WSZC01000116.1.
DR RefSeq; YP_001019034.1; NC_008821.1.
DR RefSeq; YP_001974795.1; NC_010980.1.
DR RefSeq; YP_002128400.1; NC_011140.1.
DR RefSeq; YP_976076.1; NC_008768.1.
DR PDB; 1R44; X-ray; 2.25 A; A/B/C/D/E/F=1-202.
DR PDBsum; 1R44; -.
DR AlphaFoldDB; Q06241; -.
DR SMR; Q06241; -.
DR BindingDB; Q06241; -.
DR ChEMBL; CHEMBL1681622; -.
DR DrugCentral; Q06241; -.
DR MEROPS; M15.011; -.
DR KEGG; ag:AAA65957; -.
DR BioCyc; MetaCyc:MON-15475; -.
DR BRENDA; 3.4.13.22; 2096.
DR SABIO-RK; Q06241; -.
DR EvolutionaryTrace; Q06241; -.
DR PRO; PR:Q06241; -.
DR GO; GO:0016805; F:dipeptidase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0008237; F:metallopeptidase activity; IEA:UniProtKB-KW.
DR GO; GO:0008270; F:zinc ion binding; IEA:UniProtKB-UniRule.
DR GO; GO:0071555; P:cell wall organization; IEA:UniProtKB-KW.
DR GO; GO:0006508; P:proteolysis; IEA:UniProtKB-KW.
DR GO; GO:0046677; P:response to antibiotic; IEA:UniProtKB-KW.
DR Gene3D; 3.30.1380.10; -; 1.
DR HAMAP; MF_01924; A_A_dipeptidase; 1.
DR InterPro; IPR000755; A_A_dipeptidase.
DR InterPro; IPR009045; Hedgehog_sig/DD-Pept_Zn-bd_sf.
DR Pfam; PF01427; Peptidase_M15; 1.
DR PIRSF; PIRSF026671; AA_dipeptidase; 1.
DR SUPFAM; SSF55166; SSF55166; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Antibiotic resistance; Cell wall biogenesis/degradation;
KW Dipeptidase; Direct protein sequencing; Hydrolase; Metal-binding;
KW Metalloprotease; Plasmid; Protease; Zinc.
FT CHAIN 1..202
FT /note="D-alanyl-D-alanine dipeptidase"
FT /id="PRO_0000217840"
FT ACT_SITE 181
FT /note="Proton donor/acceptor"
FT /evidence="ECO:0000305|PubMed:9702193"
FT BINDING 116
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01924,
FT ECO:0000269|PubMed:9702193"
FT BINDING 123
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01924,
FT ECO:0000269|PubMed:9702193"
FT BINDING 184
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01924,
FT ECO:0000269|PubMed:9702193"
FT SITE 71
FT /note="Transition state stabilizer"
FT /evidence="ECO:0000305"
FT STRAND 5..7
FT /evidence="ECO:0007829|PDB:1R44"
FT HELIX 8..10
FT /evidence="ECO:0007829|PDB:1R44"
FT HELIX 20..22
FT /evidence="ECO:0007829|PDB:1R44"
FT STRAND 37..39
FT /evidence="ECO:0007829|PDB:1R44"
FT STRAND 41..43
FT /evidence="ECO:0007829|PDB:1R44"
FT HELIX 44..56
FT /evidence="ECO:0007829|PDB:1R44"
FT STRAND 59..68
FT /evidence="ECO:0007829|PDB:1R44"
FT HELIX 73..83
FT /evidence="ECO:0007829|PDB:1R44"
FT HELIX 92..95
FT /evidence="ECO:0007829|PDB:1R44"
FT STRAND 97..99
FT /evidence="ECO:0007829|PDB:1R44"
FT HELIX 103..106
FT /evidence="ECO:0007829|PDB:1R44"
FT STRAND 108..110
FT /evidence="ECO:0007829|PDB:1R44"
FT HELIX 115..118
FT /evidence="ECO:0007829|PDB:1R44"
FT STRAND 121..128
FT /evidence="ECO:0007829|PDB:1R44"
FT TURN 129..131
FT /evidence="ECO:0007829|PDB:1R44"
FT HELIX 146..148
FT /evidence="ECO:0007829|PDB:1R44"
FT STRAND 153..155
FT /evidence="ECO:0007829|PDB:1R44"
FT HELIX 157..171
FT /evidence="ECO:0007829|PDB:1R44"
FT TURN 172..174
FT /evidence="ECO:0007829|PDB:1R44"
FT STRAND 175..177
FT /evidence="ECO:0007829|PDB:1R44"
FT STRAND 184..189
FT /evidence="ECO:0007829|PDB:1R44"
SQ 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
