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- PDB-2jvb: Solution Structure of Catalytic Domain of yDcp2 -

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Basic information

Entry
Database: PDB / ID: 2jvb
TitleSolution Structure of Catalytic Domain of yDcp2
ComponentsmRNA-decapping enzyme subunit 2
KeywordsHYDROLASE / Dcp2 / mRNA decay / decapping / Cytoplasm / Manganese / Metal-binding / mRNA processing / Nonsense-mediated mRNA decay / Nucleus / Phosphorylation / RNA-binding
Function / homology
Function and homology information


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 / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay ...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 / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / positive regulation of transcription initiation by RNA polymerase II / stress granule assembly / P-body / mRNA processing / manganese ion binding / hydrolase activity / mRNA binding / chromatin binding / nucleus / cytoplasm
Similarity search - Function
Dcp2, box A domain / mRNA decapping enzyme 2 , NUDIX hydrolase domain / mRNA decapping protein 2, Box A domain superfamily / mRNA decapping protein 2, Box A domain / Dcp2, box A domain / Nudix box signature. / NUDIX hydrolase, conserved site / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX domain ...Dcp2, box A domain / mRNA decapping enzyme 2 , NUDIX hydrolase domain / mRNA decapping protein 2, Box A domain superfamily / mRNA decapping protein 2, Box A domain / Dcp2, box A domain / Nudix box signature. / NUDIX hydrolase, conserved site / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
m7GpppN-mRNA hydrolase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (baker's yeast)
MethodSOLUTION NMR / simulated annealing
AuthorsDeshmukh, M. / Gross, J.
CitationJournal: Mol.Cell / Year: 2008
Title: mRNA Decapping Is Promoted by an RNA-Binding Channel in Dcp2.
Authors: Deshmukh, M.V. / Jones, B.N. / Quang-Dang, D.U. / Flinders, J. / Floor, S.N. / Kim, C. / Jemielity, J. / Kalek, M. / Darzynkiewicz, E. / Gross, J.D.
History
DepositionSep 16, 2007Deposition site: BMRB / Processing site: RCSB
Revision 1.0Mar 4, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_spectrometer ...database_2 / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: mRNA-decapping enzyme subunit 2


Theoretical massNumber of molelcules
Total (without water)17,3791
Polymers17,3791
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 50structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

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


Mass: 17378.910 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (baker's yeast)
Gene: DCP2, PSU1 / Plasmid: pET30a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (unknown) / Strain (production host): BL21 (DE3) / References: UniProt: P53550, Hydrolases

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-13C HSQC
1312D 1H-1H TOCSY
1412D 1H-1H NOESY
1533D C(CO)NH
1643D HNCO
1743D HNCA
1843D HN(CA)CB
1943D HN(CO)CA
11013D 1H-15N NOESY
11143D HN(COCA)CB
11233D H(CCO)NH
11333D C(CO)NH
11453D 13C edited NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
1500 uM [U-100% 15N] GB1-yDcp2, 90% H2O/10% D2O90% H2O/10% D2O
2500 uM [U-100% 13C] GB1-yDcp2, 90% H2O/10% D2O90% H2O/10% D2O
3500 uM [U-100% 13C, 1H ILV only; U-100% 15N; 100% 2H] GB1-yDcp2, 90% H2O/10% D2O90% H2O/10% D2O
4500 uM [U-100% 13C; U-100% 15N; 80% 2H] GB1-yDcp2, 90% H2O/10% D2O90% H2O/10% D2O
5500 uM [U-100% 13C,1H Methyl groups of I L and V; 100% 2H] GB1-yDcp2, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
500 uMGB1-yDcp2[U-100% 15N]1
500 uMGB1-yDcp2[U-100% 13C]2
500 uMGB1-yDcp2[U-100% 13C, 1H ILV only; U-100% 15N; 100% 2H]3
500 uMGB1-yDcp2[U-100% 13C; U-100% 15N; 80% 2H]4
500 uMGB1-yDcp2[U-100% 13C,1H Methyl groups of I L and V; 100% 2H]5
Sample conditionspH: 7.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE5001
Bruker AvanceBrukerAVANCE8002
Varian INOVAVarianINOVA6003

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Processing

NMR softwareName: CNS / Developer: Brunger, A.T. et al. / Classification: refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 10

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