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Protein

D-alanyl-D-alanine dipeptidase

Gene

vanX

Organism
Enterococcus faecium (Streptococcus faecium)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

Catalyzes hydrolysis of the D-alanyl-D-alanine dipeptide.UniRule annotation2 Publications

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).1 Publication

Catalytic activityi

D-Ala-D-Ala + H2O = 2 D-Ala.UniRule annotation2 Publications

Cofactori

Zn2+UniRule annotation2 Publications, Fe2+UniRule annotation2 Publications, Co2+UniRule annotation2 Publications, Ni2+UniRule annotation2 PublicationsNote: Binds 1 zinc ion per subunit. Can also be activated by other divalent cations such as iron, cobalt, or nickel.UniRule annotation2 Publications

Enzyme regulationi

Inhibited by aminoalkyl phosphinate analogs.1 Publication

Kineticsi

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.
  1. KM=1 mM for D-Ala-D-Ala (in the absence of divalent cations)1 Publication
  2. KM=2.8 mM for D-Ala-D-Ser KM=1.7 mM for D-Ser-D-Ala Vmax=12.3 nmol/min/µg enzyme with D-Ala-D-Ala as substrate1 Publication
  1. Vmax=4.7 nmol/min/µg enzyme with D-Ala-D-Ser as substrate1 Publication
  2. Vmax=1.3 nmol/min/µg enzyme with D-Ser-D-Ala as substrate1 Publication

pH dependencei

Optimum pH is 7-9.1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sitei71Transition state stabilizerCurated1
Metal bindingi116Zinc; via tele nitrogen; catalyticUniRule annotation1 Publication1
Metal bindingi123Zinc; catalyticUniRule annotation1 Publication1
Active sitei181Proton donor/acceptor1 Publication1
Metal bindingi184Zinc; via pros nitrogen; catalyticUniRule annotation1 Publication1

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionDipeptidase, Hydrolase, Metalloprotease, Protease
Biological processAntibiotic resistance, Cell wall biogenesis/degradation
LigandMetal-binding, Zinc

Enzyme and pathway databases

BioCyciMetaCyc:MONOMER-15475
BRENDAi3.4.13.22 2096
SABIO-RKQ06241

Protein family/group databases

MEROPSiM15.011

Names & Taxonomyi

Protein namesi
Recommended name:
D-alanyl-D-alanine dipeptidaseUniRule annotation (EC:3.4.13.22UniRule annotation)
Short name:
D-Ala-D-Ala dipeptidaseUniRule annotation
Alternative name(s):
Vancomycin B-type resistance protein VanX
Gene namesi
Name:vanX
Encoded oniPlasmid pIP8160 Publication
OrganismiEnterococcus faecium (Streptococcus faecium)
Taxonomic identifieri1352 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliLactobacillalesEnterococcaceaeEnterococcus

Subcellular locationi

GO - Cellular componenti

Pathology & Biotechi

Chemistry databases

ChEMBLiCHEMBL1681622
DrugBankiDB00512 Vancomycin

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002178401 – 202D-alanyl-D-alanine dipeptidaseAdd BLAST202

Expressioni

Inductioni

By vancomycin, mediated by VanS/VanR.1 Publication

Interactioni

Subunit structurei

Homodimer.2 Publications

Chemistry databases

BindingDBiQ06241

Structurei

Secondary structure

1202
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi5 – 7Combined sources3
Helixi8 – 10Combined sources3
Helixi20 – 22Combined sources3
Beta strandi37 – 39Combined sources3
Beta strandi41 – 43Combined sources3
Helixi44 – 56Combined sources13
Beta strandi59 – 68Combined sources10
Helixi73 – 83Combined sources11
Helixi92 – 95Combined sources4
Beta strandi97 – 99Combined sources3
Helixi103 – 106Combined sources4
Beta strandi108 – 110Combined sources3
Helixi115 – 118Combined sources4
Beta strandi121 – 128Combined sources8
Turni129 – 131Combined sources3
Helixi146 – 148Combined sources3
Beta strandi153 – 155Combined sources3
Helixi157 – 171Combined sources15
Turni172 – 174Combined sources3
Beta strandi175 – 177Combined sources3
Beta strandi184 – 189Combined sources6

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1R44X-ray2.25A/B/C/D/E/F1-202[»]
ProteinModelPortaliQ06241
SMRiQ06241
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ06241

Family & Domainsi

Sequence similaritiesi

Belongs to the peptidase M15D family.UniRule annotation

Phylogenomic databases

KOiK08641

Family and domain databases

Gene3Di3.30.1380.10, 1 hit
HAMAPiMF_01924 A_A_dipeptidase, 1 hit
InterProiView protein in InterPro
IPR000755 A_A_dipeptidase
IPR009045 Hedgehog_sig/DD-Pept_Zn-bd_sf
PfamiView protein in Pfam
PF01427 Peptidase_M15, 1 hit
PIRSFiPIRSF026671 AA_dipeptidase, 1 hit
SUPFAMiSSF55166 SSF55166, 1 hit

Sequencei

Sequence statusi: Complete.

Q06241-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MEIGFTFLDE IVHGVRWDAK YATWDNFTGK PVDGYEVNRI VGTYELAESL
60 70 80 90 100
LKAKELAATQ GYGLLLWDGY RPKRAVNCFM QWAAQPENNL TKESYYPNID
110 120 130 140 150
RTEMISKGYV ASKSSHSRGS AIDLTLYRLD TGELVPMGSR FDFMDERSHH
160 170 180 190 200
AANGISCNEA QNRRRLRSIM ENSGFEAYSL EWWHYVLRDE PYPNSYFDFP

VK
Length:202
Mass (Da):23,380
Last modified:October 1, 1994 - v1
Checksum:i649C00927D08669C
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M97297 Genomic DNA Translation: AAA65957.1
PIRiS72342
RefSeqiWP_000402347.1, NZ_PJZU01000110.1
YP_001019034.1, NC_008821.1
YP_001974795.1, NC_010980.1
YP_002128400.1, NC_011140.1
YP_976076.1, NC_008768.1

Genome annotation databases

GeneIDi4670250
4783136
6385878
6779646
KEGGiag:AAA65957

Similar proteinsi

Entry informationi

Entry nameiVANX_ENTFC
AccessioniPrimary (citable) accession number: Q06241
Entry historyiIntegrated into UniProtKB/Swiss-Prot: October 1, 1994
Last sequence update: October 1, 1994
Last modified: May 23, 2018
This is version 110 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Direct protein sequencing, Plasmid

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