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Yorodumi- EMDB-35612: Cryo-EM structure of cyanobacteria phosphoketolase complexed with... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-35612 | |||||||||
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Title | Cryo-EM structure of cyanobacteria phosphoketolase complexed with AMPPNPin dodecameric assembly | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Carbon metabolism / TPP-dependent enzyme / CYTOSOLIC PROTEIN | |||||||||
Function / homology | : Function and homology information | |||||||||
Biological species | Synechococcus (bacteria) / Synechococcus elongatus (strain ATCC 33912 / PCC 7942 / FACHB-805) (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.36 Å | |||||||||
Authors | Chang C-W / Tsai M-D | |||||||||
Funding support | Taiwan, 2 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_35612.map.gz | 108.3 MB | EMDB map data format | |
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Header (meta data) | emd-35612-v30.xml emd-35612.xml | 17.5 KB 17.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_35612_fsc.xml | 13.9 KB | Display | FSC data file |
Images | emd_35612.png | 2 MB | ||
Filedesc metadata | emd-35612.cif.gz | 6.5 KB | ||
Others | emd_35612_half_map_1.map.gz emd_35612_half_map_2.map.gz | 200.6 MB 200.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-35612 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-35612 | HTTPS FTP |
-Related structure data
Related structure data | 8io9MC 8io6C 8io7C 8io8C 8ioaC 8ioeC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_35612.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.82 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_35612_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_35612_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : cyanobacteria phosphoketolase complexed with AMPPNP
Entire | Name: cyanobacteria phosphoketolase complexed with AMPPNP |
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Components |
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-Supramolecule #1: cyanobacteria phosphoketolase complexed with AMPPNP
Supramolecule | Name: cyanobacteria phosphoketolase complexed with AMPPNP / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Synechococcus (bacteria) |
Molecular weight | Theoretical: 890 KDa |
-Macromolecule #1: Probable phosphoketolase
Macromolecule | Name: Probable phosphoketolase / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO |
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Source (natural) | Organism: Synechococcus elongatus (strain ATCC 33912 / PCC 7942 / FACHB-805) (bacteria) Strain: ATCC 33912 / PCC 7942 / FACHB-805 |
Molecular weight | Theoretical: 89.133211 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MTSTLQATDI ATLSPNEQAA IDAWWRAANY LSVGQIYLRD NPLLQEPLRP EHIKQRLLGH WGSDPGLSFV YVHLNRLIRR LDLNLIYVT GPGHGAPALL ANAWLEGTYS EVYPNCQQST AGLQQFFKQF SFPGGIGSHC TPETPGSIHE GGELGYSLSH A FGAALDNP ...String: MTSTLQATDI ATLSPNEQAA IDAWWRAANY LSVGQIYLRD NPLLQEPLRP EHIKQRLLGH WGSDPGLSFV YVHLNRLIRR LDLNLIYVT GPGHGAPALL ANAWLEGTYS EVYPNCQQST AGLQQFFKQF SFPGGIGSHC TPETPGSIHE GGELGYSLSH A FGAALDNP DLIVACVIGD GEAETGPLAT SWHSNKFLNP AQDGAVLPIL HLNGYKIANP TLLSRISHEE LRSLFIGYGY EP FFVEGND PAILHGVMAS TLATCVQKIQ AIQAAARSGE SSDRPMWPMI VLRTPKGWTG PATIKGHVVE GSWRSHQVPM ADV LTNPEH LQLLEDWLRS YRPEELFDAS GAPVAELQAI APIGDRRMSA NPVTNGGLLR RALTLPDFRD QAVSVPAPGK SRAD STRPL GQFLREVIRH NPDNFRLFGP DETASNRLDA VYEVTSKVWL GDRIPEDEDG GHLSDRGRVM EILSEHTLEG WLEAY LLTG RHGFFATYEA FAHVIDSMVN QHAKWLDVSK REVDWRAPVS SLNILLSSTV WRQDHNGFSH QDPGFIDLVT NKSARV TRI YLPPDANCLL SVADHCLRST DYINVIVADK QSHLQYLDAE AAARHCAKGI GIWDWASNDQ GASPDVVIAS CGDVVTL EA LAATALLREH FPDLKIRFVN VVDLFRLQPD TEHPHGLSDR DFDSLFTVDK PIIFNFHGYP WLIHKLAYRR HNHNNLHV R GYKEVGNINT PLELAIRNQV DRFNLAIDVI DRVPHLRDRG AHVKEWLKDQ IHDHIQYAYQ EGIDRPEINQ WQWPF UniProtKB: UNIPROTKB: A0A8T9U4A0 |
-Macromolecule #2: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
Macromolecule | Name: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / type: ligand / ID: 2 / Number of copies: 12 / Formula: ANP |
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Molecular weight | Theoretical: 506.196 Da |
Chemical component information | ChemComp-ANP: |
-Macromolecule #3: THIAMINE DIPHOSPHATE
Macromolecule | Name: THIAMINE DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 12 / Formula: TPP |
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Molecular weight | Theoretical: 425.314 Da |
Chemical component information | ChemComp-TPP: |
-Macromolecule #4: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 12 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.4 mg/mL |
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Buffer | pH: 7.2 |
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 40 sec. |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 165000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Detector mode: SUPER-RESOLUTION / Number grids imaged: 1 / Number real images: 2839 / Average exposure time: 4.5 sec. / Average electron dose: 59.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
-Atomic model buiding 1
Initial model | PDB ID: Chain - Source name: PDB / Chain - Initial model type: experimental model / Details: Based on S. elongatus XPK protein sequence. |
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Refinement | Space: REAL / Protocol: RIGID BODY FIT |
Output model | PDB-8io9: |