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- PDB-2deu: Cocrystal structure of an RNA sulfuration enzyme MnmA and tRNA-Gl... -

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Basic information

Entry
Database: PDB / ID: 2deu
TitleCocrystal structure of an RNA sulfuration enzyme MnmA and tRNA-Glu in the adenylated intermediate state
Components
  • tRNA
  • tRNA-specific 2-thiouridylase mnmA
KeywordsTransferase/RNA / Protein-RNA complex / adenylated intermediate of RNA / Transferase-RNA COMPLEX
Function / homology
Function and homology information


tRNA-uridine 2-sulfurtransferase / sulfurtransferase complex / tRNA wobble position uridine thiolation / sulfurtransferase activity / tRNA binding / ATP binding / cytosol
Similarity search - Function
tRNA-specific 2-thiouridylase MnmA-like, central domain / tRNA-specific 2-thiouridylase MnmA-like, C-terminal domain / tRNA methyl transferase HUP domain / Aminomethyltransferase beta-barrel domain / tRNA methyl transferase PRC-barrel domain / Adenine nucleotide alpha hydrolases-like domains / tRNA-specific 2-thiouridylase / tRNA-specific 2-thiouridylase MnmA-like, central domain superfamily / Translation factors / HUPs ...tRNA-specific 2-thiouridylase MnmA-like, central domain / tRNA-specific 2-thiouridylase MnmA-like, C-terminal domain / tRNA methyl transferase HUP domain / Aminomethyltransferase beta-barrel domain / tRNA methyl transferase PRC-barrel domain / Adenine nucleotide alpha hydrolases-like domains / tRNA-specific 2-thiouridylase / tRNA-specific 2-thiouridylase MnmA-like, central domain superfamily / Translation factors / HUPs / Elongation Factor Tu (Ef-tu); domain 3 / Rossmann-like alpha/beta/alpha sandwich fold / SH3 type barrels. / Roll / Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / RNA / RNA (> 10) / tRNA-specific 2-thiouridylase MnmA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsNumata, T. / Ikeuchi, Y. / Fukai, S. / Suzuki, T. / Nureki, O.
CitationJournal: Nature / Year: 2006
Title: Snapshots of tRNA sulphuration via an adenylated intermediate
Authors: Numata, T. / Ikeuchi, Y. / Fukai, S. / Suzuki, T. / Nureki, O.
History
DepositionFeb 17, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 15, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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 / _struct_conn.pdbx_leaving_atom_flag / _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
C: tRNA
D: tRNA
A: tRNA-specific 2-thiouridylase mnmA
B: tRNA-specific 2-thiouridylase mnmA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,4678
Polymers133,5814
Non-polymers8874
Water00
1
C: tRNA
A: tRNA-specific 2-thiouridylase mnmA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,2344
Polymers66,7902
Non-polymers4432
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: tRNA
B: tRNA-specific 2-thiouridylase mnmA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,2344
Polymers66,7902
Non-polymers4432
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)238.055, 102.133, 108.158
Angle α, β, γ (deg.)90.00, 117.03, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: RNA chain tRNA


Mass: 24378.514 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: RNA was prepared by in vitro transcription.
#2: Protein tRNA-specific 2-thiouridylase mnmA / RNA sulfuration enzyme MnmA


Mass: 42411.816 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pQE80L / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3)
References: UniProt: P25745, Transferases; Transferring sulfur-containing groups; Sulfurtransferases
#3: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4

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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: 4.38 Å3/Da / Density % sol: 71.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 100mM HEPES-Na buffer (pH 7.5), 1.3-1.5M lithium sulfate, 2.5mM ATP, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1HEPES-Na11
2lithium sulfate11
3ATP11
4HEPES-Na12
5lithium sulfate12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 1, 2005
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.4→50 Å / Num. obs: 39423 / % possible obs: 94.5 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 24.6
Reflection shellResolution: 3.4→3.52 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.334 / Mean I/σ(I) obs: 2.3 / % possible all: 91.8

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
MOLREPphasing
CNSrefinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2DET

2det


Resolution: 3.4→39.16 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.318 1456 -RANDOM
Rwork0.281 ---
obs0.281 28987 94.6 %-
Refine analyze
FreeObs
Luzzati coordinate error0.57 Å0.45 Å
Luzzati d res low-5 Å
Luzzati sigma a1.05 Å0.89 Å
Refinement stepCycle: LAST / Resolution: 3.4→39.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5708 3146 54 0 8908
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d21.6
X-RAY DIFFRACTIONc_improper_angle_d1.35
LS refinement shellResolution: 3.4→3.6 Å / Rfactor Rfree error: 0.026
RfactorNum. reflection% reflection
Rfree0.398 226 -
Rwork0.358 --
obs--91.7 %

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