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- EMDB-23326: Cyanophycin synthetase 1 from Synechocystis sp. UTEX2470 with ATP... -

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Basic information

Entry
Database: EMDB / ID: EMD-23326
TitleCyanophycin synthetase 1 from Synechocystis sp. UTEX2470 with ATP and 16x(Asp-Arg)
Map dataCyanophycin synthetase 1 from Synechocystis sp. UTEX2470 with ADPCP and 16x(Asp-Arg) map
Sample
  • Complex: Cyanophycin synthetase 1 from Synechocystis sp. UTEX2470 with ATP and 16x(Asp-Arg)
    • Other: Cyanophycin synthetase 1 from Synechocystis sp. UTEX2470 with ATP and 16x(Asp-Arg)
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) / biosynthetic process / ATP binding / metal ion binding
Similarity search - Function
Cyanophycin synthase-like, N-terminal / Cyanophycin synthase-like N-terminal domain / Cyanophycin synthetase / ATP-grasp fold, RimK-type / RimK-like ATP-grasp domain / Mur ligase, C-terminal / Mur ligase, C-terminal domain superfamily / Mur ligase, glutamate ligase domain / Mur ligase, central / Mur-like, catalytic domain superfamily ...Cyanophycin synthase-like, N-terminal / Cyanophycin synthase-like N-terminal domain / Cyanophycin synthetase / ATP-grasp fold, RimK-type / RimK-like ATP-grasp domain / 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 / ATP-grasp fold profile.
Similarity search - Domain/homology
Cyanophycin synthetase
Similarity search - Component
Biological speciesSynechocystis sp. PCC 6714 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsSharon I / Grogg M / Hilvert D / 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-
UpdateOct 6, 2021-
Current statusOct 6, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.8
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.8
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23326.png

Downloads & links

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Map

FileDownload / File: emd_23326.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCyanophycin synthetase 1 from Synechocystis sp. UTEX2470 with ADPCP and 16x(Asp-Arg) map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 512 pix.
= 437.76 Å		0.86 Å/pix.
x 512 pix.
= 437.76 Å		0.86 Å/pix.
x 512 pix.
= 437.76 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.855 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.8 / Movie #1: 0.8
Minimum - Maximum-4.084533 - 6.3807025
Average (Standard dev.)-0.00091906043 (±0.11798249)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 437.76 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8550.8550.855
M x/y/z512512512
origin x/y/z0.0000.0000.000
length x/y/z437.760437.760437.760
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ450450450
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS512512512
D min/max/mean-4.0856.381-0.001

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Supplemental data

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Mask #1

Fileemd_23326_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Cyanophycin synthetase 1 from Synechocystis sp. UTEX2470 with...

Fileemd_23326_half_map_1.map
AnnotationCyanophycin synthetase 1 from Synechocystis sp. UTEX2470 with ADPCP and 16x(Asp-Arg) half map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Cyanophycin synthetase 1 from Synechocystis sp. UTEX2470 with...

Fileemd_23326_half_map_2.map
AnnotationCyanophycin synthetase 1 from Synechocystis sp. UTEX2470 with ADPCP and 16x(Asp-Arg) half map A
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 Synechocystis sp. UTEX2470 with ATP...

EntireName: Cyanophycin synthetase 1 from Synechocystis sp. UTEX2470 with ATP and 16x(Asp-Arg)
Components
  • Complex: Cyanophycin synthetase 1 from Synechocystis sp. UTEX2470 with ATP and 16x(Asp-Arg)
    • Other: Cyanophycin synthetase 1 from Synechocystis sp. UTEX2470 with ATP and 16x(Asp-Arg)

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Supramolecule #1: Cyanophycin synthetase 1 from Synechocystis sp. UTEX2470 with ATP...

SupramoleculeName: Cyanophycin synthetase 1 from Synechocystis sp. UTEX2470 with ATP and 16x(Asp-Arg)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Synechocystis sp. PCC 6714 (bacteria)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)

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Macromolecule #1: Cyanophycin synthetase 1 from Synechocystis sp. UTEX2470 with ATP...

MacromoleculeName: Cyanophycin synthetase 1 from Synechocystis sp. UTEX2470 with ATP and 16x(Asp-Arg)
type: other / ID: 1 / Classification: other
Source (natural)Organism: Synechocystis sp. PCC 6714 (bacteria)
SequenceString: 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 expressionOrganism: Escherichia coli BL21(DE3) (bacteria)

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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

Concentration3 mg/mL
BufferpH: 8
GridModel: 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
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: D2 (2x2 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 687356
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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