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- PDB-7wad: Trichodesmium erythraeum cyanophycin synthetase 1 (TeCphA1) with ... -

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Basic information

Entry
Database: PDB / ID: 7wad
TitleTrichodesmium erythraeum cyanophycin synthetase 1 (TeCphA1) with ATPgammaS
ComponentsCyanophycin synthase
KeywordsLIGASE / Cyanophycin / Non-ribosomal peptide synthesis / ATP / Aspartate / Arginine
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) / tetrahydrofolylpolyglutamate synthase activity / macromolecule biosynthetic process / ATP binding / metal ion binding
Similarity search - Function
Cyanophycin synthase-like, N-terminal / Cyanophycin synthase-like N-terminal domain / Folylpolyglutamate synthase signature 1. / Cyanophycin synthetase / Folylpolyglutamate synthetase, conserved site / ATP-grasp fold, RimK-type / RimK-like ATP-grasp domain / Mur ligase, C-terminal / Mur ligase family, glutamate ligase domain / Mur ligase, C-terminal domain superfamily ...Cyanophycin synthase-like, N-terminal / Cyanophycin synthase-like N-terminal domain / Folylpolyglutamate synthase signature 1. / Cyanophycin synthetase / Folylpolyglutamate synthetase, conserved site / ATP-grasp fold, RimK-type / RimK-like ATP-grasp domain / Mur ligase, C-terminal / Mur ligase family, glutamate ligase domain / Mur ligase, C-terminal domain superfamily / Mur ligase, central / Mur-like, catalytic domain superfamily / Mur ligase middle domain / ATP-grasp fold / ATP-grasp fold profile.
Similarity search - Domain/homology
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / Cyanophycin synthetase
Similarity search - Component
Biological speciesTrichodesmium erythraeum IMS101 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.96 Å
AuthorsKawasaki, M. / Miyakawa, T. / Yang, J. / Adachi, N. / Fujii, A. / Miyauchi, Y. / Muramatsu, T. / Moriya, T. / Senda, T. / Tanokura, M.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP21am0101077 Japan
Japan Agency for Medical Research and Development (AMED)JP21am0101071 Japan
CitationJournal: Nat Commun / Year: 2022
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
DepositionDec 14, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 7, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cyanophycin synthase
B: Cyanophycin synthase
C: Cyanophycin synthase
D: Cyanophycin synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)400,60316
Polymers396,3204
Non-polymers4,28312
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Cyanophycin synthase / / Cyanophycin synthetase


Mass: 99079.914 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trichodesmium erythraeum IMS101 (bacteria)
Strain: IMS101 / Gene: Tery_1965 / Production host: Escherichia coli (E. coli)
References: UniProt: Q113V7, cyanophycin synthase (L-aspartate-adding), cyanophycin synthase (L-arginine-adding)
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: TeCphA1 with ATPgammaS / Type: COMPLEX / Details: Homotetramer / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.40 MDa / Experimental value: NO
Source (natural)Organism: Trichodesmium erythraeum IMS101 (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli) / Cell: BL21(DE3) / Plasmid: pET-22b(+)
Buffer solutionpH: 8.2
Details: The buffer contains 4 mM ATPgammaS, 5 mM aspartate, 0.5 mM arginine and 10 mM 4-mer cyanophycin peptide as ligands.
Buffer component
IDConc.NameBuffer-ID
150 mMtris(hydroxymethyl)aminomethane1
2200 mMsodium chloride1
320 mMpotassium chloride1
420 mMmagnesium chloride1
51 mMdithiothreitol1
SpecimenConc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: This sample was mono-disperse.
Specimen supportDetails: 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
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 291 K / Details: Blotting time was 15 seconds (blot force 10).

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 120000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Specimen holderCryogen: NITROGEN
Image recordingAverage exposure time: 56.18 sec. / Electron dose: 50 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 1730

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
EM software
IDNameVersionCategoryDetails
1SPHIREparticle selectioncrYOLO
2EPUimage acquisition
4GctfCTF correctionInitial estimation
5RELION3.1CTF correctionCTF refinement
8UCSF Chimera1.13.1model fitting
9Coot0.8.9.2model fitting
11Coot0.8.9.2model refinement
12PHENIX1.19.2model refinement
13RELION3.1initial Euler assignment
14RELION3.1final Euler assignment
15RELION3.1classification
16RELION3.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 927603
SymmetryPoint symmetry: D2 (2x2 fold dihedral)
3D reconstructionResolution: 2.96 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 49842 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00322640
ELECTRON MICROSCOPYf_angle_d0.51330760
ELECTRON MICROSCOPYf_dihedral_angle_d7.8673196
ELECTRON MICROSCOPYf_chiral_restr0.0453616
ELECTRON MICROSCOPYf_plane_restr0.0043920

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