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- PDB-6g5r: Structure of the UB2H domain of E.coli PBP1B in complex with LpoB -

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Basic information

Entry
Database: PDB / ID: 6g5r
TitleStructure of the UB2H domain of E.coli PBP1B in complex with LpoB
ComponentsPenicillin-binding protein 1B
KeywordsTRANSFERASE / Murein polymerase / Complex / LpoB / PBP1B / E. coli / Transpeptidase / Glycosyltransferase / Peptidoglican
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 (E. coli)
MethodSOLUTION NMR / simulated annealing
Model detailsRegulatory domain of Penicillin-Binding Protein
AuthorsSimorre, J.P. / Maya Martinez, R.C. / Bougault, C.
Funding support France, United Kingdom, 3items
OrganizationGrant numberCountry
French National Research AgencyANR-14-JAMR-0003 France
Wellcome Trust101824/Z/13/Z United Kingdom
French National Research AgencyANR-10-INSB-05-02 France
Citation
Journal: 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.
#1: Journal: J. Biol. Chem. / Year: 2017
Title: Structural Insights into Inhibition of Escherichia coli Penicillin-binding Protein 1B.
Authors: King, D.T. / Wasney, G.A. / Nosella, M. / Fong, A. / Strynadka, N.C.
History
DepositionMar 29, 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:
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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 area8390 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: UB2H domain (108-200)
Source method: isolated from a genetically manipulated source
Details: UB2H is a domain of E. coli of PBP1B (residues 108-200)
Source: (gene. exp.) Escherichia coli (strain K12) (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
111isotropic22D 1H-15N HSQC
121isotropic23D HNCO
131isotropic23D HN(CA)CO
141isotropic43D BESTROSY-HN(CA)CB
151isotropic43D BESTROSY-HN(CO)CACB
161isotropic42D 1H-13C HSQC aliphatic
171isotropic42D 1H-13C HSQC aromatic
181isotropic43D (H)CCH-TOCSY
191isotropic43D (H)CCH-TOCSY
1101isotropic33D 1H-15N NOESY
1111isotropic33D 1H-13C NOESY aliphatic
1121isotropic43D 1H-13C NOESY aromatic

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution1400 uM [U-13C; U-15N] UB2H domain, 480 uM None LpoB, 90% H2O and 10% D2O15N,13C-UB2H in complex 1:1 with unlabeled LpoB15N_13C-UB2H_LpoB90% H2O and 10% D2O
solution2450 uM [U-15N] UB2H, 540 uM None LpoB, 90% H2O/10% D2O15N-UB2H in complex 1:1 with unlabeled LpoB15N_UB2H_LpoB90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
400 uMUB2H domain[U-13C; U-15N]1
480 uMLpoBNone1
450 uMUB2H[U-15N]2
540 uMLpoBNone2
Sample conditionsDetails: 10 mM Tris/HCl, 200 mM NaCl / Ionic strength: 210 mM / Ionic strength err: 5 / Label: condition_1 / pH: 7.5 / Pressure: 1 atm / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE7002
Bruker AVANCE IIIBrukerAVANCE III8504
Bruker US2BrukerUS29503

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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 Analysis2.4CCPNchemical shift assignment
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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