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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-23327 | |||||||||
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Title | Cyanophycin synthetase from A. baylyi DSM587 with ATP | |||||||||
![]() | Cyanophycin synthetase from A. baylyi DSM587 with ATP map | |||||||||
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![]() | Cyanophycin / CphA1 / ATP-grasp / LIGASE | |||||||||
Function / homology | ![]() 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 | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.4 Å | |||||||||
![]() | Sharon I / Haque AS / Lahiri I / Leschziner A / Schmeing TM | |||||||||
![]() | ![]() 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 |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 117.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 14.5 KB 14.5 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 11.1 KB | Display | ![]() |
Images | ![]() | 162.4 KB | ||
Masks | ![]() | 125 MB | ![]() | |
Filedesc metadata | ![]() | 5.6 KB | ||
Others | ![]() ![]() | 116.2 MB 116.2 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 800 KB | Display | ![]() |
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Full document | ![]() | 799.5 KB | Display | |
Data in XML | ![]() | 19.1 KB | Display | |
Data in CIF | ![]() | 24.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7lgmMC ![]() 7lg5C ![]() 7lgjC ![]() 7lgnC ![]() 7lgqC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Cyanophycin synthetase from A. baylyi DSM587 with ATP map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.16 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
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Projections & Slices |
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Density Histograms |
-Half map: Cyanophycin synthetase from A. baylyi DSM587 with ATP half map A
File | emd_23327_half_map_1.map | ||||||||||||
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Annotation | Cyanophycin synthetase from A. baylyi DSM587 with ATP half map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Cyanophycin synthetase from A. baylyi DSM587 with ATP half map B
File | emd_23327_half_map_2.map | ||||||||||||
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Annotation | Cyanophycin synthetase from A. baylyi DSM587 with ATP half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Cyanophycin synthetase 1 from A. baylyi with ATP
Entire | Name: Cyanophycin synthetase 1 from A. baylyi with ATP |
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Components |
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-Supramolecule #1: Cyanophycin synthetase 1 from A. baylyi with ATP
Supramolecule | Name: Cyanophycin synthetase 1 from A. baylyi with ATP / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: Cyanophycin synthase
Macromolecule | Name: Cyanophycin synthase / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: cyanophycin synthase (L-aspartate-adding) |
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Source (natural) | Organism: ![]() Strain: ATCC 33305 / BD413 / ADP1 |
Molecular weight | Theoretical: 101.783664 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MNIISTSVYV GPNVYASIPL IRLVIDLNPH YITQLASMGS EVLENLEKVI PTLKTEQDAK LQHKLEELRQ APQQQIGELV AILALHLQR LAGQKGGAAF SAYCHEDETE ILYSYESEEI GIEAGEVVCD MLVALAKAHE AGDQIDLNRD VKGFLRYADR F ALGPSALA ...String: MNIISTSVYV GPNVYASIPL IRLVIDLNPH YITQLASMGS EVLENLEKVI PTLKTEQDAK LQHKLEELRQ APQQQIGELV AILALHLQR LAGQKGGAAF SAYCHEDETE ILYSYESEEI GIEAGEVVCD MLVALAKAHE AGDQIDLNRD VKGFLRYADR F ALGPSALA LVQAAEERNI PWYRLNDASL IQVGQGKYQK RIEAALTSGT SHIAVEIAGD KNVCNQLLQD LGLPVPKQRV VY DIDDAVR AARRVGFPVV LKPLDGNHGR GVSVNLTTDE AVEAAFDIAM SEGSAVIVES MLYGDDHRLL VVNGELVAAA RRV PGHIVG DGKHNVEALI EIVNQDPRRG VGHENMLTKI ELDEQALKLL AEKGYDKDSI PAKDEVVYLR RTANISTGGT AIDV TDTIH PENKLMAERA IRAVGLDIGA VDFLTTDITK SYRDIGGGIC EVNAGPGLRM HISPSEGPSR DVGGKIMDML FPQGS QSRV PIAAITGTNG KTTCSRMLAH ILKMAGHVVG QTSTDAVYID GNVTVKGDMT GPVSAKMVLR DPSVDIAVLE TARGGI VRS GLGYQFCDVG AVLNVSSDHL GLGGVDTLDG LAEVKRVIAE VTKDTVVLNA DNAYTLKMAG HSPAKHIMYV TRDAENK LV REHIRLGKRA VVLEKGLNGD QIVIYENGTQ IPLIWTHLIP ATLEGKAIHN VENAMFAAGM AYALGKNLDQ IRIGLRTF D NTFFQSPGRM NVFDKHGFRV ILDYGHNEAA VGAMTELVDR LNPRGRRLLG VTCPGDRRDE DVVAIAAKVA GHFDEYYCH RDDDLRGRAP DETPKIMRDA LIQLGVPESR IHIVEQEEDS LAAVLTEAQV DDLVLFFCEN ITRSWKQIVH FTPEFNIEND HETLELKIA EQGFDIPEGY HAVSNDRGVM ILPRGENLYF QGHHHHHHHH UniProtKB: Cyanophycin synthase |
-Macromolecule #2: ADENOSINE-5'-TRIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 2 / Formula: ATP |
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Molecular weight | Theoretical: 507.181 Da |
Chemical component information | ![]() ChemComp-ATP: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 57.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Illumination mode: OTHER / Imaging mode: OTHER |
Experimental equipment | ![]() Model: Talos Arctica / Image courtesy: FEI Company |