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- PDB-3ovb: How the CCA-adding Enzyme Selects Adenine over Cytosine in Positi... -

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Basic information

Entry
Database: PDB / ID: 3ovb
TitleHow the CCA-adding Enzyme Selects Adenine over Cytosine in Position 76 of tRNA
Components
  • CCA-Adding Enzyme
  • RNA (35-MER)
KeywordsTransferase/RNA / Protein-RNA / Rossmann Fold / CCA-adding / tRNA / nucleotidyltransfer / Transferase-RNA complex
Function / homology
Function and homology information


CCACCA tRNA nucleotidyltransferase activity / CCA tRNA nucleotidyltransferase / tRNA 3'-terminal CCA addition / tRNA surveillance / RNA repair / tRNA binding / magnesium ion binding / ATP binding
Similarity search - Function
CCA tRNA nucleotidyltransferase, domain 2 / Archaeal tRNA CCA-adding enzyme catalytic domain / tRNA nucleotidyltransferase, archaea / tRNA nucleotidyltransferase, substrate binding / tRNA nucleotidyltransferase, domain 2 / : / tRNA nucleotidyltransferase, second domain / CCA-adding enzyme, C-terminal domain / Poly(A) polymerase predicted RNA binding domain / Nucleotidyltransferase, class I-like, C-terminal ...CCA tRNA nucleotidyltransferase, domain 2 / Archaeal tRNA CCA-adding enzyme catalytic domain / tRNA nucleotidyltransferase, archaea / tRNA nucleotidyltransferase, substrate binding / tRNA nucleotidyltransferase, domain 2 / : / tRNA nucleotidyltransferase, second domain / CCA-adding enzyme, C-terminal domain / Poly(A) polymerase predicted RNA binding domain / Nucleotidyltransferase, class I-like, C-terminal / 2-5OAS/ClassI-CCAase, nucleotidyltransferase domain / Polymerase, nucleotidyl transferase domain / Poly(a)-polymerase, middle domain / Nucleotidyltransferase domain / Beta Polymerase, domain 2 / Beta Polymerase; domain 2 / Nucleotidyltransferase superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / PYROPHOSPHATE 2- / RNA / RNA (> 10) / CCA-adding enzyme
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsPan, B.C. / Xiong, Y. / Steitz, T.A.
CitationJournal: Science / Year: 2010
Title: How the CCA-Adding Enzyme Selects Adenine over Cytosine at Position 76 of tRNA.
Authors: Pan, B. / Xiong, Y. / Steitz, T.A.
History
DepositionSep 16, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 1, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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_conn.ptnr2_label_seq_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: CCA-Adding Enzyme
B: CCA-Adding Enzyme
C: RNA (35-MER)
D: RNA (35-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,57118
Polymers126,1474
Non-polymers2,42514
Water8,557475
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14940 Å2
ΔGint-97 kcal/mol
Surface area49380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.978, 215.826, 58.390
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein / RNA chain , 2 types, 4 molecules ABCD

#1: Protein CCA-Adding Enzyme / tRNA nucleotidyltransferase / tRNA adenylyl-/cytidylyl- transferase / tRNA CCA-pyrophosphorylase / tRNA-NT


Mass: 51906.691 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Archaeoglobus fulgidus (archaea) / References: UniProt: O28126, EC: 2.7.7.25, EC: 2.7.7.21
#2: RNA chain RNA (35-MER) / tRNA nucleotidyltransferase / tRNA adenylyl-/cytidylyl- transferase / tRNA CCA-pyrophosphorylase / tRNA-NT


Mass: 11166.653 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: chemical synthesis

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Non-polymers , 6 types, 489 molecules

#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-POP / PYROPHOSPHATE 2-


Mass: 175.959 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H2O7P2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 475 / 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: 2.77 Å3/Da / Density % sol: 55.62 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG 4000, 0.2 M tri-lithium citrate, 80 mM ammonium sulfate, 50 mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 12, 2007
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 100973 / % possible obs: 97.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.3 % / Rsym value: 0.098 / Net I/σ(I): 15.8
Reflection shell
Resolution (Å)% possible all
1.95-2.0281.3
2.02-2.198.6
2.1-2.299.8
2.2-2.3199.8
2.31-2.4699.7
2.46-2.6599.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→46.63 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.93 / SU B: 8.261 / SU ML: 0.125 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24775 5031 5 %RANDOM
Rwork0.21126 ---
obs0.21309 95658 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.329 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å20 Å2
2--0.03 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.95→46.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7285 1476 143 475 9379
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0229283
X-RAY DIFFRACTIONr_angle_refined_deg1.3532.19212850
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4635880
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.28622.813391
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.656151397
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.441580
X-RAY DIFFRACTIONr_chiral_restr0.090.21408
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026488
X-RAY DIFFRACTIONr_nbd_refined0.1920.24192
X-RAY DIFFRACTIONr_nbtor_refined0.2980.26125
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1840.2520
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2650.253
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3940.222
X-RAY DIFFRACTIONr_mcbond_it0.6341.54547
X-RAY DIFFRACTIONr_mcangle_it0.98827093
X-RAY DIFFRACTIONr_scbond_it1.54235812
X-RAY DIFFRACTIONr_scangle_it2.4384.55757
LS refinement shellResolution: 1.953→2.003 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 304 -
Rwork0.304 5760 -
obs--100 %
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)
11.94590.6025-0.52651.32720.23280.91470.0113-0.0011-0.1577-0.08330.0161-0.03450.02610.0275-0.0274-0.0603-0.0084-0.02010.0316-0.0253-0.1148-1.558-58.691-37.746
20.90680.1990.39711.0388-0.1130.9917-0.02260.1153-0.0616-0.06750.0126-0.1256-0.0510.17540.01-0.049-0.00360.02990.0666-0.0144-0.099418.564-43.951-39.754
31.39110.2924-0.06021.08580.37141.4390.0473-0.0738-0.03650.1184-0.0321-0.09570.1238-0.0451-0.0153-0.032-0.0208-0.01230.01350.0038-0.119317.998-41.89-8.194
41.24680.09890.30467.6631-0.60211.55610.04540.00910.56580.4468-0.01531.02570.1961-0.4256-0.0301-0.1879-0.03090.09110.0626-0.04920.229415.921-10.3095.531
58.65270.9434-1.18525.69271.23834.76020.4365-0.58941.78350.4333-0.27790.4039-0.5790.3431-0.1586-0.0182-0.09080.1638-0.4467-0.17980.472543.76326.3318.111
65.75931.2778-0.88023.00680.80173.48630.2456-0.34451.47190.2844-0.23131.2051-0.3917-0.2813-0.0142-0.13050.06360.1954-0.2336-0.130.644522.04813.849.085
72.26251.3737-0.12813.53830.51161.27050.1859-0.07810.10.3516-0.1116-0.26420.09420.0093-0.0743-0.0913-0.0326-0.05-0.0756-0.023-0.025239.025-12.3573.948
81.5751-0.05051.83570.1248-0.18464.8374-0.06780.13390.0988-0.09680.0864-0.1649-0.15070.1928-0.0186-0.0675-0.0340.01920.0056-0.0014-0.014431.943-31.324-23.128
90.99250.04180.14154.01435.00156.2396-0.0058-0.24790.1928-0.8879-0.61770.5395-0.7839-0.63760.62350.06910.0807-0.07550.0295-0.13550.0752-1.388-26.075-14.605
101.1830.60040.155113.56718.60955.5077-0.30720.36250.1809-2.82370.41220.2338-1.75930.0802-0.1050.5141-0.1499-0.0523-0.06320.116-0.064639.107-1.881-19.593
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A16 - 143
2X-RAY DIFFRACTION2A1 - 15
3X-RAY DIFFRACTION2A144 - 259
4X-RAY DIFFRACTION3A260 - 339
5X-RAY DIFFRACTION3A384 - 441
6X-RAY DIFFRACTION4A340 - 383
7X-RAY DIFFRACTION5B16 - 143
8X-RAY DIFFRACTION6B2 - 15
9X-RAY DIFFRACTION6B144 - 259
10X-RAY DIFFRACTION7B260 - 339
11X-RAY DIFFRACTION7B384 - 437
12X-RAY DIFFRACTION8B340 - 383
13X-RAY DIFFRACTION9C1 - 33
14X-RAY DIFFRACTION10D1 - 33

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