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- PDB-8xz2: The structural model of a homodimeric D-Ala-D-Ala metallopeptidas... -

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Basic information

Entry
Database: PDB / ID: 8xz2
TitleThe structural model of a homodimeric D-Ala-D-Ala metallopeptidase, VanX, from vancomycin-resistant bacteria
ComponentsD-alanyl-D-alanine dipeptidase
KeywordsMETAL BINDING PROTEIN / acid-selective unlabeling / antimicrobial resistance / homodimer / residual dipolar coupling (RDC) / transfer cross saturation (TCS) / vancomycin-resistant enterococci / VanX
Function / homology
Function and homology information


D-Ala-D-Ala dipeptidase / dipeptidase activity / cell wall organization / metallopeptidase activity / response to antibiotic / proteolysis / zinc ion binding
Similarity search - Function
D-alanyl-D-alanine dipeptidase / D-ala-D-ala dipeptidase / Hedgehog signalling/DD-peptidase zinc-binding domain superfamily
Similarity search - Domain/homology
D-alanyl-D-alanine dipeptidase
Similarity search - Component
Biological speciesEnterococcus faecium (bacteria)
MethodSOLUTION NMR / molecular dynamics
AuthorsKonuma, T. / Takai, T. / Tsuchiya, C. / Nishida, M. / Hashiba, M. / Yamada, Y. / Shirai, H. / Motoda, Y. / Nagadoi, A. / Chikaishi, E. ...Konuma, T. / Takai, T. / Tsuchiya, C. / Nishida, M. / Hashiba, M. / Yamada, Y. / Shirai, H. / Motoda, Y. / Nagadoi, A. / Chikaishi, E. / Akagi, K. / Akashi, S. / Yamazaki, T. / Akutsu, H. / Oe, A. / Ikegami, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: Protein Sci. / Year: 2024
Title: Analysis of the homodimeric structure of a D-Ala-D-Ala metallopeptidase, VanX, from vancomycin-resistant bacteria.
Authors: Konuma, T. / Takai, T. / Tsuchiya, C. / Nishida, M. / Hashiba, M. / Yamada, Y. / Shirai, H. / Motoda, Y. / Nagadoi, A. / Chikaishi, E. / Akagi, K.I. / Akashi, S. / Yamazaki, T. / Akutsu, H. / Ikegami, T.
History
DepositionJan 20, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 22, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: D-alanyl-D-alanine dipeptidase
C: D-alanyl-D-alanine dipeptidase


Theoretical massNumber of molelcules
Total (without water)46,8162
Polymers46,8162
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints, transfer cross saturation inter-subunit NOE
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area2110 Å2
ΔGint-2 kcal/mol
Surface area16850 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)4 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein D-alanyl-D-alanine dipeptidase / D-Ala-D-Ala dipeptidase / Vancomycin B-type resistance protein VanX


Mass: 23408.168 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecium (bacteria) / Gene: vanX / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: Q06241, D-Ala-D-Ala dipeptidase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111anisotropic11H/15N TROSY IPAP
121isotropic2Transfer cross saturation

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Sample preparation

DetailsType: solution
Contents: 0.154 mM [U-13C; U-15N; U-2H] VanX, 90% H2O/10% D2O
Details: The coat protein of Pf1 filamentous bacteriophage was added as an alignment medium at a concentration of 27 mg/mL to a solution of 0.154 mM [2H, 15N, 13C]-VanX.
Label: 15N_13C_2H_labelled / Solvent system: 90% H2O/10% D2O
SampleConc.: 0.154 mM / Component: VanX / Isotopic labeling: [U-13C; U-15N; U-2H]
Sample conditionsIonic strength: 50 mM / Label: conditions_1 / pH: 7 / Pressure: 1 atm / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE III HDBrukerAVANCE III HD8001
Bruker AVANCE III HDBrukerAVANCE III HD5002

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Processing

NMR software
NameVersionDeveloperClassification
HADDOCK2.4Bonvinstructure calculation
PALESZweckstetter M and Bax Adata analysis
NMRFAM-SPARKYLee W, Tonelli M, and Markley JL.peak picking
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: molecular dynamics / Software ordinal: 1
Details: In total, 132 RDC-based orientational restraints and seven TCS-based intersubunit ambiguous restraints were imposed in the calculations. The latter restraints involved residues in segments B ...Details: In total, 132 RDC-based orientational restraints and seven TCS-based intersubunit ambiguous restraints were imposed in the calculations. The latter restraints involved residues in segments B (selected from residues exhibiting remarkable TCS effects) and C (selected from residues exhibiting both remarkable and minor TCS effects). These constraints were applied c2-symmetrically between the subunits B and C in the calculations.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 4

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