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- PDB-3bt7: Structure of E. coli 5-Methyluridine Methyltransferase TrmA in co... -

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Basic information

Entry
Database: PDB / ID: 3bt7
TitleStructure of E. coli 5-Methyluridine Methyltransferase TrmA in complex with 19 nucleotide T-arm analogue
Components
  • RNA (5'-D(P*GP*CP*UP*GP*UP*GP*(5MU)P*UP*CP*GP*AP*UP*CP*CP*AP*CP*AP*GP*C)-3')
  • tRNA (uracil-5-)-methyltransferaseTRNA (uracil-5-)-methyltransferase
KeywordsTRANSFERASE/RNA / methyluridine / methyltransferase / TrmA / RUMT / S-adenosyl-L-methionine / tRNA processing / TRANSFERASE-RNA COMPLEX
Function / homology
Function and homology information


tRNA (uracil(54)-C5)-methyltransferase activity, S-adenosyl methionine-dependent / tRNA (uracil54-C5)-methyltransferase / tRNA methylation / Transferases; Transferring one-carbon groups; Methyltransferases / tRNA binding / rRNA binding / cytosol
Similarity search - Function
tRNA/tmRNA (uracil-C(5))-methyltransferase, TrmA / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #1070 / RNA methyltransferase TrmA, active site / RNA methyltransferase TrmA, conserved site / RNA methyltransferase trmA family signature 1. / RNA methyltransferase trmA family signature 2. / (Uracil-5)-methyltransferase family / tRNA (Uracil-5-)-methyltransferase / SAM-dependent methyltransferase RNA m(5)U-type domain profile. / Vaccinia Virus protein VP39 ...tRNA/tmRNA (uracil-C(5))-methyltransferase, TrmA / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #1070 / RNA methyltransferase TrmA, active site / RNA methyltransferase TrmA, conserved site / RNA methyltransferase trmA family signature 1. / RNA methyltransferase trmA family signature 2. / (Uracil-5)-methyltransferase family / tRNA (Uracil-5-)-methyltransferase / SAM-dependent methyltransferase RNA m(5)U-type domain profile. / Vaccinia Virus protein VP39 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / tRNA/tmRNA (uracil-C(5))-methyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / MAD / Resolution: 2.43 Å
AuthorsAlian, A. / Stroud, R.M. / Finer-Moore, J.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2008
Title: Structure of a TrmA-RNA complex: A consensus RNA fold contributes to substrate selectivity and catalysis in m5U methyltransferases.
Authors: Alian, A. / Lee, T.T. / Griner, S.L. / Stroud, R.M. / Finer-Moore, J.
History
DepositionDec 27, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 25, 2013Group: Derived calculations
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Source and taxonomy
Category: database_2 / pdbx_entity_src_syn ...database_2 / pdbx_entity_src_syn / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: tRNA (uracil-5-)-methyltransferase
B: tRNA (uracil-5-)-methyltransferase
C: RNA (5'-D(P*GP*CP*UP*GP*UP*GP*(5MU)P*UP*CP*GP*AP*UP*CP*CP*AP*CP*AP*GP*C)-3')
D: RNA (5'-D(P*GP*CP*UP*GP*UP*GP*(5MU)P*UP*CP*GP*AP*UP*CP*CP*AP*CP*AP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)96,6864
Polymers96,6864
Non-polymers00
Water4,702261
1
A: tRNA (uracil-5-)-methyltransferase
C: RNA (5'-D(P*GP*CP*UP*GP*UP*GP*(5MU)P*UP*CP*GP*AP*UP*CP*CP*AP*CP*AP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)48,3432
Polymers48,3432
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2580 Å2
ΔGint-17 kcal/mol
Surface area18310 Å2
MethodPISA
2
B: tRNA (uracil-5-)-methyltransferase
D: RNA (5'-D(P*GP*CP*UP*GP*UP*GP*(5MU)P*UP*CP*GP*AP*UP*CP*CP*AP*CP*AP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)48,3432
Polymers48,3432
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2590 Å2
ΔGint-20 kcal/mol
Surface area18480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)184.407, 70.131, 107.950
Angle α, β, γ (deg.)90.00, 120.88, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B
51A
61B
71A
81B
91A
101B
111A
121B
131A
141B
12C
22D

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111METMETASPASP1AA1 - 654 - 68
211METMETASPASP1BB1 - 654 - 68
321GLNGLNTHRTHR1AA67 - 6870 - 71
421GLNGLNTHRTHR1BB67 - 6870 - 71
531SERSERSERSER1AA7073
631SERSERSERSER1BB7073
741ILEILESERSER1AA72 - 8175 - 84
841ILEILESERSER1BB72 - 8175 - 84
951LEULEULEULEU1AA83 - 10186 - 104
1051LEULEULEULEU1BB83 - 10186 - 104
1161HISHISASPASP1AA103 - 233106 - 236
1261HISHISASPASP1BB103 - 233106 - 236
1371VALVALLYSLYS1AA235 - 366238 - 369
1471VALVALLYSLYS1BB235 - 366238 - 369
112GGCC4CC48 - 661 - 19
212GGCC4DD48 - 661 - 19

NCS ensembles :
ID
1
2

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Components

#1: Protein tRNA (uracil-5-)-methyltransferase / TRNA (uracil-5-)-methyltransferase / tRNAM-5-U54 / methyltransferase / RUMT


Mass: 42298.137 Da / Num. of mol.: 2 / Mutation: E358Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: trmA / Plasmid: pET28b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P23003, tRNA (uracil54-C5)-methyltransferase
#2: RNA chain RNA (5'-D(P*GP*CP*UP*GP*UP*GP*(5MU)P*UP*CP*GP*AP*UP*CP*CP*AP*CP*AP*GP*C)-3')


Mass: 6044.636 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 261 / 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: 3.1 Å3/Da / Density % sol: 60.3 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 100 mM sodium cacodylate pH 7.4, 200 mM sodium sulfate, and 22 % PEG-8000, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Components of the solutions
IDNameCrystal-IDSol-ID
1sodium cacodylate11
2sodium cacodylate12
3sodium sulfate11
4sodium sulfate12
5PEG-800011
6PEG-800012

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 24, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11 Å / Relative weight: 1
ReflectionResolution: 2.43→35.1 Å / Num. all: 90859 / Num. obs: 42023 / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.2 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 5.7
Reflection shellResolution: 2.43→2.49 Å / Redundancy: 2 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 1.7 / % possible all: 83.7

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SOLVEphasing
DMphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3.004data extraction
ADSCQuantumdata collection
SCALAdata scaling
RefinementMethod to determine structure: SAD
Starting model: PDB entry 2BH2

2bh2


Resolution: 2.43→35.07 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.907 / SU B: 11.218 / SU ML: 0.247 / Cross valid method: THROUGHOUT / ESU R: 0.461 / ESU R Free: 0.31 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28635 3230 7.7 %RANDOM
Rwork0.22509 ---
obs0.2297 38764 93.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.563 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å2-0.01 Å2
2--0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.43→35.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5914 804 0 261 6979
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0226929
X-RAY DIFFRACTIONr_bond_other_d0.0020.024378
X-RAY DIFFRACTIONr_angle_refined_deg1.7812.1059568
X-RAY DIFFRACTIONr_angle_other_deg1.4343.00110684
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7155736
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.58724.304309
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.099151055
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1691546
X-RAY DIFFRACTIONr_chiral_restr0.0850.21102
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0217116
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021292
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2130.2257
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0070.21
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1350.222
X-RAY DIFFRACTIONr_symmetry_vdw_other0.250.274
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2750.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.781.53692
X-RAY DIFFRACTIONr_mcbond_other0.1431.51470
X-RAY DIFFRACTIONr_mcangle_it1.45325963
X-RAY DIFFRACTIONr_scbond_it2.10233237
X-RAY DIFFRACTIONr_scangle_it3.3924.53605
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 2 / Auth asym-ID: A / Ens-ID: 2 / Number: 531 / Refine-ID: X-RAY DIFFRACTION / Rms dev position: 0 Å

TypeWeight position
medium positional0.5
medium thermal5
LS refinement shellResolution: 2.43→2.493 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.42 209 -
Rwork0.366 2533 -
obs--82.81 %

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