[English] 日本語
Yorodumi
- EMDB-35609: Cryo-EM structure of phosphoketolase from Bifidobacterium longum ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-35609
TitleCryo-EM structure of phosphoketolase from Bifidobacterium longum in octameric assembly
Map data
Sample
  • Complex: Bifidobacterium longum XFPK in complex with TPP/Mg2+
    • Protein or peptide: Xylulose5phosphatefructose6phosphate phosphoketolase
  • Ligand: THIAMINE DIPHOSPHATE
  • Ligand: MAGNESIUM ION
KeywordsCarbon metabolism / TPP-dependent enzyme / CYTOSOLIC PROTEIN
Function / homology
Function and homology information


aldehyde-lyase activity / carbohydrate metabolic process
Similarity search - Function
Xylulose 5-phosphate/Fructose 6-phosphate phosphoketolase / Xylulose 5-phosphate/Fructose 6-phosphate phosphoketolase, C-terminal / Xylulose 5-phosphate/Fructose 6-phosphate phosphoketolase, N-terminal / Xylulose 5-phosphate/Fructose 6-phosphate phosphoketolase, thiamine diphosphate binding site / Xylulose 5-phosphate/Fructose 6-phosphate phosphoketolase, conserved site / D-xylulose 5-phosphate/D-fructose 6-phosphate phosphoketolase / XFP C-terminal domain / XFP N-terminal domain / Phosphoketolase signature 1. / Phosphoketolase signature 2. ...Xylulose 5-phosphate/Fructose 6-phosphate phosphoketolase / Xylulose 5-phosphate/Fructose 6-phosphate phosphoketolase, C-terminal / Xylulose 5-phosphate/Fructose 6-phosphate phosphoketolase, N-terminal / Xylulose 5-phosphate/Fructose 6-phosphate phosphoketolase, thiamine diphosphate binding site / Xylulose 5-phosphate/Fructose 6-phosphate phosphoketolase, conserved site / D-xylulose 5-phosphate/D-fructose 6-phosphate phosphoketolase / XFP C-terminal domain / XFP N-terminal domain / Phosphoketolase signature 1. / Phosphoketolase signature 2. / Transketolase C-terminal/Pyruvate-ferredoxin oxidoreductase domain II / Thiamin diphosphate-binding fold
Similarity search - Domain/homology
Xylulose5phosphatefructose6phosphate phosphoketolase
Similarity search - Component
Biological speciesBifidobacteriaceae bacterium (bacteria) / Bifidobacterium longum subsp. longum F8 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.68 Å
AuthorsChang C-W / Tsai M-D
Funding support Taiwan, 2 items
OrganizationGrant numberCountry
Academia Sinica (Taiwan)Grant No. AS-CFII-108-110 Taiwan
Academia Sinica (Taiwan)Grant No. AS-KPQ-109-TPP2 Taiwan
CitationJournal: Nat Metab / Year: 2023
Title: An ATP-sensitive phosphoketolase regulates carbon fixation in cyanobacteria.
Authors: Kuan-Jen Lu / Chiung-Wen Chang / Chun-Hsiung Wang / Frederic Y-H Chen / Irene Y Huang / Pin-Hsuan Huang / Cheng-Han Yang / Hsiang-Yi Wu / Wen-Jin Wu / Kai-Cheng Hsu / Meng-Chiao Ho / Ming- ...Authors: Kuan-Jen Lu / Chiung-Wen Chang / Chun-Hsiung Wang / Frederic Y-H Chen / Irene Y Huang / Pin-Hsuan Huang / Cheng-Han Yang / Hsiang-Yi Wu / Wen-Jin Wu / Kai-Cheng Hsu / Meng-Chiao Ho / Ming-Daw Tsai / James C Liao /
Abstract: Regulation of CO fixation in cyanobacteria is important both for the organism and global carbon balance. Here we show that phosphoketolase in Synechococcus elongatus PCC7942 (SeXPK) possesses a ...Regulation of CO fixation in cyanobacteria is important both for the organism and global carbon balance. Here we show that phosphoketolase in Synechococcus elongatus PCC7942 (SeXPK) possesses a distinct ATP-sensing mechanism, where a drop in ATP level allows SeXPK to divert precursors of the RuBisCO substrate away from the Calvin-Benson-Bassham cycle. Deleting the SeXPK gene increased CO fixation particularly during light-dark transitions. In high-density cultures, the Δxpk strain showed a 60% increase in carbon fixation and unexpectedly resulted in sucrose secretion without any pathway engineering. Using cryo-EM analysis, we discovered that these functions were enabled by a unique allosteric regulatory site involving two subunits jointly binding two ATP, which constantly suppresses the activity of SeXPK until the ATP level drops. This magnesium-independent ATP allosteric site is present in many species across all three domains of life, where it may also play important regulatory functions.
History
DepositionMar 10, 2023-
Header (metadata) releaseJun 28, 2023-
Map releaseJun 28, 2023-
UpdateNov 15, 2023-
Current statusNov 15, 2023Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_35609.png

Downloads & links

-
Map

FileDownload / File: emd_35609.map.gz / Format: CCP4 / Size: 216 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 384 pix.
= 318.72 Å		0.83 Å/pix.
x 384 pix.
= 318.72 Å		0.83 Å/pix.
x 384 pix.
= 318.72 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: 0.238
Minimum - Maximum-0.4946258 - 1.32146
Average (Standard dev.)0.0038830866 (±0.053200353)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 318.72 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_35609_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_35609_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Bifidobacterium longum XFPK in complex with TPP/Mg2+

EntireName: Bifidobacterium longum XFPK in complex with TPP/Mg2+
Components
  • Complex: Bifidobacterium longum XFPK in complex with TPP/Mg2+
    • Protein or peptide: Xylulose5phosphatefructose6phosphate phosphoketolase
  • Ligand: THIAMINE DIPHOSPHATE
  • Ligand: MAGNESIUM ION

-
Supramolecule #1: Bifidobacterium longum XFPK in complex with TPP/Mg2+

SupramoleculeName: Bifidobacterium longum XFPK in complex with TPP/Mg2+ / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Bifidobacteriaceae bacterium (bacteria)
Molecular weightTheoretical: 750 KDa

-
Macromolecule #1: Xylulose5phosphatefructose6phosphate phosphoketolase

MacromoleculeName: Xylulose5phosphatefructose6phosphate phosphoketolase / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Bifidobacterium longum subsp. longum F8 (bacteria)
Molecular weightTheoretical: 92.621125 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MTSPVIGTPW KKLNAPVSEE ALEGVDKYWR VANYLSIGQI YLRSNPLMKE PFTREDVKHR LVGHWGTTPG LNFLIGHINR FIADHGQNT VIIMGPGHGG PAGTSQSYLD GTYTETFPKI TKDEAGLQKF FRQFSYPGGI PSHFAPETPG SIHEGGELGY A LSHAYGAI ...String:
MTSPVIGTPW KKLNAPVSEE ALEGVDKYWR VANYLSIGQI YLRSNPLMKE PFTREDVKHR LVGHWGTTPG LNFLIGHINR FIADHGQNT VIIMGPGHGG PAGTSQSYLD GTYTETFPKI TKDEAGLQKF FRQFSYPGGI PSHFAPETPG SIHEGGELGY A LSHAYGAI MDNPSLFVPA IVGDGEAETG PLATGWQSNK LVNPRTDGIV LPILHLNGYK IANPTILSRI SDEELHEFFH GM GYEPYEF VAGFDDEDHM SIHRRFAELW ETIWDEICDI KATAQTDNVH RPFYPMLIFR TPKGWTCPKY IDGKKTEGSW RSH QVPLAS ARDTEAHFEV LKNWLESYKP EELFDANGAV KDDVLAFMPK GELRIGANPN ANGGVIRNDL KLPNLEDYEV KEVA EYGHG WGQLEATRTL GAYTRDIIKN NPRDFRIFGP DETASNRLQA SYEVTNKQWD AGYISDEVDE HMHVSGQVVE QLSEH QMEG FLEAYLLTGR HGIWSSYESF VHVIDSMLNQ HAKWLEATVR EIPWRKPIAS MNLLVSSHVW RQDHNGFSHQ DPGVTS VLL NKCFHNDHVI GIYFATDANM LLAIAEKCYK STNKINAIIA GKQPAATWLT LDEARAELEK GAAAWDWAST AKNNDEA EV VLAAAGDVPT QEIMAASDKL KELGVKFKVV NVADLLSLQS AKENDEALTD EEFADIFTAD KPVLFAYHSY AHDVRGLI Y DRPNHDNFNV HGYEEEGSTT TPYDMVRVNR IDRYELTAEA LRMIDADKYA DKIDELEKFR DEAFQFAVDN GYDHPDYTD WVYSGVNTDK KGAVTATAAT AGDNE

UniProtKB: Xylulose5phosphatefructose6phosphate phosphoketolase

-
Macromolecule #2: THIAMINE DIPHOSPHATE

MacromoleculeName: THIAMINE DIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 8 / Formula: TPP
Molecular weightTheoretical: 425.314 Da
Chemical component information

ChemComp-TPP:
THIAMINE DIPHOSPHATE

-
Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 8 / Formula: MG
Molecular weightTheoretical: 24.305 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.4 mg/mL
BufferpH: 7.2
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 40 sec.
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Detector mode: SUPER-RESOLUTION / Number grids imaged: 1 / Number real images: 6289 / Average exposure time: 2.5 sec. / Average electron dose: 42.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

3ai7

Final reconstructionNumber classes used: 3 / Resolution.type: BY AUTHOR / Resolution: 2.68 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.0) / Number images used: 590627
Initial angle assignmentType: OTHER
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

3ai7


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-8io6:
Cryo-EM structure of phosphoketolase from Bifidobacterium longum in octameric assembly

+
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