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- PDB-4kg4: Crystal structure of Saccharomyces cerevisiae Dcp2 Nudix domain (... -

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Basic information

Entry
Database: PDB / ID: 4kg4
TitleCrystal structure of Saccharomyces cerevisiae Dcp2 Nudix domain (E198Q mutation)
ComponentsmRNA-decapping enzyme subunit 2
KeywordsHYDROLASE / Nudix / mRNA decay / mRNA decapping
Function / homology
Function and homology information


RNA decapping complex / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / Tristetraprolin (TTP, ZFP36) 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 / 5'-(N(7)-methylguanosine 5'-triphospho)-[mRNA] hydrolase activity / cytoplasmic side of membrane / deadenylation-dependent decapping of nuclear-transcribed mRNA / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay ...RNA decapping complex / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / Tristetraprolin (TTP, ZFP36) 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 / 5'-(N(7)-methylguanosine 5'-triphospho)-[mRNA] hydrolase activity / cytoplasmic side of membrane / 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
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 ...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 / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
m7GpppN-mRNA hydrolase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsAglietti, R.A. / Floor, S.N. / Gross, J.D.
CitationJournal: Structure / Year: 2013
Title: Active site conformational dynamics are coupled to catalysis in the mRNA decapping enzyme dcp2.
Authors: Aglietti, R.A. / Floor, S.N. / McClendon, C.L. / Jacobson, M.P. / Gross, J.D.
History
DepositionApr 28, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Feb 28, 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

Downloads & links

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Assembly

Deposited unit
A: mRNA-decapping enzyme subunit 2
B: mRNA-decapping enzyme subunit 2


Theoretical massNumber of molelcules
Total (without water)34,7562
Polymers34,7562
Non-polymers00
Water2,306128
1
A: mRNA-decapping enzyme subunit 2


Theoretical massNumber of molelcules
Total (without water)17,3781
Polymers17,3781
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: mRNA-decapping enzyme subunit 2


Theoretical massNumber of molelcules
Total (without water)17,3781
Polymers17,3781
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.352, 47.804, 60.957
Angle α, β, γ (deg.)90.000, 97.290, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 17377.924 Da / Num. of mol.: 2 / Fragment: catalytic Nudix domain / Mutation: E198Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: DCP2, N1917, PSU1, YNL118C / Plasmid: pET-Duet1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P53550, Hydrolases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.42 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 10 mM HEPES, 1 mM DTT, 50 mM NaCl, 100 mM Na2SO4, 0.25 M Na Acetate, 20% PEG 3350, pH 6.5, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 Å
DetectorDetector: CCD / Date: Apr 23, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11587 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 29367 / % possible obs: 96.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 1.8 % / Rmerge(I) obs: 0.04 / Χ2: 1.986 / Net I/σ(I): 18.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.8-1.831.80.38314871.346197.1
1.83-1.861.80.33414381.466197.2
1.86-1.91.80.23415001.277197.9
1.9-1.941.80.21414511.47197.1
1.94-1.981.80.16815091.508197.7
1.98-2.031.80.13914421.544198
2.03-2.081.80.1314872.112197.4
2.08-2.131.80.10814921.771197.7
2.13-2.21.80.09214801.838197.6
2.2-2.271.80.08614822.015197.6
2.27-2.351.80.06514901.87198
2.35-2.441.80.06314671.913197.4
2.44-2.551.80.05314862.086197.2
2.55-2.691.80.04714712.106196.9
2.69-2.861.80.04414972.212197.1
2.86-3.081.90.04214512.683195.5
3.08-3.391.80.03914592.822194.2
3.39-3.881.90.03314292.718193.3
3.88-4.881.90.02914112.47191.4
4.88-501.90.02814382.418189.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→44.336 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8494 / SU ML: 0.19 / σ(F): 0 / Phase error: 22.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.214 1919 6.77 %Random
Rwork0.1871 ---
obs0.1889 28350 92.87 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 160.11 Å2 / Biso mean: 39.0297 Å2 / Biso min: 17.08 Å2
Refinement stepCycle: LAST / Resolution: 1.8→44.336 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2331 0 0 128 2459
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072377
X-RAY DIFFRACTIONf_angle_d1.1663189
X-RAY DIFFRACTIONf_chiral_restr0.091337
X-RAY DIFFRACTIONf_plane_restr0.004408
X-RAY DIFFRACTIONf_dihedral_angle_d14.662917
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.84640.28361380.23591625176382
1.8464-1.89630.30271120.21521761187387
1.8963-1.95210.24371300.21451795192589
1.9521-2.01510.27971330.19891855198892
2.0151-2.08710.24231300.18931907203794
2.0871-2.17070.23931410.18921940208195
2.1707-2.26950.21461350.19731944207996
2.2695-2.38910.2381500.18591937208796
2.3891-2.53880.22711390.19831945208496
2.5388-2.73480.22871490.19931957210697
2.7348-3.00990.22841360.20311978211497
3.0099-3.44540.21991510.19331951210296
3.4454-4.34020.17921330.16311916204993
4.3402-44.34980.18381420.17621920206291
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)
14.45871.4280.86553.62822.74446.1258-0.0675-0.11270.04670.0063-0.0615-0.030.0522-0.23390.16480.25630.01220.04710.215-0.02490.27932.823118.007723.9462
24.85970.4233-0.58153.53352.28646.7985-0.11290.22390.5449-0.9720.0935-0.2194-0.6040.5115-0.23440.3809-0.04470.09240.2519-0.02020.337342.133623.221618.3978
31.4037-0.15931.75291.56662.12785.6846-0.16040.82310.0185-0.63090.2435-0.3049-0.1897-0.1597-0.34430.4064-0.09660.1410.5358-0.12640.308133.365411.53697.1529
42.7230.55663.27282.30261.69024.8881-0.09420.0604-0.2166-0.22410.0505-0.1169-0.0902-0.20760.04980.27430.01060.08550.2565-0.01870.241135.1229.851215.1496
56.3512-0.71810.93382.823-0.08182.1454-0.02120.0618-0.0694-0.3098-0.02110.2270.0734-0.14730.09470.3327-0.01650.03440.2542-0.04240.244529.975214.658419.9941
66.2839-3.1832-4.68549.13380.35374.69650.35530.11250.517-0.328-0.2345-0.1232-0.43430.05560.0420.27040.0290.05490.19810.02220.28147.312112.90217.457
76.7543-3.914-2.89186.89122.71525.6496-0.104-0.52740.6140.05210.1519-0.1307-0.4285-0.0222-0.05080.3033-0.00860.00430.2483-0.09810.306536.69124.634629.6718
86.69412.27980.62884.8077-0.18654.7553-0.36020.21681.1914-0.8154-0.04580.5442-1.09440.1350.41970.3671-0.02850.03630.22450.01390.513135.719730.250121.5797
96.19052.0417-0.67547.8451-5.58076.7481-0.1251-0.49960.41010.88170.24870.6644-0.5413-1.4278-0.12580.34180.01410.09920.4266-0.15610.384521.17921.989629.8411
106.35361.8512-1.72862.352-0.07833.5043-0.0853-0.1885-0.27710.07080.12390.0188-0.1411-0.073-0.07880.20630.00830.01540.10470.01610.13646.350527.925650.7003
113.4482-2.30592.79676.6723-2.61542.3769-0.12240.63860.063-0.00630.43290.6033-0.6581-0.98-0.35380.34420.0127-0.05150.33480.07680.200343.998435.763642.022
124.2573-0.7214-0.78533.87810.58314.12040.0522-0.012-0.1508-0.07020.03820.36220.1681-0.4081-0.08520.2579-0.0309-0.01950.20580.04280.285441.349922.632950.1543
135.2694-4.87394.99759.9235-2.74565.3896-0.1287-0.74260.00781.59850.01790.4510.2117-0.22770.04360.4184-0.0682-0.01880.4131-0.12820.446641.887424.178834.1218
145.9442.59280.21145.76391.12752.53540.17210.08730.0696-0.19560.1475-0.0926-0.47760.379-0.17690.2411-0.05350.07310.15580.00040.163853.307633.244546.4708
154.6401-2.32710.88511.7637-0.67769.2632-0.12120.00811.41480.3738-0.168-0.2462-1.15460.61730.32620.66720.0178-0.02260.3181-0.00330.5449.584742.367950.1439
166.0014-3.76032.35374.8162-2.40511.2750.0188-1.41110.07641.01770.1467-0.5038-0.2001-0.3502-0.1240.4677-0.0888-0.0580.34870.00050.344852.584229.106963.1352
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN A AND (RESID 103:122 )A0
2X-RAY DIFFRACTION2CHAIN A AND (RESID 123:132 )A0
3X-RAY DIFFRACTION3CHAIN A AND (RESID 133:141 )A0
4X-RAY DIFFRACTION4CHAIN A AND (RESID 142:154 )A0
5X-RAY DIFFRACTION5CHAIN A AND (RESID 155:192 )A0
6X-RAY DIFFRACTION6CHAIN A AND (RESID 193:200 )A0
7X-RAY DIFFRACTION7CHAIN A AND (RESID 201:212 )A0
8X-RAY DIFFRACTION8CHAIN A AND (RESID 213:227 )A0
9X-RAY DIFFRACTION9CHAIN A AND (RESID 228:243 )A0
10X-RAY DIFFRACTION10CHAIN B AND (RESID 101:123 )B0
11X-RAY DIFFRACTION11CHAIN B AND (RESID 124:131 )B0
12X-RAY DIFFRACTION12CHAIN B AND (RESID 132:192 )B0
13X-RAY DIFFRACTION13CHAIN B AND (RESID 193:198 )B0
14X-RAY DIFFRACTION14CHAIN B AND (RESID 199:211 )B0
15X-RAY DIFFRACTION15CHAIN B AND (RESID 212:227 )B0
16X-RAY DIFFRACTION16CHAIN B AND (RESID 228:241 )B0

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