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- PDB-6khs: Crystal structure of HEMK2/TRMT112 in complex with SAH and MEQ -

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Basic information

Entry
Database: PDB / ID: 6khs
TitleCrystal structure of HEMK2/TRMT112 in complex with SAH and MEQ
Components
  • Methyltransferase N6AMT1
  • Multifunctional methyltransferase subunit TRM112-like protein
KeywordsSTRUCTURAL PROTEIN / Glutamine Methyltransferase
Function / homology
Function and homology information


arsonoacetate metabolic process / arsenite methyltransferase activity / histone H4K12 methyltransferase activity / eRF1 methyltransferase complex / protein-glutamine N-methyltransferase activity / peptidyl-glutamine methylation / rRNA (guanine-N7)-methylation / tRNA methyltransferase activator activity / toxin metabolic process / site-specific DNA-methyltransferase (adenine-specific) activity ...arsonoacetate metabolic process / arsenite methyltransferase activity / histone H4K12 methyltransferase activity / eRF1 methyltransferase complex / protein-glutamine N-methyltransferase activity / peptidyl-glutamine methylation / rRNA (guanine-N7)-methylation / tRNA methyltransferase activator activity / toxin metabolic process / site-specific DNA-methyltransferase (adenine-specific) activity / tRNA modification in the nucleus and cytosol / Methylation / protein methyltransferase activity / positive regulation of rRNA processing / tRNA methylation / S-adenosyl-L-methionine binding / S-adenosylmethionine-dependent methyltransferase activity / rRNA methylation / rRNA modification in the nucleus and cytosol / negative regulation of gene expression, epigenetic / Eukaryotic Translation Termination / transcription initiation-coupled chromatin remodeling / Transferases; Transferring one-carbon groups; Methyltransferases / positive regulation of cell growth / methylation / nucleic acid binding / protein heterodimerization activity / perinuclear region of cytoplasm / protein-containing complex / nucleoplasm / nucleus / cytosol
Similarity search - Function
Eukaryotic/archaeal PrmC-related / : / Multifunctional methyltransferase subunit Trm112 / Trm112-like / Trm112p-like protein / Methyltransferase small domain / Methyltransferase small domain / N-6 Adenine-specific DNA methylases signature. / DNA methylase, N-6 adenine-specific, conserved site / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
N5-METHYLGLUTAMINE / S-ADENOSYL-L-HOMOCYSTEINE / Multifunctional methyltransferase subunit TRM112-like protein / Methyltransferase N6AMT1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.895 Å
AuthorsLiao, S. / Guo, Q. / Zhu, Z.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China31500601 China
National Natural Science Foundation of China31501093 China
CitationJournal: To Be Published
Title: Crystal structure of HEMK2/TRMT112 in complex with SAH and MEQ
Authors: Liao, S. / Guo, Q. / Zhu, Z.
History
DepositionJul 16, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 15, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Methyltransferase N6AMT1
B: Multifunctional methyltransferase subunit TRM112-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7384
Polymers37,1942
Non-polymers5452
Water3,873215
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2310 Å2
ΔGint-15 kcal/mol
Surface area13870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.218, 110.218, 130.747
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11B-264-

HOH

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Components

#1: Protein Methyltransferase N6AMT1 / HemK methyltransferase family member 2 / M.HsaHemK2P


Mass: 22978.367 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HEMK2
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q9Y5N5, Transferases; Transferring one-carbon groups; Methyltransferases, site-specific DNA-methyltransferase (adenine-specific)
#2: Protein Multifunctional methyltransferase subunit TRM112-like protein


Mass: 14215.359 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRMT112
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q9UI30
#3: Chemical ChemComp-MEQ / N5-METHYLGLUTAMINE


Type: L-peptide linking / Mass: 160.171 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12N2O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.28 Å3/Da / Density % sol: 62.45 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 1.26 Msodium phosphate monobasic monohydrate 0.14 Mpotassium phosphate dibasic pH 5.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.895→50 Å / Num. obs: 37766 / % possible obs: 100 % / Redundancy: 37.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.141 / Net I/σ(I): 3.7
Reflection shellResolution: 1.895→1.97 Å / Redundancy: 35.8 % / Rmerge(I) obs: 1.27 / Mean I/σ(I) obs: 3 / Num. unique obs: 3686 / CC1/2: 0.877 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3Q87, 4QTU

3q87

4qtu


Resolution: 1.895→47.726 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 20.03
RfactorNum. reflection% reflection
Rfree0.2198 1943 5.15 %
Rwork0.1874 --
obs0.189 37702 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 85.79 Å2 / Biso mean: 25.0376 Å2 / Biso min: 7.3 Å2
Refinement stepCycle: final / Resolution: 1.895→47.726 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2449 0 37 215 2701
Biso mean--25.47 33.48 -
Num. residues----318
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.895-1.9420.25221170.2183241596
1.942-1.99450.27681270.21042508100
1.9945-2.05320.23211340.20082528100
2.0532-2.11950.21751560.18352510100
2.1195-2.19530.23071340.18452517100
2.1953-2.28310.20541530.1872506100
2.2831-2.38710.23341400.18482527100
2.3871-2.51290.26431390.22563100
2.5129-2.67030.24461260.2042540100
2.6703-2.87650.26051460.20142536100
2.8765-3.16590.22941470.19722582100
3.1659-3.62390.17911360.17532594100
3.6239-4.56510.19531280.15782651100
4.5651-47.720.2011600.19262782100
Refinement TLS params.Method: refined / Origin x: 9.1972 Å / Origin y: 45.4774 Å / Origin z: 75.9758 Å
111213212223313233
T0.0552 Å20.0111 Å20.0058 Å2-0.0789 Å20.013 Å2--0.0753 Å2
L0.551 °2-0.4808 °2-0.3835 °2-0.7098 °2-0.021 °2--1.0486 °2
S0.056 Å °0.0742 Å °0.0275 Å °-0.041 Å °-0.1018 Å °-0.063 Å °-0.0134 Å °0.0667 Å °-0.0321 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA20 - 214
2X-RAY DIFFRACTION1allB1 - 123
3X-RAY DIFFRACTION1allD1
4X-RAY DIFFRACTION1allS1 - 242
5X-RAY DIFFRACTION1allC301

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