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- PDB-8p3a: bacteriophage T5 l-alanoyl-d-glutamate peptidase Zn2+/Ca2+ form -

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Basic information

Entry
Database: PDB / ID: 8p3a
Titlebacteriophage T5 l-alanoyl-d-glutamate peptidase Zn2+/Ca2+ form
ComponentsL-alanyl-D-glutamate peptidase
KeywordsANTIMICROBIAL PROTEIN / l-alanoyl-d-glutamate peptidase / bacteriophage T5 / endolysin / Zn2+ and Ca2+ containing form
Function / homologyHedgehog signalling/DD-peptidase zinc-binding domain superfamily / Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / viral release from host cell by cytolysis / cell wall organization / peptidase activity / defense response to bacterium / metal ion binding / L-alanyl-D-glutamate peptidase
Function and homology information
Biological speciesEscherichia phage T5 (virus)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsProkhorov, D.A. / Kutyshenko, V.P. / Mikoulinskaia, G.V.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Science Foundation23-24-00210 Russian Federation
CitationJournal: Int J Mol Sci / Year: 2023
Title: Conservative Tryptophan Residue in the Vicinity of an Active Site of the M15 Family l,d-Peptidases: A Key Element in the Catalysis.
Authors: Mikoulinskaia, G.V. / Prokhorov, D.A. / Chernyshov, S.V. / Sitnikova, D.S. / Arakelian, A.G. / Uversky, V.N.
History
DepositionMay 17, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 5, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI
Revision 1.2Jan 15, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: L-alanyl-D-glutamate peptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3923
Polymers15,2861
Non-polymers1052
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology, https://doi.org/10.1107/S0907444908007890 and https://doi.org/10.1039/c9mt00020h
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area190 Å2
ΔGint-36 kcal/mol
Surface area8270 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1target function

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Components

#1: Protein L-alanyl-D-glutamate peptidase / Endolysin / Lysozyme


Mass: 15286.202 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: ZN - ZN2+ ION CA - CA2+ ION / Source: (gene. exp.) Escherichia phage T5 (virus) / Gene: lys, T5.040, T5p039, orf10c / Production host: Escherichia coli B (bacteria)
References: UniProt: Q6QGP7, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
112isotropic12D 1H-15N HSQC
122isotropic12D 1H-13C HSQC
132isotropic13D HN(CA)CB
142isotropic13D CBCA(CO)NH
152isotropic13D C(CO)NH
162isotropic13D 1H-15N TOCSY
172isotropic13D (H)CCH-TOCSY
182isotropic12D CBHD
1122isotropic13D HNCO
1112isotropic12D 1H-13C HSQC aromatic
1102isotropic13D 1H-13C NOESY aliphatic
192isotropic13D 1H-15N NOESY
1132isotropic13D HN(CO)CA
1142isotropic13D 1H-13C NOESY aromatic

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Sample preparation

DetailsType: solution
Contents: 0.8 mM [U-100% 13C; U-100% 15N] l-alanoyl-d-glutamate peptidase, 50 mM [U-100% 2H] sodium acetate, 3 mM Zn(NO3)2, 3 mM CaCl2, 0.03 % sodium azide, 90% H2O/10% D2O
Details: The sample was obtained by renaturation from a solution of 8 M urea in the presence of Zn2+ and Ca2+ salts
Label: endo_T5 Zn-Ca / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.8 mMl-alanoyl-d-glutamate peptidase[U-100% 13C; U-100% 15N]2
50 mMsodium acetate[U-100% 2H]2
3 mMZn(NO3)2natural abundance2
3 mMCaCl2natural abundance2
0.03 %sodium azidenatural abundance2
Sample conditionsDetails: The sample remained stable throughout the entire data collection period. The stability of the sample was monitored by periodically recording 15N-HSQC spectra and comparing them.
Ionic strength: 50 mM / Ionic strength err: 5 / Label: conditions_1 / pH: 4.1 / PH err: 0.05 / Pressure: AMBIENT atm / Pressure err: 0.01 / Temperature: 298 K / Temperature err: 0.2

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 600 MHz / Details: TXI probehead

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure calculation
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
CARARelease: 1.8.4.2Keller and Wuthrichchemical shift assignment
TopSpin2.1Bruker Biospinprocessing
TopSpin2.1Bruker Biospinpeak picking
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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