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- PDB-7wae: Trichodesmium erythraeum cyanophycin synthetase 1 (TeCphA1) with ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7wae | |||||||||
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Title | Trichodesmium erythraeum cyanophycin synthetase 1 (TeCphA1) with ATPgammaS, 4x(beta-Asp-Arg), and aspartate | |||||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() Synthetic construct (others) | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Miyakawa, T. / Yang, J. / Kawasaki, M. / Adachi, N. / Fujii, A. / Miyauchi, Y. / Muramatsu, T. / Moriya, T. / Senda, T. / Tanokura, M. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural bases for aspartate recognition and polymerization efficiency of cyanobacterial cyanophycin synthetase. Authors: Takuya Miyakawa / Jian Yang / Masato Kawasaki / Naruhiko Adachi / Ayumu Fujii / Yumiko Miyauchi / Tomonari Muramatsu / Toshio Moriya / Toshiya Senda / Masaru Tanokura / ![]() ![]() Abstract: Cyanophycin is a natural biopolymer consisting of equimolar amounts of aspartate and arginine as the backbone and branched sidechain, respectively. It is produced by a single enzyme, cyanophycin ...Cyanophycin is a natural biopolymer consisting of equimolar amounts of aspartate and arginine as the backbone and branched sidechain, respectively. It is produced by a single enzyme, cyanophycin synthetase (CphA1), and accumulates as a nitrogen reservoir during N fixation by most cyanobacteria. A recent structural study showed that three constituent domains of CphA1 function as two distinct catalytic sites and an oligomerization interface in cyanophycin synthesis. However, it remains unclear how the ATP-dependent addition of aspartate to cyanophycin is initiated at the catalytic site of the glutathione synthetase-like domain. Here, we report the cryogenic electron microscopy structures of CphA1, including a complex with aspartate, cyanophycin primer peptide, and ATP analog. These structures reveal the aspartate binding mode and phosphate-binding loop movement to the active site required for the reaction. Furthermore, structural and mutational data show a potential role of protein dynamics in the catalytic efficiency of the arginine condensation reaction. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 545 KB | Display | ![]() |
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PDB format | ![]() | 448.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 32383MC ![]() 7wacC ![]() 7wadC ![]() 7wafC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
-Protein / Protein/peptide , 2 types, 8 molecules ABCDJKLM
#1: Protein | ![]() Mass: 99079.914 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: IMS101 / Gene: Tery_1965 / Production host: ![]() ![]() ![]() References: UniProt: Q113V7, ![]() ![]() #2: Protein/peptide | Mass: 478.366 Da / Num. of mol.: 4 / Source method: obtained synthetically Details: Backbone peptide bonds are formed between Asp residues. An Arg residue forms a peptide bond with the beta-carboxy group of Asp. Source: (synth.) Synthetic construct (others) |
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-Non-polymers , 4 types, 28 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/AGS.gif)
![](data/chem/img/ASP.gif)
![](data/chem/img/ARG.gif)
![](data/chem/img/AGS.gif)
![](data/chem/img/ASP.gif)
![](data/chem/img/ARG.gif)
#3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-AGS / #5: Chemical | ChemComp-ASP / | ![]() #6: Chemical | ChemComp-ARG / ![]() |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: ![]() |
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Sample preparation
Component | Name: TeCphA1 with ATPgammaS, 4x(beta-Asp-Arg) and aspartate Type: COMPLEX / Details: Homotetramer / Entity ID: #1 / Source: RECOMBINANT | ||||||||||||||||||||||||
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Molecular weight | Value: 0.40 MDa / Experimental value: NO | ||||||||||||||||||||||||
Source (natural) | Organism: ![]() ![]() | ||||||||||||||||||||||||
Source (recombinant) | Organism: ![]() ![]() ![]() ![]() | ||||||||||||||||||||||||
Buffer solution | pH: 8.2 Details: The buffer contains 10 mM ATPgammaS, 100 mM aspartate and 20 mM 4-mer cyanophycin peptide as ligands. | ||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied![]() ![]() | ||||||||||||||||||||||||
Specimen support | Details: The grid was washed by acetone prior to use. / Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 | ||||||||||||||||||||||||
Vitrification![]() | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 291 K / Details: Blotting time was 10 seconds (blot force 10). |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source![]() ![]() |
Electron lens | Mode: BRIGHT FIELD![]() ![]() |
Specimen holder | Cryogen: NITROGEN |
Image recording | Average exposure time: 4.63 sec. / Electron dose: 49 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 3843 |
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Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction![]() | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 1371057 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction![]() | Resolution: 2.64 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 198918 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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