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- PDB-2a6t: Crystal structure of S.pombe mRNA decapping enzyme Dcp2p -

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Basic information

Entry
Database: PDB / ID: 2a6t
TitleCrystal structure of S.pombe mRNA decapping enzyme Dcp2p
ComponentsSPAC19A8.12
KeywordsRNA BINDING PROTEIN / HYDROLASE / alpha/beta/alpha
Function / homology
Function and homology information


: / RNA decapping complex / mRNA methylguanosine-cap decapping / 5'-(N(7)-methyl 5'-triphosphoguanosine)-[mRNA] diphosphatase activity / 5'-(N(7)-methylguanosine 5'-triphospho)-[mRNA] hydrolase activity / Hydrolases / deadenylation-dependent decapping of nuclear-transcribed mRNA / mRNA cap binding / : / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay ...: / RNA decapping complex / mRNA methylguanosine-cap decapping / 5'-(N(7)-methyl 5'-triphosphoguanosine)-[mRNA] diphosphatase activity / 5'-(N(7)-methylguanosine 5'-triphospho)-[mRNA] hydrolase activity / Hydrolases / deadenylation-dependent decapping of nuclear-transcribed mRNA / mRNA cap binding / : / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / P-body / mRNA processing / cytoplasmic stress granule / manganese ion binding / single-stranded RNA binding / magnesium ion binding / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Dcp2, box A domain / mRNA decapping protein 2, Box A domain / mRNA decapping protein 2, Box A domain superfamily / mRNA decapping enzyme 2 , NUDIX hydrolase domain / Dcp2, box A domain / Dcp2, box A domain / NUDIX hydrolase, conserved site / Nudix box signature. / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase ...Dcp2, box A domain / mRNA decapping protein 2, Box A domain / mRNA decapping protein 2, Box A domain superfamily / mRNA decapping enzyme 2 , NUDIX hydrolase domain / Dcp2, box A domain / Dcp2, box A domain / NUDIX hydrolase, conserved site / Nudix box signature. / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily / Arc Repressor Mutant, subunit A / Alpha-Beta Complex / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
mRNA decapping complex subunit 2
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsShe, M. / Chen, N. / Song, H.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2006
Title: Crystal structure and functional analysis of Dcp2p from Schizosaccharomyces pombe
Authors: She, M. / Decker, C.J. / Chen, N. / Tumati, S. / Parker, R. / Song, H.
History
DepositionJul 4, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 20, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SPAC19A8.12
B: SPAC19A8.12


Theoretical massNumber of molelcules
Total (without water)62,7162
Polymers62,7162
Non-polymers00
Water1,928107
1
A: SPAC19A8.12


Theoretical massNumber of molelcules
Total (without water)31,3581
Polymers31,3581
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: SPAC19A8.12


Theoretical massNumber of molelcules
Total (without water)31,3581
Polymers31,3581
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.481, 56.481, 301.528
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein SPAC19A8.12 / mRNA decapping enzyme Dcp2


Mass: 31358.084 Da / Num. of mol.: 2 / Fragment: N-terminal conserved region
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Plasmid: pGEX-6p-1 / Production host: Escherichia coli (E. coli) / References: UniProt: O13828
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 107 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: Na/K phosphate, PEG200, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9798 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 31, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. obs: 18700 / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.5→2.56 Å

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→15 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.881 / SU B: 13.618 / SU ML: 0.297 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.591 / ESU R Free: 0.324 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28878 953 5.1 %RANDOM
Rwork0.2476 ---
all0.2549 18635 --
obs0.24981 17682 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 22.666 Å2
Baniso -1Baniso -2Baniso -3
1-2.8 Å21.4 Å20 Å2
2--2.8 Å20 Å2
3----4.2 Å2
Refinement stepCycle: LAST / Resolution: 2.5→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3334 0 0 107 3441
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223411
X-RAY DIFFRACTIONr_bond_other_d0.0020.023076
X-RAY DIFFRACTIONr_angle_refined_deg1.3171.9394586
X-RAY DIFFRACTIONr_angle_other_deg0.85137171
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4085393
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0790.2488
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023688
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02729
X-RAY DIFFRACTIONr_nbd_refined0.2170.2812
X-RAY DIFFRACTIONr_nbd_other0.2220.23612
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0850.22014
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2120.2110
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.150.234
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2030.285
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2060.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4641.52008
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.86723247
X-RAY DIFFRACTIONr_scbond_it1.23331403
X-RAY DIFFRACTIONr_scangle_it2.0194.51339
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.563 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.404 69
Rwork0.311 1321
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
1-0.08140.9938-0.61491.5041-2.30852.72770.0095-0.00710.1285-0.1342-0.0773-0.042-0.29820.02440.06780.37910.18070.04970.36480.03990.306-0.729339.20347.0678
25.3463-0.7276-1.83731.8360.7793.7941-0.05330.0702-0.29050.0849-0.3020.3958-0.0223-0.43780.35530.08810.06390.02790.1614-0.0320.2479-24.760225.066334.5956
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 946 - 99
2X-RAY DIFFRACTION1AA95 - 244100 - 249
3X-RAY DIFFRACTION2BB35 - 9440 - 99
4X-RAY DIFFRACTION2BB95 - 243100 - 248

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