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

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Basic information

Entry
Database: PDB / ID: 3ova
TitleHow the CCA-adding Enzyme Selects Adenine over Cytosine in Position 76 of tRNA
Components
  • CCA-adding enzyme
  • RNA (34-MER)
KeywordsTransferase/RNA / Protein-RNA / Rossmann Fold / CCA-adding / tRNA / nucleotidyltransfer / Transferase-RNA complex
Function / homology
Function and homology information


CCA tRNA nucleotidyltransferase activity / tRNA surveillance / CCACCA tRNA nucleotidyltransferase activity / CCA tRNA nucleotidyltransferase / tRNA 3'-terminal CCA addition / 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 / Poly(a)-polymerase, middle domain / Polymerase, nucleotidyl transferase 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
DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / RNA / RNA (> 10) / CCA-adding enzyme / CCA-adding enzyme
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
Synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 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 ...Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity / entity_name_com / entity_src_nat / pdbx_entity_src_syn / struct_ref / struct_ref_seq / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _entity.pdbx_ec / _entity_src_nat.pdbx_beg_seq_num / _entity_src_nat.pdbx_end_seq_num / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific / _pdbx_entity_src_syn.pdbx_beg_seq_num / _pdbx_entity_src_syn.pdbx_end_seq_num / _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
C: RNA (34-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,8588
Polymers62,0462
Non-polymers8126
Water3,945219
1
A: CCA-adding enzyme
C: RNA (34-MER)
hetero molecules

A: CCA-adding enzyme
C: RNA (34-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,71616
Polymers124,0924
Non-polymers1,62412
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_645y+1,x-1,-z1
Buried area14200 Å2
ΔGint-92 kcal/mol
Surface area47470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.942, 57.942, 427.945
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-628-

HOH

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Components

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Protein / RNA chain , 2 types, 2 molecules AC

#1: Protein CCA-adding enzyme / CCA tRNA nucleotidyltransferase / tRNA CCA-pyrophosphorylase / tRNA adenylyl-/cytidylyl- ...CCA tRNA nucleotidyltransferase / tRNA CCA-pyrophosphorylase / tRNA adenylyl-/cytidylyl- transferase / tRNA nucleotidyltransferase / tRNA-NT


Mass: 51208.762 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Archaeoglobus fulgidus (archaea)
References: UniProt: A0A101DCH0, UniProt: O28126*PLUS, CCA tRNA nucleotidyltransferase
#2: RNA chain RNA (34-MER)


Mass: 10837.447 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: chemistry synthesis / Source: (synth.) Synthetic construct (others)

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Non-polymers , 5 types, 225 molecules

#3: Chemical ChemComp-APC / DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-CPP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 219 / 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: 2.89 Å3/Da / Density % sol: 57.5 %
Crystal growTemperature: 300 K / 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: APS / Beamline: 19-ID / Wavelength: 1
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 20, 2007
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.98→50 Å / Num. obs: 46253 / % possible obs: 87.2 % / Observed criterion σ(I): 2 / Redundancy: 8.3 % / Rsym value: 0.118
Reflection shellResolution: 1.98→2.05 Å / % possible all: 77

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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: 1.98→48 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.928 / SU B: 8.275 / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.158 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.244 2326 5.1 %RANDOM
Rwork0.214 ---
obs0.216 43725 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: 31.451 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.98→48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3570 720 49 219 4558
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0224499
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2792.1846217
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4585428
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.62722.76192
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.50615679
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7811540
X-RAY DIFFRACTIONr_chiral_restr0.0840.2684
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023150
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1940.22030
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2970.23031
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.2245
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1830.288
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1710.216
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5351.52211
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.89623452
X-RAY DIFFRACTIONr_scbond_it1.33232797
X-RAY DIFFRACTIONr_scangle_it2.1884.52765
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.98→2.03 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 122 -
Rwork0.293 2753 -
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)
10.9646-0.0843-0.31110.7825-0.07491.9761-0.02870.13120.01720.00170.10450.0581-0.1217-0.0715-0.0758-0.06870-0.0282-0.02170.0145-0.041111.2899-1.9639-42.8428
21.24520.16260.00930.9097-0.11641.97680.058-0.18610.02890.0267-0.00990.0505-0.1529-0.0429-0.0481-0.06440.00370.0138-0.0220.0046-0.03968.9486-3.4559-18.1892
31.2322-0.39340.22740.8886-0.08242.4173-0.03920.07470.09340.0471-0.0456-0.0104-0.1540.07430.0848-0.0798-0.0381-0.0143-0.03940.0285-0.024540.7583-5.1404-17.1304
40.70320.79350.05247.648-1.96530.61080.08050.20480.004-0.4416-0.0083-0.02360.1830.0606-0.07220.07870.0169-0.0204-0.0086-0.0209-0.085252.7514-32.0677-0.4975
55.5788-3.85693.33242.8119-1.98032.71080.73440.2108-0.9125-0.1814-0.19520.7550.53860.2566-0.53920.09210.0304-0.1548-0.01720.01790.085533.5982-28.0669-24.8047
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A16 - 143
2X-RAY DIFFRACTION2A3 - 15
3X-RAY DIFFRACTION2A144 - 256
4X-RAY DIFFRACTION3A262 - 339
5X-RAY DIFFRACTION3A384 - 437
6X-RAY DIFFRACTION4A340 - 383
7X-RAY DIFFRACTION5C1 - 34

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