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- PDB-7lgn: Cyanophycin synthetase 1 from T. morbirosei -

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Basic information

Entry
Database: PDB / ID: 7lgn
TitleCyanophycin synthetase 1 from T. morbirosei
ComponentsCyanophycin synthase
KeywordsLIGASE / Cyanophycin / CphA1 / ATP-grasp
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
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, subdomain 1 ...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, subdomain 1 / ATP-grasp fold / ATP-grasp fold profile.
Similarity search - Domain/homology
Cyanophycin synthetase
Similarity search - Component
Biological speciesTatumella morbirosei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / molecular replacement / Resolution: 3.1 Å
AuthorsSharon, I. / Schmeing, T.M.
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, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 18, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 1, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 6, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cyanophycin synthase
B: Cyanophycin synthase


Theoretical massNumber of molelcules
Total (without water)197,2972
Polymers197,2972
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3560 Å2
ΔGint-11 kcal/mol
Surface area70770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)222.561, 222.561, 105.216
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number80
Space group name H-MI41

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Components

#1: Protein Cyanophycin synthase / Cyanophycin synthetase


Mass: 98648.547 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tatumella morbirosei (bacteria) / Gene: HA49_14190 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A095T5Z8, cyanophycin synthase (L-aspartate-adding), cyanophycin synthase (L-arginine-adding)

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.3 Å3/Da / Density % sol: 62.75 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 6.8
Details: 13.25% PEG3350, 320mM NaFormate, 1% glycerol, 100mM Na/K phosphate pH6.8. protein concentration 6mg/ml.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.1→72.31 Å / Num. obs: 46806 / % possible obs: 99.89 % / Redundancy: 2 % / Biso Wilson estimate: 130.26 Å2 / CC1/2: 0.995 / CC star: 0.999 / Rmerge(I) obs: 0.06706 / Rpim(I) all: 0.06706 / Rrim(I) all: 0.09484 / Net I/σ(I): 11.47
Reflection shellResolution: 3.1→3.211 Å / Redundancy: 2 % / Rmerge(I) obs: 0.4044 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 4632 / CC1/2: 0.768 / CC star: 0.932 / Rpim(I) all: 0.4044 / Rrim(I) all: 0.5719 / % possible all: 99.42

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5refinement
Aimlessdata scaling
CRANK2phasing
PDB_EXTRACT3.27data extraction
DIALSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 3.1→72.31 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflectionSelection details
Rfree0.326 2413 5 %RANDOM
Rwork0.2703 ---
obs-46760 99.89 %-
Displacement parametersBiso max: 314.63 Å2 / Biso mean: 130.1855 Å2 / Biso min: 36.34 Å2
Refinement stepCycle: LAST / Resolution: 3.1→72.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11790 0 0 0 11790
LS refinement shellResolution: 3.1→3.211 Å
RfactorNum. reflection% reflection
Rfree0.5121 255 5 %
Rwork0.4696 4605 -
obs--99.42 %

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