[English] 日本語
Yorodumi
- EMDB-41299: Structural basis of peptidoglycan synthesis by E. coli RodA-PBP2 ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-41299
TitleStructural basis of peptidoglycan synthesis by E. coli RodA-PBP2 complex
Map data
Sample
  • Complex: RodA-PBP2
    • Protein or peptide: Peptidoglycan glycosyltransferase MrdB
    • Protein or peptide: Peptidoglycan D,D-transpeptidase MrdA
KeywordsPeptidoglycan / glycosyltransferase / enzyme / MEMBRANE PROTEIN
Function / homology
Function and homology information


lipid-linked peptidoglycan transporter activity / peptidoglycan glycosyltransferase / peptidoglycan L,D-transpeptidase activity / peptidoglycan glycosyltransferase activity / serine-type D-Ala-D-Ala carboxypeptidase / serine-type D-Ala-D-Ala carboxypeptidase activity / cell division site / glycosyltransferase activity / penicillin binding / peptidoglycan biosynthetic process ...lipid-linked peptidoglycan transporter activity / peptidoglycan glycosyltransferase / peptidoglycan L,D-transpeptidase activity / peptidoglycan glycosyltransferase activity / serine-type D-Ala-D-Ala carboxypeptidase / serine-type D-Ala-D-Ala carboxypeptidase activity / cell division site / glycosyltransferase activity / penicillin binding / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / cell division / proteolysis / plasma membrane
Similarity search - Function
Probable peptidoglycan glycosyltransferase RodA/MrdB / Cell cycle, FtsW / RodA / SpoVE, conserved site / Cell cycle proteins ftsW / rodA / spoVE signature. / Penicillin-binding protein 2 / Probable peptidoglycan glycosyltransferase FtsW/RodA / Cell cycle protein / Penicillin-binding protein, dimerisation domain / Penicillin-binding Protein dimerisation domain / Penicillin-binding protein, dimerisation domain superfamily / : ...Probable peptidoglycan glycosyltransferase RodA/MrdB / Cell cycle, FtsW / RodA / SpoVE, conserved site / Cell cycle proteins ftsW / rodA / spoVE signature. / Penicillin-binding protein 2 / Probable peptidoglycan glycosyltransferase FtsW/RodA / Cell cycle protein / Penicillin-binding protein, dimerisation domain / Penicillin-binding Protein dimerisation domain / Penicillin-binding protein, dimerisation domain superfamily / : / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Beta-lactamase/transpeptidase-like
Similarity search - Domain/homology
Peptidoglycan glycosyltransferase MrdB / Peptidoglycan D,D-transpeptidase MrdA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsNygaard R / Mancia F
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM132120 United States
CitationJournal: Nat Commun / Year: 2023
Title: Structural basis of peptidoglycan synthesis by E. coli RodA-PBP2 complex.
Authors: Rie Nygaard / Chris L B Graham / Meagan Belcher Dufrisne / Jonathan D Colburn / Joseph Pepe / Molly A Hydorn / Silvia Corradi / Chelsea M Brown / Khuram U Ashraf / Owen N Vickery / Nicholas ...Authors: Rie Nygaard / Chris L B Graham / Meagan Belcher Dufrisne / Jonathan D Colburn / Joseph Pepe / Molly A Hydorn / Silvia Corradi / Chelsea M Brown / Khuram U Ashraf / Owen N Vickery / Nicholas S Briggs / John J Deering / Brian Kloss / Bruno Botta / Oliver B Clarke / Linda Columbus / Jonathan Dworkin / Phillip J Stansfeld / David I Roper / Filippo Mancia /
Abstract: Peptidoglycan (PG) is an essential structural component of the bacterial cell wall that is synthetized during cell division and elongation. PG forms an extracellular polymer crucial for cellular ...Peptidoglycan (PG) is an essential structural component of the bacterial cell wall that is synthetized during cell division and elongation. PG forms an extracellular polymer crucial for cellular viability, the synthesis of which is the target of many antibiotics. PG assembly requires a glycosyltransferase (GT) to generate a glycan polymer using a Lipid II substrate, which is then crosslinked to the existing PG via a transpeptidase (TP) reaction. A Shape, Elongation, Division and Sporulation (SEDS) GT enzyme and a Class B Penicillin Binding Protein (PBP) form the core of the multi-protein complex required for PG assembly. Here we used single particle cryo-electron microscopy to determine the structure of a cell elongation-specific E. coli RodA-PBP2 complex. We combine this information with biochemical, genetic, spectroscopic, and computational analyses to identify the Lipid II binding sites and propose a mechanism for Lipid II polymerization. Our data suggest a hypothesis for the movement of the glycan strand from the Lipid II polymerization site of RodA towards the TP site of PBP2, functionally linking these two central enzymatic activities required for cell wall peptidoglycan biosynthesis.
History
DepositionJul 20, 2023-
Header (metadata) releaseAug 30, 2023-
Map releaseAug 30, 2023-
UpdateMay 1, 2024-
Current statusMay 1, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_41299.png

Downloads & links

-
Map

FileDownload / File: emd_41299.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 400 pix.
= 332. Å		0.83 Å/pix.
x 400 pix.
= 332. Å		0.83 Å/pix.
x 400 pix.
= 332. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.043
Minimum - Maximum-0.16517833 - 0.8442311
Average (Standard dev.)0.00046289113 (±0.00810673)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 332.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

-
Entire : RodA-PBP2

EntireName: RodA-PBP2
Components
  • Complex: RodA-PBP2
    • Protein or peptide: Peptidoglycan glycosyltransferase MrdB
    • Protein or peptide: Peptidoglycan D,D-transpeptidase MrdA

-
Supramolecule #1: RodA-PBP2

SupramoleculeName: RodA-PBP2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Nanodisc were formed using MSP1E3D1 and POPG lipid
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 111.803 KDa

-
Macromolecule #1: Peptidoglycan glycosyltransferase MrdB

MacromoleculeName: Peptidoglycan glycosyltransferase MrdB / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 40.508766 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MTDNPNKKTF WDKVHLDPTM LLILLALLVY SALVIWSASG QDIGMMERKI GQIAMGLVIM VVMAQIPPRV YEGWAPYLYI ICIILLVAV DAFGAISKGA QRWLDLGIVR FQPSEIAKIA VPLMVARFIN RDVCPPSLKN TGIALVLIFM PTLLVAAQPD L GTSILVAL ...String:
MTDNPNKKTF WDKVHLDPTM LLILLALLVY SALVIWSASG QDIGMMERKI GQIAMGLVIM VVMAQIPPRV YEGWAPYLYI ICIILLVAV DAFGAISKGA QRWLDLGIVR FQPSEIAKIA VPLMVARFIN RDVCPPSLKN TGIALVLIFM PTLLVAAQPD L GTSILVAL SGLFVLFLSG LSWRLIGVAV VLVAAFIPIL WFFLMHDYQR QRVMMLLDPE SDPLGAGYHI IQSKIAIGSG GL RGKGWLH GTQSQLEFLP ERHTDFIFAV LAEELGLVGI LILLALYILL IMRGLWIAAR AQTTFGRVMA GGLMLILFVY VFV NIGMVS GILPVVGVPL PLVSYGGSAL IVLMAGFGIV MSIHTHRKML SKSV

UniProtKB: Peptidoglycan glycosyltransferase MrdB

-
Macromolecule #2: Peptidoglycan D,D-transpeptidase MrdA

MacromoleculeName: Peptidoglycan D,D-transpeptidase MrdA / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 70.943414 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKLQNSFRDY TAESALFVRR ALVAFLGILL LTGVLIANLY NLQIVRFTDY QTRSNENRIK LVPIAPSRGI IYDRNGIPLA LNRTIYQIE MMPEKVDNVQ QTLDALRSVV DLTDDDIAAF RKERARSHRF TSIPVKTNLT EVQVARFAVN QYRFPGVEVK G YKRRYYPY ...String:
MKLQNSFRDY TAESALFVRR ALVAFLGILL LTGVLIANLY NLQIVRFTDY QTRSNENRIK LVPIAPSRGI IYDRNGIPLA LNRTIYQIE MMPEKVDNVQ QTLDALRSVV DLTDDDIAAF RKERARSHRF TSIPVKTNLT EVQVARFAVN QYRFPGVEVK G YKRRYYPY GSALTHVIGY VSKINDKDVE RLNNDGKLAN YAATHDIGKL GIERYYEDVL HGQTGYEEVE VNNRGRVIRQ LK EVPPQAG HDIYLTLDLK LQQYIETLLA GSRAAVVVTD PRTGGVLALV STPSYDPNLF VDGISSKDYS ALLNDPNTPL VNR ATQGVY PPASTVKPYV AVSALSAGVI TRNTTLFDPG WWQLPGSEKR YRDWKKWGHG RLNVTRSLEE SADTFFYQVA YDMG IDRLS EWMGKFGYGH YTGIDLAEER SGNMPTREWK QKRFKKPWYQ GDTIPVGIGQ GYWTATPIQM SKALMILIND GIVKV PHLL MSTAEDGKQV PWVQPHEPPV GDIHSGYWEL AKDGMYGVAN RPNGTAHKYF ASAPYKIAAK SGTAQVFGLK ANETYN AHK IAERLRDHKL MTAFAPYNNP QVAVAMILEN GGAGPAVGTL MRQILDHIML GDNNTDLPAE NPAVAAAEDH

UniProtKB: Peptidoglycan D,D-transpeptidase MrdA

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.66 mg/mL
BufferpH: 7
Component:
ConcentrationNameFormula
20.0 mMHEPES
150.0 mMSodium ChlorideNaCl
1.0 mMTCEPtris(2-carboxyethyl)phosphine
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 11120 / Average exposure time: 2.5 sec. / Average electron dose: 58.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm

+
Image processing

Particle selectionNumber selected: 4415933
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.12 and 3.2) / Software - details: Local refinement / Number images used: 399000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

-
Atomic model buiding 1

Initial modelPDB ID:

4f0a


Chain - Source name: PDB / Chain - Initial model type: experimental model
Output model

PDB-8tj3:
Structural basis of peptidoglycan synthesis by E. coli RodA-PBP2 complex

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more