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- PDB-6y3z: Crystal structure of the Pby1 ATP-grasp enzyme bound to the S. ce... -

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Basic information

Entry
Database: PDB / ID: 6y3z
TitleCrystal structure of the Pby1 ATP-grasp enzyme bound to the S. cerevisiae mRNA decapping complex (Dcp1-Dcp2-Edc3)
Components
  • Enhancer of mRNA-decapping protein 3
  • Probable tubulin--tyrosine ligase PBY1
  • m7GpppN-mRNA hydrolase
  • mRNA-decapping enzyme subunit 1
KeywordsHYDROLASE / RNA decay enzyme
Function / homology
Function and homology information


tubulin-tyrosine ligase / Dcp1-Dcp2 complex / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / deadenylation-independent decapping of nuclear-transcribed mRNA / mRNA decay by 5' to 3' exoribonuclease / 5'-(N7-methylguanosine 5'-triphospho)-[mRNA] hydrolase / cytoplasmic side of membrane / m7G(5')pppN diphosphatase activity / deadenylation-dependent decapping of nuclear-transcribed mRNA ...tubulin-tyrosine ligase / Dcp1-Dcp2 complex / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / deadenylation-independent decapping of nuclear-transcribed mRNA / mRNA decay by 5' to 3' exoribonuclease / 5'-(N7-methylguanosine 5'-triphospho)-[mRNA] hydrolase / cytoplasmic side of membrane / m7G(5')pppN diphosphatase activity / deadenylation-dependent decapping of nuclear-transcribed mRNA / P-body assembly / tubulin-tyrosine ligase activity / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / positive regulation of catalytic activity / enzyme activator activity / stress granule assembly / positive regulation of transcription initiation by RNA polymerase II / P-body / mRNA processing / manganese ion binding / hydrolase activity / mRNA binding / chromatin binding / nucleus / cytoplasm
Similarity search - Function
Probable tubulin-tyrosine ligase / FDF domain / FDF / DFDF domain profile. / FDF domain / DFDF domain / mRNA-decapping enzyme subunit 1 / Dcp1-like decapping family / Survival protein SurE-like phosphatase/nucleotidase / Survival protein SurE ...Probable tubulin-tyrosine ligase / FDF domain / FDF / DFDF domain profile. / FDF domain / DFDF domain / mRNA-decapping enzyme subunit 1 / Dcp1-like decapping family / Survival protein SurE-like phosphatase/nucleotidase / Survival protein SurE / SurE-like phosphatase/nucleotidase superfamily / YjeF-related protein N-terminus / YjeF N-terminal domain superfamily / YjeF N-terminal domain profile. / YjeF N-terminal domain / mRNA decapping protein 2, Box A domain superfamily / mRNA decapping enzyme 2 , NUDIX hydrolase domain / Dcp2, box A domain / Dcp2, box A domain / mRNA decapping protein 2, Box A domain / Tubulin-tyrosine ligase/Tubulin polyglutamylase / Tubulin-tyrosine ligase family / TTL domain profile. / NUDIX hydrolase, conserved site / Nudix box signature. / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily / PH-like domain superfamily
Similarity search - Domain/homology
Probable tubulin--tyrosine ligase PBY1 / Enhancer of mRNA-decapping protein 3 / m7GpppN-mRNA hydrolase / mRNA-decapping enzyme subunit 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (unknown)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.49 Å
AuthorsGraille, M.
Funding support France, 3items
OrganizationGrant numberCountry
ATIP-Avenir France
French National Research AgencyANR-11-BSV800902 France
French National Research AgencyANR-10-LABX-0030-INRT France
CitationJournal: Nucleic Acids Res. / Year: 2020
Title: Pby1 is a direct partner of the Dcp2 decapping enzyme.
Authors: Charenton, C. / Gaudon-Plesse, C. / Back, R. / Ulryck, N. / Cosson, L. / Seraphin, B. / Graille, M.
History
DepositionFeb 19, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 29, 2020Provider: repository / Type: Initial release
Revision 1.1May 20, 2020Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jun 24, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: m7GpppN-mRNA hydrolase
B: mRNA-decapping enzyme subunit 1
C: Enhancer of mRNA-decapping protein 3
P: Probable tubulin--tyrosine ligase PBY1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,0215
Polymers116,9974
Non-polymers241
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4530 Å2
ΔGint-24 kcal/mol
Surface area36020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.210, 90.600, 194.240
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein m7GpppN-mRNA hydrolase / / Protein PSU1 / mRNA-decapping enzyme subunit 2


Mass: 32946.887 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (unknown)
Gene: DCP2, PSU1, YNL118C, N1917
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (unknown)
References: UniProt: P53550, 5'-(N7-methylguanosine 5'-triphospho)-[mRNA] hydrolase
#2: Protein mRNA-decapping enzyme subunit 1


Mass: 26705.814 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (unknown)
Gene: DCP1, YOL149W
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (unknown)
References: UniProt: Q12517
#3: Protein Enhancer of mRNA-decapping protein 3


Mass: 7448.622 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (unknown)
Gene: EDC3, LSM16, YEL015W
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (unknown)
References: UniProt: P39998
#4: Protein Probable tubulin--tyrosine ligase PBY1 / P-body-associated protein 1


Mass: 49895.680 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (unknown)
Gene: PBY1, YBR094W, YBR0821
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (unknown)
References: UniProt: P38254, tubulin-tyrosine ligase
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: 2.68 Å3/Da / Density % sol: 54.07 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 0.05 M calcium acetate; 0.1 M sodium cacodylate pH6; 25% MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97626 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 3.49→48.5 Å / Num. obs: 16546 / % possible obs: 99.5 % / Redundancy: 10.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.034 / Rsym value: 0.107 / Net I/σ(I): 9.6
Reflection shellResolution: 3.49→3.55 Å / Rmerge(I) obs: 1.409 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 828 / CC1/2: 0.07 / Rpim(I) all: 0.479 / Rsym value: 1.494

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4K6E, 6Y3P, 5LOP
Resolution: 3.49→48.5 Å / Cor.coef. Fo:Fc: 0.899 / Cor.coef. Fo:Fc free: 0.876 / Rfactor Rfree error: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.638
RfactorNum. reflection% reflectionSelection details
Rfree0.321 766 4.63 %RANDOM
Rwork0.246 ---
obs0.25 16539 99.5 %-
Displacement parametersBiso max: 300 Å2 / Biso mean: 193.18 Å2 / Biso min: 83.52 Å2
Baniso -1Baniso -2Baniso -3
1-14.7068 Å20 Å20 Å2
2---16.5042 Å20 Å2
3---1.7973 Å2
Refine analyzeLuzzati coordinate error obs: 0.54 Å
Refinement stepCycle: final / Resolution: 3.49→48.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5569 0 1 0 5570
Biso mean--128.98 --
Num. residues----672
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2038SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes176HARMONIC2
X-RAY DIFFRACTIONt_gen_planes781HARMONIC5
X-RAY DIFFRACTIONt_it5682HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion728SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact6605SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d5682HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg7660HARMONIC21.27
X-RAY DIFFRACTIONt_omega_torsion2.92
X-RAY DIFFRACTIONt_other_torsion27.31
LS refinement shellResolution: 3.49→3.73 Å / Rfactor Rfree error: 0 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.273 124 4.29 %
Rwork0.229 2767 -
all0.231 2891 -
obs--98.2 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
14.0178-0.914-3.92940.5938-1.01435.6324-0.04710.43920.4969-0.246-0.0657-1.08850.96740.25230.11280.18470.20180.304-0.2654-0.2910.150924.6037-6.632420.9765
27.15534.9102-0.5069.037-3.944711.4522-0.014-0.49680.01810.2210.1444-0.4870.19310.0968-0.13050.6078-0.12880.304-0.0401-0.304-0.512427.8621-20.3561-13.4558
33.77332.60282.16168.64611.30963.61140.29830.12790.20460.7459-0.36850.17750.59580.17810.07030.17240.0517-0.0581-0.4735-0.0424-0.36843.35970.182648.6714
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A14 - 266
2X-RAY DIFFRACTION2{ C|* }C2 - 64
3X-RAY DIFFRACTION3{ P|* }P335 - 751

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