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- PDB-1rfl: NMR data driven structural model of G-domain of MnmE protein -

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Basic information

Entry
Database: PDB / ID: 1rfl
TitleNMR data driven structural model of G-domain of MnmE protein
ComponentsProbable tRNA modification GTPase trmE
KeywordsUNKNOWN FUNCTION / GTPase domain / alpha/beta
Function / homology
Function and homology information


cytosolic tRNA wobble base thiouridylase complex / regulation of cytoplasmic translational fidelity / tRNA wobble base 5-methoxycarbonylmethyl-2-thiouridinylation / tRNA wobble uridine modification / Hydrolases; Acting on acid anhydrides / tRNA methylation / response to pH / potassium ion binding / chaperone-mediated protein folding / GDP binding ...cytosolic tRNA wobble base thiouridylase complex / regulation of cytoplasmic translational fidelity / tRNA wobble base 5-methoxycarbonylmethyl-2-thiouridinylation / tRNA wobble uridine modification / Hydrolases; Acting on acid anhydrides / tRNA methylation / response to pH / potassium ion binding / chaperone-mediated protein folding / GDP binding / GTPase activity / GTP binding / protein homodimerization activity / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
tRNA modification GTPase MnmE / GTP-binding protein TrmE, N-terminal / MnmE, helical domain / tRNA modification GTPase MnmE domain 2 / TrmE-type guanine nucleotide-binding domain / GTP-binding protein TrmE N-terminus / MnmE helical domain / TrmE-type guanine nucleotide-binding (G) domain profile. / GTP-binding protein TrmE/Aminomethyltransferase GcvT, domain 1 / 50S ribosome-binding GTPase ...tRNA modification GTPase MnmE / GTP-binding protein TrmE, N-terminal / MnmE, helical domain / tRNA modification GTPase MnmE domain 2 / TrmE-type guanine nucleotide-binding domain / GTP-binding protein TrmE N-terminus / MnmE helical domain / TrmE-type guanine nucleotide-binding (G) domain profile. / GTP-binding protein TrmE/Aminomethyltransferase GcvT, domain 1 / 50S ribosome-binding GTPase / GTP binding domain / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
tRNA modification GTPase MnmE
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / NMR restraints were obtained from the backbone assignment (TALOS analysis for dihedral angle constraints), from the 15N-edited 3D NOESY. Additional structural information was obtained from the homologous GTPAse protein structures.
AuthorsMonleon, D. / Esteve, V. / Martinez-Vicente, M. / Yim, L. / Armengod, M.E. / Celda, B.
CitationJournal: Proteins / Year: 2007
Title: Structural insights into the GTPase domain of Escherichia coli MnmE protein.
Authors: Monleon, D. / Martinez-Vicente, M. / Esteve, V. / Yim, L. / Prado, S. / Armengod, M.E. / Celda, B.
History
DepositionNov 10, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 2, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable tRNA modification GTPase trmE


Theoretical massNumber of molelcules
Total (without water)18,7231
Polymers18,7231
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1fewest violations

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Components

#1: Protein Probable tRNA modification GTPase trmE


Mass: 18723.354 Da / Num. of mol.: 1 / Fragment: gdomain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: TRME, THDF, MNME, B3706 / Production host: Escherichia coli (E. coli) / References: UniProt: P25522

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111Triple resonance experiments for BB assignment
1213D 15N-separated NOESY
NMR detailsText: Backbone assignment would not be possible without cryoprobe spectrometers because of the low solubility and stability of the protein.

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Sample preparation

DetailsContents: 0.3 Gdomain MnmE, phosphate buffer, NaCl / Solvent system: 95% H2O/5% D2O
Sample conditionsIonic strength: 50 mM / pH: 7 / Pressure: 1 atm / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DPXBrukerDPX5001
Bruker AMXBrukerAMX5002
Bruker AMXBrukerAMX8003

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2002DelAglio et al.processing
Sparky2002Goddard et al.data analysis
DYANA2000Guntert et al.structure solution
DYANA2000Guntert et al.refinement
RefinementMethod: NMR restraints were obtained from the backbone assignment (TALOS analysis for dihedral angle constraints), from the 15N-edited 3D NOESY. Additional structural information was obtained from ...Method: NMR restraints were obtained from the backbone assignment (TALOS analysis for dihedral angle constraints), from the 15N-edited 3D NOESY. Additional structural information was obtained from the homologous GTPAse protein structures.
Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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