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- PDB-1oy5: Crystal structure of tRNA (m1G37) methyltransferase from Aquifex ... -

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Basic information

Entry
Database: PDB / ID: 1oy5
TitleCrystal structure of tRNA (m1G37) methyltransferase from Aquifex aeolicus
ComponentstRNA (Guanine-N(1)-)-methyltransferase
KeywordsTRANSFERASE / structural genomics / trmD / tRNA (m1G37) methyltransferase / BSGC structure funded by NIH / Protein Structure Initiative / PSI / Berkeley Structural Genomics Center
Function / homology
Function and homology information


: / tRNA N1-guanine methylation / tRNA (guanine37-N1)-methyltransferase / tRNA (guanine(37)-N1)-methyltransferase activity / cytosol
Similarity search - Function
tRNA(m1g37)methyltransferase, domain 2 / Trp Operon Repressor; Chain A / tRNA (guanine-N1-)-methyltransferase, bacteria / tRNA (guanine-N(1)-)-methyltransferase, C-terminal domain superfamily / tRNA methyltransferase TRMD/TRM10-type domain / tRNA (Guanine-1)-methyltransferase / SPOUT methyltransferase, trefoil knot domain / Alpha/beta knot / tRNA (guanine-N1-)-methyltransferase, N-terminal / Alpha/beta knot methyltransferases ...tRNA(m1g37)methyltransferase, domain 2 / Trp Operon Repressor; Chain A / tRNA (guanine-N1-)-methyltransferase, bacteria / tRNA (guanine-N(1)-)-methyltransferase, C-terminal domain superfamily / tRNA methyltransferase TRMD/TRM10-type domain / tRNA (Guanine-1)-methyltransferase / SPOUT methyltransferase, trefoil knot domain / Alpha/beta knot / tRNA (guanine-N1-)-methyltransferase, N-terminal / Alpha/beta knot methyltransferases / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
tRNA (guanine-N(1)-)-methyltransferase
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.6 Å
AuthorsLiu, J. / Wang, W. / Shin, D.H. / Yokota, H. / Kim, R. / Kim, S.H. / Berkeley Structural Genomics Center (BSGC)
CitationJournal: Proteins / Year: 2003
Title: Crystal structure of tRNA (m1G37) methyltransferase from Aquifex aeolicus at 2.6 A resolution: a novel methyltransferase fold.
Authors: Liu, J. / Wang, W. / Shin, D.H. / Yokota, H. / Kim, R. / Kim, S.H.
History
DepositionApr 3, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Remark 300BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 3 CHAIN(S). ...BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 3 CHAIN(S). THE AUTHORS STATE THAT THE BIOLOGICAL UNIT IS NOT CLEAR.
Remark 400COMPOUND THE AUTHORS STATE THE FOLLOWING: BASED ON THE PROTEIN SEQUENCE, THIS PROTEIN, AQ_TRMD, IS ...COMPOUND THE AUTHORS STATE THE FOLLOWING: BASED ON THE PROTEIN SEQUENCE, THIS PROTEIN, AQ_TRMD, IS ANNOTATED AS A TRNA (M1G37) METHYLTRANSFERASE, SAME AS ANOTHER TRNA (M1G37) METHYLTRANSFERASE OF KNOWN STRUCTURE (SUCH AS 1UAJ, 1UAK, 1UAL, 1UAM). THE MAJOR DIFFERENCE IS THAT THE LATTER STRUCTURES HAVE "TRIFOIL KNOTS", WHICH IS PROPOSED AS ESSENTIAL FOR S-ADENOSYL-L-METHIONINE BINDING, WHILE THIS STRUCTURE DOES NOT HAVE THE KNOT. THEREFORE, IT IS POSSIBLE THAT THE PROTEIN IN THIS ENTRY MAY HAVE A BIOCHEMICAL FUNCTION DIFFERENT FROM TRNA (1MG37) METHYLTRANSFERASE DESPITE THE SEQUENCE-BASED ANNOTATION AS SUCH.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: tRNA (Guanine-N(1)-)-methyltransferase
B: tRNA (Guanine-N(1)-)-methyltransferase
C: tRNA (Guanine-N(1)-)-methyltransferase


Theoretical massNumber of molelcules
Total (without water)89,0813
Polymers89,0813
Non-polymers00
Water1,36976
1
A: tRNA (Guanine-N(1)-)-methyltransferase
C: tRNA (Guanine-N(1)-)-methyltransferase


Theoretical massNumber of molelcules
Total (without water)59,3872
Polymers59,3872
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6480 Å2
ΔGint-41 kcal/mol
Surface area21450 Å2
MethodPISA
2
B: tRNA (Guanine-N(1)-)-methyltransferase

B: tRNA (Guanine-N(1)-)-methyltransferase


Theoretical massNumber of molelcules
Total (without water)59,3872
Polymers59,3872
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Unit cell
Length a, b, c (Å)153.351, 96.139, 57.426
Angle α, β, γ (deg.)90.00, 96.24, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein tRNA (Guanine-N(1)-)-methyltransferase / M1G-methyltransferase / tRNA [GM37] methyltransferase


Mass: 29693.562 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Gene: TRMD OR AQ_1489 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)/pSJ1244 / References: UniProt: O67463, EC: 2.1.1.31
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 2.36 Å3/Da / Density % sol: 47.89 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 100 mM Sodium Citrate, 20 % PEG3000, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 278K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Details: Jancarik, J., (1991) J. Appl. Crystallogr., 24, 409.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
20.1 Msodium cirtate1reservoirpH5.5
320 %PEG30001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9640,0.9793
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 23, 2002
RadiationMonochromator: YALE MIRRORS / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9641
20.97931
ReflectionResolution: 2.58→20 Å / Num. obs: 31977 / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2.58→2.64 Å / % possible all: 96.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data reduction
REFMAC5refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.6→20 Å / SU B: 20.353 / SU ML: 0.454 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 1.086 / ESU R Free: 0.377 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30029 1312 5.2 %RANDOM
Rwork0.27937 ---
obs0.28048 24034 99.35 %-
all-24191 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 29.025 Å2
Baniso -1Baniso -2Baniso -3
1--0.75 Å20 Å20.16 Å2
2--1.89 Å20 Å2
3----1.1 Å2
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5303 0 0 76 5379
LS refinement shellResolution: 2.6→2.666 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.343 90
Rwork0.298 1734
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)
12.54780.5433-0.67144.41060.22624.9878-0.2551-0.0388-0.18830.01630.2507-0.35950.27350.38990.00440.06660.0124-0.00990.1279-0.08750.1293-37.5218-10.1929.4359
24.1335-0.69570.82791.5050.14643.9270.0042-0.0960.0696-0.0264-0.01450.001-0.00950.02650.01030.055-0.01030.00130.05450.00430.0294-14.344542.277924.2227
34.12942.1136-1.39695.7814-1.01573.6675-0.0354-0.20380.0383-0.2687-0.0343-0.5903-0.03970.18150.06960.1551-0.09050.0010.1425-0.14620.2362-25.394710.23094.8704
413.29340.51642.26446.5572-2.56749.1935-0.28860.5279-2.4543-1.2192-0.3898-1.46081.88691.02170.67841.0256-0.1660.76490.552-0.15371.3512-9.6145.791-9.9538
58.8721-0.86643.25919.6893-1.37873.14730.1145-0.57821.61540.4607-0.20110.9953-0.99430.30860.08670.4929-0.23340.18560.3624-0.22410.51128.589657.680148.8469
618.5065-3.7492-4.28624.44094.2074-1.0641-0.813-0.75010.31960.94490.9271-1.02071.35930.4979-0.11411.12120.5794-0.31770.55480.00030.53-26.7051-20.398225.9528
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA4 - 1644 - 164
2X-RAY DIFFRACTION2BB304 - 4644 - 164
3X-RAY DIFFRACTION3CC604 - 7644 - 164
4X-RAY DIFFRACTION4AA179 - 235179 - 235
5X-RAY DIFFRACTION5BB479 - 535179 - 235
6X-RAY DIFFRACTION6CC779 - 835179 - 235
Refinement
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 20 Å / Rfactor Rfree: 0.3 / Rfactor Rwork: 0.279
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.018
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg1.97

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