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Yorodumi- EMDB-23326: Cyanophycin synthetase 1 from Synechocystis sp. UTEX2470 with ATP... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-23326 | |||||||||
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Title | Cyanophycin synthetase 1 from Synechocystis sp. UTEX2470 with ATP and 16x(Asp-Arg)Cyanophycin synthase (L-aspartate-adding) | |||||||||
Map data | Cyanophycin synthetase 1 from Synechocystis sp. UTEX2470 with ADPCP and 16x(Asp-Arg) mapCyanophycin synthase (L-aspartate-adding) | |||||||||
Sample |
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Function / homology | Function and homology information cyanophycin synthase (L-aspartate-adding) / cyanophycin synthase (L-arginine-adding) / cyanophycin synthetase activity (L-aspartate-adding) / cyanophycin synthetase activity (L-arginine-adding) / macromolecule biosynthetic process / ATP binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Synechocystis sp. PCC 6714 (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.6 Å | |||||||||
Authors | Sharon I / Grogg M / Hilvert D / Schmeing TM | |||||||||
Citation | Journal: Nat Chem Biol / Year: 2021 Title: Structures and function of the amino acid polymerase cyanophycin synthetase. Authors: Itai Sharon / Asfarul S Haque / Marcel Grogg / Indrajit Lahiri / Dieter Seebach / Andres E Leschziner / Donald Hilvert / T Martin Schmeing / Abstract: Cyanophycin is a natural biopolymer produced by a wide range of bacteria, consisting of a chain of poly-L-Asp residues with L-Arg residues attached to the β-carboxylate sidechains by isopeptide ...Cyanophycin is a natural biopolymer produced by a wide range of bacteria, consisting of a chain of poly-L-Asp residues with L-Arg residues attached to the β-carboxylate sidechains by isopeptide bonds. Cyanophycin is synthesized from ATP, aspartic acid and arginine by a homooligomeric enzyme called cyanophycin synthetase (CphA1). CphA1 has domains that are homologous to glutathione synthetases and muramyl ligases, but no other structural information has been available. Here, we present cryo-electron microscopy and X-ray crystallography structures of cyanophycin synthetases from three different bacteria, including cocomplex structures of CphA1 with ATP and cyanophycin polymer analogs at 2.6 Å resolution. These structures reveal two distinct tetrameric architectures, show the configuration of active sites and polymer-binding regions, indicate dynamic conformational changes and afford insight into catalytic mechanism. Accompanying biochemical interrogation of substrate binding sites, catalytic centers and oligomerization interfaces combine with the structures to provide a holistic understanding of cyanophycin biosynthesis. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_23326.map.gz | 483.6 MB | EMDB map data format | |
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Header (meta data) | emd-23326-v30.xml emd-23326.xml | 15 KB 15 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_23326_fsc.xml | 17.7 KB | Display | FSC data file |
Images | emd_23326.png | 211.8 KB | ||
Masks | emd_23326_msk_1.map | 512 MB | Mask map | |
Others | emd_23326_half_map_1.map.gz emd_23326_half_map_2.map.gz | 474.5 MB 474.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-23326 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-23326 | HTTPS FTP |
-Related structure data
Related structure data | 7txuM 7lg5C 7lgjC 7lgmC 7lgnC 7lgqC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_23326.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cyanophycin synthetase 1 from Synechocystis sp. UTEX2470 with ADPCP and 16x(Asp-Arg) map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.855 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_23326_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: Cyanophycin synthetase 1 from Synechocystis sp. UTEX2470 with...
File | emd_23326_half_map_1.map | ||||||||||||
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Annotation | Cyanophycin synthetase 1 from Synechocystis sp. UTEX2470 with ADPCP and 16x(Asp-Arg) half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Cyanophycin synthetase 1 from Synechocystis sp. UTEX2470 with...
File | emd_23326_half_map_2.map | ||||||||||||
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Annotation | Cyanophycin synthetase 1 from Synechocystis sp. UTEX2470 with ADPCP and 16x(Asp-Arg) half map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Cyanophycin synthetase 1 from Synechocystis sp. UTEX2470 with ATP...
Entire | Name: Cyanophycin synthetase 1 from Synechocystis sp. UTEX2470 with ATP and 16x(Asp-Arg)Cyanophycin synthase (L-aspartate-adding) |
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Components |
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-Supramolecule #1: Cyanophycin synthetase 1 from Synechocystis sp. UTEX2470 with ATP...
Supramolecule | Name: Cyanophycin synthetase 1 from Synechocystis sp. UTEX2470 with ATP and 16x(Asp-Arg) type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Synechocystis sp. PCC 6714 (bacteria) |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
-Macromolecule #1: Cyanophycin synthetase 1 from Synechocystis sp. UTEX2470 with ATP...
Macromolecule | Name: Cyanophycin synthetase 1 from Synechocystis sp. UTEX2470 with ATP and 16x(Asp-Arg) type: other / ID: 1 / Classification: other |
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Source (natural) | Organism: Synechocystis sp. PCC 6714 (bacteria) |
Sequence | String: MKILKTLTLR GPNYWSIRRK KLIVMRLDLE DLAERPSNSI PGFYEGLIKV LPSLVEHFCS PGYQGGFLER VKEGTYMGHI VEHVALELQE LVGMTAGFGR TRETSTPGV YNVVYEYVDE QAGRYAGRAA VRLCRSLVDT GDYPRLELEK DLEDLRDLGA NSALGPSTET ...String: MKILKTLTLR GPNYWSIRRK KLIVMRLDLE DLAERPSNSI PGFYEGLIKV LPSLVEHFCS PGYQGGFLER VKEGTYMGHI VEHVALELQE LVGMTAGFGR TRETSTPGV YNVVYEYVDE QAGRYAGRAA VRLCRSLVDT GDYPRLELEK DLEDLRDLGA NSALGPSTET IVTEAEARKI PWMLLSARAM VQLGYGVYQQ R IQATLSSH SGILGVELAC DKEGTKTILQ DAGIPVPRGT TIQYFDDLEE AINDVGGYPV VIKPLDGNHG RGITINVRHW QEAIAAYDLA AEESKSRAII VE RYYEGSD HRVLVVNGKL VAVAERIPAH VTGDGSSTIS ELIEKTNQDP NRGDGHDNIL TKIVVNKTAI DVMERQGYNL DSVLPKDEVV YLRATANLST GGI AIDRTD DIHPENIWLM ERVAKVIGLD IAGIDVVTSD ISKPLRETNG VIVEVNAAPG FRMHVAPSQG LPRNVAAPVL DMLFPPGTPS RIPILAVTGT NGKT TTTRL LAHIYRQTGK TVGYTSTDAI YINEYCVEKG DNTGPQSAGV ILRDPTVEVA VLETARGGIL RAGLAFDSCD VGVVLNVAAD HLGLGDIDTI EQMAK VKSV IAEVVDPSGY AVLNADDPLV AAMADKVKAK VAYFSMNPDN PIIQAHVRRN GIAAVYESGY LSILEGSWTL RVEQAKLIPM TMGGMAPFMI ANALAA CLA AFVNGLDVEV IRQGVRTFTT SAEQTPGRMN LFNLGQHHAL VDYAHNPAGY RAVGDFVKNW QGQRFGVVGG PGDRRDSDLI ELGQIAAQVF DRIIVKE DD DKRGRSEGET ADLIVKGILQ ENPGASYEVI LDETIALNKA LDQVEEKGLV VVFPESVTRA IDLIKVRNPI GENLYFQ |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 3 mg/mL |
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Buffer | pH: 8 |
Grid | Model: C-flat-1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-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: OTHER / Imaging mode: OTHER |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |