[English] 日本語
Yorodumi
- EMDB-50185: KS + AT di-domain of polyketide synthase 13 in Mycobacterium tube... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-50185
TitleKS + AT di-domain of polyketide synthase 13 in Mycobacterium tuberculosis
Map dataFinal map for Pks13 from M. tuberculosis
Sample
  • Complex: Subunit of Pks13
    • Protein or peptide: Polyketide synthase Pks13
KeywordsMycolic acid synthesis / Claisen condensation / cell wall synthesis / BIOSYNTHETIC PROTEIN
Function / homology
Function and homology information


DIM/DIP cell wall layer assembly / fatty acid synthase activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / fatty acid biosynthetic process / cytoplasm
Similarity search - Function
: / Thioesterase / Thioesterase domain / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / Malonyl-CoA ACP transacylase, ACP-binding / : / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. ...: / Thioesterase / Thioesterase domain / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / Malonyl-CoA ACP transacylase, ACP-binding / : / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase domain superfamily / Acyl transferase/acyl hydrolase/lysophospholipase / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Beta-ketoacyl synthase / Ketosynthase family 3 (KS3) domain profile. / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal domain / Beta-ketoacyl synthase, C-terminal domain / Thiolase-like / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
Polyketide synthase Pks13
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria) / Mycobacterium tuberculosis H37Rv (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsJohnston HE / Futterer K
Funding support United Kingdom, 2 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/S000542/1 United Kingdom
Medical Research Council (MRC, United Kingdom)MR/R001154/1 United Kingdom
CitationJournal: Microbiology (Reading) / Year: 2024
Title: Cryo-electron microscopy structure of the di-domain core of polyketide synthase 13, essential for mycobacterial mycolic acid synthesis.
Authors: Hannah E Johnston / Sarah M Batt / Alistair K Brown / Christos G Savva / Gurdyal S Besra / Klaus Fütterer /
Abstract: Mycobacteria are known for their complex cell wall, which comprises layers of peptidoglycan, polysaccharides and unusual fatty acids known as mycolic acids that form their unique outer membrane. ...Mycobacteria are known for their complex cell wall, which comprises layers of peptidoglycan, polysaccharides and unusual fatty acids known as mycolic acids that form their unique outer membrane. Polyketide synthase 13 (Pks13) of , the bacterial organism causing tuberculosis, catalyses the last step of mycolic acid synthesis prior to export to and assembly in the cell wall. Due to its essentiality, Pks13 is a target for several novel anti-tubercular inhibitors, but its 3D structure and catalytic reaction mechanism remain to be fully elucidated. Here, we report the molecular structure of the catalytic core domains of Pks13 (Mt-Pks13), determined by transmission cryo-electron microscopy (cryoEM) to a resolution of 3.4 Å. We observed a homodimeric assembly comprising the ketoacyl synthase (KS) domain at the centre, mediating dimerization, and the acyltransferase (AT) domains protruding in opposite directions from the central KS domain dimer. In addition to the KS-AT di-domains, the cryoEM map includes features not covered by the di-domain structural model that we predicted to contain a dimeric domain similar to dehydratases, yet likely lacking catalytic function. Analytical ultracentrifugation data indicate a pH-dependent equilibrium between monomeric and dimeric assembly states, while comparison with the previously determined structures of Pks13 indicates architectural flexibility. Combining the experimentally determined structure with modelling in AlphaFold2 suggests a structural scaffold with a relatively stable dimeric core, which combines with considerable conformational flexibility to facilitate the successive steps of the Claisen-type condensation reaction catalysed by Pks13.
History
DepositionApr 26, 2024-
Header (metadata) releaseMay 22, 2024-
Map releaseMay 22, 2024-
UpdateOct 30, 2024-
Current statusOct 30, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_50185.png

Downloads & links

-
Map

FileDownload / File: emd_50185.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFinal map for Pks13 from M. tuberculosis
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 360 pix.
= 392.4 Å		1.09 Å/pix.
x 360 pix.
= 392.4 Å		1.09 Å/pix.
x 360 pix.
= 392.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.09 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.000747
Minimum - Maximum-0.058972042 - 0.115474425
Average (Standard dev.)0.00008320585 (±0.0017154444)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 392.40002 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: Half map 1

Fileemd_50185_half_map_1.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map 2

Fileemd_50185_half_map_2.map
AnnotationHalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Subunit of Pks13

EntireName: Subunit of Pks13
Components
  • Complex: Subunit of Pks13
    • Protein or peptide: Polyketide synthase Pks13

-
Supramolecule #1: Subunit of Pks13

SupramoleculeName: Subunit of Pks13 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mycobacterium tuberculosis (bacteria) / Strain: H37Rv
Molecular weightTheoretical: 187 KDa

-
Macromolecule #1: Polyketide synthase Pks13

MacromoleculeName: Polyketide synthase Pks13 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
EC number: Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
Source (natural)Organism: Mycobacterium tuberculosis H37Rv (bacteria)
Molecular weightTheoretical: 186.642188 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MADVAESQEN APAERAELTV PEMRQWLRNW VGKAVGKAPD SIDESVPMVE LGLSSRDAVA MAADIEDLTG VTLSVAVAFA HPTIESLAT RIIEGEPETD LAGDDAEDWS RTGPAERVDI AIVGLSTRFP GEMNTPEQTW QALLEGRDGI TDLPDGRWSE F LEEPRLAA ...String:
MADVAESQEN APAERAELTV PEMRQWLRNW VGKAVGKAPD SIDESVPMVE LGLSSRDAVA MAADIEDLTG VTLSVAVAFA HPTIESLAT RIIEGEPETD LAGDDAEDWS RTGPAERVDI AIVGLSTRFP GEMNTPEQTW QALLEGRDGI TDLPDGRWSE F LEEPRLAA RVAGARTRGG YLKDIKGFDS EFFAVAKTEA DNIDPQQRMA LELTWEALEH ARIPASSLRG QAVGVYIGSS TN DYSFLAV SDPTVAHPYA ITGTSSSIIA NRVSYFYDFH GPSVTIDTAC SSSLVAIHQG VQALRNGEAD VVVAGGVNAL ITP MVTLGF DEIGAVLAPD GRIKSFSADA DGYTRSEGGG MLVLKRVDDA RRDGDAILAV IAGSAVNHDG RSNGLIAPNQ DAQA DVLRR AYKDAGIDPR TVDYIEAHGT GTILGDPIEA EALGRVVGRG RPADRPALLG AVKTNVGHLE SAAGAASMAK VVLAL QHDK LPPSINFAGP SPYIDFDAMR LKMITTPTDW PRYGGYALAG VSSFGFGGAN AHVVVREVLP RDVVEKEPEP EPEPKA AAE PAEAPTLAGH ALRFDEFGNI ITDSAVAEEP EPELPGVTEE ALRLKEAALE ELAAQEVTAP LVPLAVSAFL TSRKKAA AA ELADWMQSPE GQASSLESIG RSLSRRNHGR SRAVVLAHDH DEAIKGLRAV AAGKQAPNVF SVDGPVTTGP VWVLAGFG A QHRKMGKSLY LRNEVFAAWI EKVDALVQDE LGYSVLELIL DDAQDYGIET TQVTIFAIQI ALGELLRHHG AKPAAVIGQ SLGEAASAYF AGGLSLRDAT RAICSRSHLM GEGEAMLFGE YIRLMALVEY SADEIREVFS DFPDLEVCVY AAPTQTVIGG PPEQVDAIL ARAEAEGKFA RKFATKGASH TSQMDPLLGE LTAELQGIKP TSPTCGIFST VHEGRYIKPG GEPIHDVEYW K KGLRHSVY FTHGIRNAVD SGHTTFLELA PNPVALMQVA LTTADAGLHD AQLIPTLARK QDEVSSMVST MAQLYVYGHD LD IRTLFSR ASGPQDYANI PPTRFKRKEH WLPAHFSGDG STYMPGTHVA LPDGRHVWEY APRDGNVDLA ALVRAAAAHV LPD AQLTAA EQRAVPGDGA RLVTTMTRHP GGASVQVHAR IDESFTLVYD ALVSRAGSES VLPTAVGAAT AIAVADGAPV APET PAEDA DAETLSDSLT TRYMPSGMTR WSPDSGETIA ERLGLIVGSA MGYEPEDLPW EVPLIELGLD SLMAVRIKNR VEYDF DLPP IQLTAVRDAN LYNVEKLIEY AVEHRDEVQQ LHEHQKTQTA EEIARAQAEL LHGKVGKTEP VDSEAGVALP SPQNGE QPN PTGPALNVDV PPRDAAERVT FATWAIVTGK SPGGIFNELP RLDDEAAAKI AQRLSERAEG PITAEDVLTS SNIEALA DK VRTYLEAGQI DGFVRTLRAR PEAGGKVPVF VFHPAGGSTV VYEPLLGRLP ADTPMYGFER VEGSIEERAQ QYVPKLIE M QGDGPYVLVG WSLGGVLAYA CAIGLRRLGK DVRFVGLIDA VRAGEEIPQT KEEIRKRWDR YAAFAEKTFN VTIPAIPYE QLEELDDEGQ VRFVLDAVSQ SGVQIPAGII EHQRTSYLDN RAIDTAQIQP YDGHVTLYMA DRYHDDAIMF EPRYAVRQPD GGWGEYVSD LEVVPIGGEH IQAIDEPIIA KVGEHMSRAL GQIEADRTSE VGKQ

UniProtKB: Polyketide synthase Pks13

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.9 mg/mL
BufferpH: 7.9 / Component - Concentration: 20.0 mM / Component - Formula: C4H11NO3 / Component - Name: Tris
Details: 20 mM Tris-HCl pH 7.9, 50 mM NaCl, 2.5 mM beta-mercaptoethanol
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 291 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 1412 / Average exposure time: 3.0 sec. / Average electron dose: 16.5 e/Å2 / Details: movie mode
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: OTHER / Cs: 2.7 mm / Nominal defocus max: 2.7 µm / Nominal defocus min: 1.5 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 310055
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: OTHER / Number images used: 168566
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

+
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