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- PDB-6fzk: NMR structure of UB2H, regulatory domain of PBP1b from E. coli -

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Basic information

Entry
Database: PDB / ID: 6fzk
TitleNMR structure of UB2H, regulatory domain of PBP1b from E. coli
ComponentsPenicillin-binding protein 1B
KeywordsTRANSFERASE / UB2H domain of PBP1b / regulatory domain
Function / homology
Function and homology information


positive regulation of bipolar cell growth / cell wall repair / peptidoglycan glycosyltransferase / peptidoglycan glycosyltransferase activity / serine-type D-Ala-D-Ala carboxypeptidase / serine-type D-Ala-D-Ala carboxypeptidase activity / penicillin binding / peptidoglycan biosynthetic process / peptidoglycan-based cell wall / regulation of cell shape ...positive regulation of bipolar cell growth / cell wall repair / peptidoglycan glycosyltransferase / peptidoglycan glycosyltransferase activity / serine-type D-Ala-D-Ala carboxypeptidase / serine-type D-Ala-D-Ala carboxypeptidase activity / penicillin binding / peptidoglycan biosynthetic process / peptidoglycan-based cell wall / regulation of cell shape / outer membrane-bounded periplasmic space / response to antibiotic / proteolysis / membrane / plasma membrane
Similarity search - Function
Penicillin-binding protein 1B / Bifunctional transglycosylase second domain / Transglycosylase PBP1b, N-terminal transmembrane domain / Transmembrane domain of transglycosylase PBP1 at N-terminal / Bifunctional transglycosylase second domain / Glycosyl transferase, family 51 / Penicillin binding protein transglycosylase domain / Transglycosylase / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain ...Penicillin-binding protein 1B / Bifunctional transglycosylase second domain / Transglycosylase PBP1b, N-terminal transmembrane domain / Transmembrane domain of transglycosylase PBP1 at N-terminal / Bifunctional transglycosylase second domain / Glycosyl transferase, family 51 / Penicillin binding protein transglycosylase domain / Transglycosylase / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Beta-lactamase/transpeptidase-like / Lysozyme-like domain superfamily
Similarity search - Domain/homology
Penicillin-binding protein 1B
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailsRegulatory domain of Penicillin-Binding Protein
AuthorsSimorre, J.P. / Maya Martinez, R.C. / Bougault, C. / Egan, A.J.F. / Vollmer, W.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research Agency60- 60900-98-207 France
CitationJournal: Mol. Microbiol. / Year: 2018
Title: Induced conformational changes activate the peptidoglycan synthase PBP1B.
Authors: Egan, A.J.F. / Maya-Martinez, R. / Ayala, I. / Bougault, C.M. / Banzhaf, M. / Breukink, E. / Vollmer, W. / Simorre, J.P.
History
DepositionMar 15, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 20, 2019Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_spectrometer.model
Revision 1.3Jun 19, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Penicillin-binding protein 1B


Theoretical massNumber of molelcules
Total (without water)13,1841
Polymers13,1841
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7840 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 75020
RepresentativeModel #1lowest energy

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Components

#1: Protein Penicillin-binding protein 1B / PBP1b / Murein polymerase


Mass: 13183.969 Da / Num. of mol.: 1 / Fragment: PBP1b (108-200)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: mrcB, pbpF, ponB, b0149, JW0145 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P02919, peptidoglycan glycosyltransferase, serine-type D-Ala-D-Ala carboxypeptidase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
1131isotropic32D 1H-15N HSQC
121isotropic23D HNCO
131isotropic23D HN(CA)CO
141isotropic33D BESTROSY-HN(CA)CB
151isotropic33D BESTROSY-HN(CO)CACB
161isotropic22D 1H-13C HSQC aliphatic
171isotropic22D 1H-13C HSQC aromatic
181isotropic23D (H)CCH-TOCSY
191isotropic23D (H)CCH-TOCSY
1101isotropic43D 1H-15N NOESY
1111isotropic43D 1H-13C NOESY aliphatic
1121isotropic43D 1H-13C NOESY aromatic

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Sample preparation

DetailsType: solution
Contents: 500 uM [U-13C; U-15N] UB2H, 450 uM [U-99% 15N] UB2H, 100 uM not label UB2H_Lys-Oxyl, 90% H2O and 10% D2O
Label: 15N-13C sample / Solvent system: 90% H2O and 10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
500 uMUB2H double label[U-13C; U-15N]1
450 uMUB2H single label[U-99% 15N]1
100 uMUB2H_Lys-Oxylnot label1
Sample conditionsIonic strength: 200 mM / Label: General condition / pH: 7.5 / Pressure: 1 atm / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III6001
Bruker AVANCE IIIBrukerAVANCE III7002
Bruker AVANCE IIIBrukerAVANCE III8503
Bruker AVANCE IIIBrukerAVANCE III9504

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Processing

NMR software
NameVersionDeveloperClassification
ARIA2.3Rieping W., Habeck M., Bardiaux B., Bernard A , Nilges M.structure calculation
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
CcpNmr Analysis2.4CCPNdata analysis
TALOS+Yang Shen, Frank Delaglio, Gabriel Cornilescu, and Ad Baxdata analysis
UNIO2.0.2Torsten Herrmannstructure calculation
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: 20 / Conformers calculated total number: 750 / Conformers submitted total number: 20

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