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- PDB-4kg3: Crystal structure of Saccharomyces cerevisiae Dcp2 Nudix domain i... -

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Basic information

Entry
Database: PDB / ID: 4kg3
TitleCrystal structure of Saccharomyces cerevisiae Dcp2 Nudix domain in complex with Mg (E153Q 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: 1.7 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 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
C: mRNA-decapping enzyme subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2076
Polymers52,1343
Non-polymers733
Water6,413356
1
A: mRNA-decapping enzyme subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4022
Polymers17,3781
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: mRNA-decapping enzyme subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4022
Polymers17,3781
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: mRNA-decapping enzyme subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4022
Polymers17,3781
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)140.789, 49.270, 84.022
Angle α, β, γ (deg.)90.000, 91.370, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-503-

HOH

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Components

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


Mass: 17377.926 Da / Num. of mol.: 3 / Fragment: Dcp2 Nudix domain / Mutation: E153Q
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: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 356 / 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: 2.79 Å3/Da / Density % sol: 55.98 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 20% Peg 3350, 0.1 M Mg Formate, 10 mM HEPES, 1 mM DTT, 50 mM NaCl, 100 mM Na2SO4, pH 7.4, 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
ReflectionAv R equivalents: 0.084 / Number: 230321
ReflectionResolution: 1.7→50 Å / Num. obs: 54471 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Rmerge(I) obs: 0.072 / Rsym value: 0.072 / Net I/σ(I): 19.711
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0 / Mean I/σ(I) obs: 0.684 / Rsym value: 0 / % possible all: 99.8
Cell measurementReflection used: 230321

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.7 Å46.5 Å
Translation1.7 Å46.5 Å

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASERphasing
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→46.503 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8454 / SU ML: 0.2 / σ(F): 0.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2127 1713 3.14 %random
Rwork0.177 ---
obs0.1781 54471 85.68 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 129.39 Å2 / Biso mean: 35.7096 Å2 / Biso min: 13.12 Å2
Refinement stepCycle: LAST / Resolution: 1.7→46.503 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3567 0 3 356 3926
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073639
X-RAY DIFFRACTIONf_angle_d1.114884
X-RAY DIFFRACTIONf_chiral_restr0.085513
X-RAY DIFFRACTIONf_plane_restr0.004627
X-RAY DIFFRACTIONf_dihedral_angle_d13.7551405
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7-1.75110.4151980.35453075317360
1.7511-1.80760.32091110.29063387349867
1.8076-1.87220.32281250.24583680380572
1.8722-1.94720.22081240.20333946407077
1.9472-2.03580.21081380.19274335447385
2.0358-2.14310.20561490.17554646479590
2.1431-2.27740.1931540.17324720487493
2.2774-2.45320.2211560.17074815497194
2.4532-2.70010.24281550.18114899505495
2.7001-3.09070.20851690.17664993516297
3.0907-3.89370.20811640.16645074523898
3.8937-46.52040.17871700.15195188535898
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)
13.53330.57850.7774.70590.52722.7984-0.1465-0.02890.22730.04440.13790.2306-0.0417-0.2303-0.00740.13150.008-0.04750.14850.04970.154544.510831.281391.8506
23.31690.38620.40223.4845-0.44854.3405-0.0690.2665-0.2075-0.24780.1534-0.05570.2158-0.0296-0.10140.1895-0.0139-0.04550.17420.01140.183347.417822.785789.5886
33.93371.0949-0.6423.7897-2.40043.4453-0.15750.116-0.0565-0.00590.2384-0.5521-0.0776-0.00260.01760.15140.0002-0.09410.1594-0.00280.245458.663430.447298.374
42.4818-2.0587-0.21772.3282-0.29322.2725-0.2750.14660.4925-0.06080.17860.2673-0.5071-0.51760.06160.25780.0422-0.10620.26980.02680.362539.250539.084892.1007
56.37870.24370.29135.3338-0.44547.8922-0.20170.65640.269-0.4179-0.1191.0689-0.3876-0.56240.06430.2570.0173-0.12270.3409-0.01960.410932.480228.11285.6636
62.7131-0.00950.68332.8105-0.18835.27460.0699-0.0130.0258-0.00660.08240.0737-0.1036-0.1962-0.04310.1410.035-0.00040.15420.02560.105664.1918-0.637565.8897
73.68780.11560.68582.7973-0.15813.56580.05010.1429-0.2438-0.18540.13310.16070.1939-0.2799-0.10620.1699-0.0017-0.03140.18070.01290.147463.4224-9.347463.6362
84.9844-0.4935-2.96422.28130.86525.902-0.1153-0.37870.25090.19190.1968-0.0487-0.13880.256-0.08910.22190.021-0.03810.1183-0.02540.140768.55273.129468.5978
95.51441.84291.11215.01943.69082.7267-0.0928-0.04840.6825-0.37010.29290.7211-0.7189-0.50230.15290.39530.14410.03130.30330.09680.287958.07418.844667.7425
103.09091.7753-0.02822.20731.47691.87750.3151-0.0332-0.01680.5586-0.01730.3487-0.2249-0.6533-0.05790.20860.03010.0320.2690.04230.153953.8319-7.397280.4863
114.24430.28980.43372.78130.37722.435-0.0997-0.230.07770.22310.29160.1125-0.4306-0.066-0.05210.270.1066-0.00060.27730.00510.135552.546715.81337.1053
121.4917-0.1783-0.37862.72770.22482.5226-0.272-0.3608-0.20030.15120.27760.57730.1585-0.46570.07630.24380.08130.02990.34360.09740.23749.36227.246436.3587
132.73260.89650.78971.85621.29585.8152-0.1741-0.05680.3110.20150.24110.0078-0.52150.5450.00320.38270.0442-0.05080.1863-0.01620.202556.484618.652833.3845
145.45010.8543-1.22590.2692-1.00165.1409-0.2105-0.85680.75420.65650.26290.1664-1.1289-0.1637-1.28130.66810.30760.01650.4476-0.06570.340150.82125.795243.4106
152.8081-0.8720.45333.1757-0.28860.08130.1218-0.3194-0.10730.3929-0.04280.3066-0.9906-0.6071-0.06070.57520.16390.01090.44560.04190.205758.31289.120453.0554
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN A AND (RESID 102:131 )A0
2X-RAY DIFFRACTION2CHAIN A AND (RESID 132:192 )A0
3X-RAY DIFFRACTION3CHAIN A AND (RESID 193:198 )A0
4X-RAY DIFFRACTION4CHAIN A AND (RESID 199:223 )A0
5X-RAY DIFFRACTION5CHAIN A AND (RESID 224:239 )A0
6X-RAY DIFFRACTION6CHAIN B AND (RESID 101:131 )B0
7X-RAY DIFFRACTION7CHAIN B AND (RESID 132:192 )B0
8X-RAY DIFFRACTION8CHAIN B AND (RESID 193:213 )B0
9X-RAY DIFFRACTION9CHAIN B AND (RESID 214:227 )B0
10X-RAY DIFFRACTION10CHAIN B AND (RESID 228:245 )B0
11X-RAY DIFFRACTION11CHAIN C AND (RESID 102:132 )C0
12X-RAY DIFFRACTION12CHAIN C AND (RESID 133:192 )C0
13X-RAY DIFFRACTION13CHAIN C AND (RESID 193:211 )C0
14X-RAY DIFFRACTION14CHAIN C AND (RESID 212:227 )C0
15X-RAY DIFFRACTION15CHAIN C AND (RESID 228:245 )C0

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