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- EMDB-23327: Cyanophycin synthetase from A. baylyi DSM587 with ATP -

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Basic information

Entry
Database: EMDB / ID: EMD-23327
TitleCyanophycin synthetase from A. baylyi DSM587 with ATP
Map dataCyanophycin synthetase from A. baylyi DSM587 with ATP map
Sample
  • Complex: Cyanophycin synthetase 1 from A. baylyi with ATP
    • Protein or peptide: Cyanophycin synthase
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
KeywordsCyanophycin / CphA1 / ATP-grasp / LIGASE
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) / ATP binding / metal ion binding
Similarity search - Function
ATP-grasp domain / Cyanophycin synthetase / Mur ligase, C-terminal / Mur ligase, C-terminal domain superfamily / Mur ligase, glutamate ligase domain / Mur ligase, central / Mur-like, catalytic domain superfamily / Mur ligase middle domain / ATP-grasp fold, subdomain 1 / ATP-grasp fold / ATP-grasp fold profile.
Similarity search - Domain/homology
Cyanophycin synthetase
Similarity search - Component
Biological speciesAcinetobacter baylyi ADP1 (bacteria) / Acinetobacter baylyi (strain ATCC 33305 / BD413 / ADP1) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.4 Å
AuthorsSharon I / Haque AS / Lahiri I / Leschziner A / Schmeing TM
CitationJournal: 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
DepositionJan 20, 2021-
Header (metadata) releaseAug 18, 2021-
Map releaseAug 18, 2021-
UpdateMay 29, 2024-
Current statusMay 29, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.63
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.63
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7lgm
  • Surface level: 0.63
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23327.png

Downloads & links

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Map

FileDownload / File: emd_23327.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCyanophycin synthetase from A. baylyi DSM587 with ATP map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.16 Å/pix.
x 320 pix.
= 371.2 Å		1.16 Å/pix.
x 320 pix.
= 371.2 Å		1.16 Å/pix.
x 320 pix.
= 371.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.16 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.63 / Movie #1: 0.63
Minimum - Maximum-1.8378305 - 3.3070047
Average (Standard dev.)0.00022550921 (±0.052535728)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 371.19998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.161.161.16
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z371.200371.200371.200
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ500500500
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-1.8383.3070.000

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Supplemental data

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Mask #1

Fileemd_23327_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Cyanophycin synthetase from A. baylyi DSM587 with ATP half map A

Fileemd_23327_half_map_1.map
AnnotationCyanophycin synthetase from A. baylyi DSM587 with ATP half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Cyanophycin synthetase from A. baylyi DSM587 with ATP half map B

Fileemd_23327_half_map_2.map
AnnotationCyanophycin synthetase from A. baylyi DSM587 with ATP half map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Cyanophycin synthetase 1 from A. baylyi with ATP

EntireName: Cyanophycin synthetase 1 from A. baylyi with ATP
Components
  • Complex: Cyanophycin synthetase 1 from A. baylyi with ATP
    • Protein or peptide: Cyanophycin synthase
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE

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Supramolecule #1: Cyanophycin synthetase 1 from A. baylyi with ATP

SupramoleculeName: Cyanophycin synthetase 1 from A. baylyi with ATP / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Acinetobacter baylyi ADP1 (bacteria)

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Macromolecule #1: Cyanophycin synthase

MacromoleculeName: Cyanophycin synthase / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: cyanophycin synthase (L-aspartate-adding)
Source (natural)Organism: Acinetobacter baylyi (strain ATCC 33305 / BD413 / ADP1) (bacteria)
Strain: ATCC 33305 / BD413 / ADP1
Molecular weightTheoretical: 101.783664 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: 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 synthetase

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Macromolecule #2: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 2 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 57.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 296574
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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