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- PDB-1mlv: Structure and Catalytic Mechanism of a SET Domain Protein Methylt... -

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Basic information

Entry
Database: PDB / ID: 1mlv
TitleStructure and Catalytic Mechanism of a SET Domain Protein Methyltransferase
ComponentsRibulose-1,5 biphosphate carboxylase/oxygenase large subunit N-methyltransferase
KeywordsTRANSFERASE / SET Domain / Lysine N-Methylation / Photosynthesis / Post-translational Modification
Function / homology
Function and homology information


[ribulose-bisphosphate carboxylase]-lysine N-methyltransferase / [fructose-bisphosphate aldolase]-lysine N-methyltransferase / [ribulose-bisphosphate carboxylase]-lysine N-methyltransferase activity / protein-lysine N-methyltransferase activity / chloroplast / methylation
Similarity search - Function
Rubisco LSMT methyltransferase, plant / RBCMT, SET domain / Plant LSMT protein-lysine methyltransferase family profile. / set domain protein methyltransferase, domain 1 / set domain protein methyltransferase, domain 1 / set domain protein methyltransferase, domain 2 / Rubisco LSMT, substrate-binding domain / Rubisco LSMT, substrate-binding domain / Rubisco LSMT, substrate-binding domain superfamily / Rubisco LSMT substrate-binding ...Rubisco LSMT methyltransferase, plant / RBCMT, SET domain / Plant LSMT protein-lysine methyltransferase family profile. / set domain protein methyltransferase, domain 1 / set domain protein methyltransferase, domain 1 / set domain protein methyltransferase, domain 2 / Rubisco LSMT, substrate-binding domain / Rubisco LSMT, substrate-binding domain / Rubisco LSMT, substrate-binding domain superfamily / Rubisco LSMT substrate-binding / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain superfamily / SET domain / SET domain profile. / SET domain / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / Ribulose-1,5 bisphosphate carboxylase/oxygenase large subunit N-methyltransferase, chloroplastic
Similarity search - Component
Biological speciesPisum sativum (garden pea)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2.6 Å
AuthorsTrievel, R.C. / Beach, B.M. / Dirk, L.M.A. / Houtz, R.L. / Hurley, J.H.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2002
Title: Structure and catalytic mechanism of a SET domain protein methyltransferase.
Authors: Trievel, R.C. / Beach, B.M. / Dirk, L.M. / Houtz, R.L. / Hurley, J.H.
History
DepositionAug 30, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 999SEQUENCE AUTHOR INFORMED THAT RESIDUES 483-488 RESULT FROM A C-TERMINAL TEV PROTEASE CLEAVAGE SITE ...SEQUENCE AUTHOR INFORMED THAT RESIDUES 483-488 RESULT FROM A C-TERMINAL TEV PROTEASE CLEAVAGE SITE THAT WAS ENGINEERED INTO THE ENZYME AFTER LEU 482. AFTER CLEAVAGE, THESE SIX RESIDUES WERE LEFT ON THE C-TERMINUS OF THIS CONSTRUCT.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribulose-1,5 biphosphate carboxylase/oxygenase large subunit N-methyltransferase
B: Ribulose-1,5 biphosphate carboxylase/oxygenase large subunit N-methyltransferase
C: Ribulose-1,5 biphosphate carboxylase/oxygenase large subunit N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,7569
Polymers151,8873
Non-polymers1,8686
Water11,998666
1
A: Ribulose-1,5 biphosphate carboxylase/oxygenase large subunit N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2523
Polymers50,6291
Non-polymers6232
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ribulose-1,5 biphosphate carboxylase/oxygenase large subunit N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2523
Polymers50,6291
Non-polymers6232
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Ribulose-1,5 biphosphate carboxylase/oxygenase large subunit N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2523
Polymers50,6291
Non-polymers6232
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9730 Å2
ΔGint-35 kcal/mol
Surface area59800 Å2
MethodPISA
5
A: Ribulose-1,5 biphosphate carboxylase/oxygenase large subunit N-methyltransferase
B: Ribulose-1,5 biphosphate carboxylase/oxygenase large subunit N-methyltransferase
C: Ribulose-1,5 biphosphate carboxylase/oxygenase large subunit N-methyltransferase
hetero molecules

A: Ribulose-1,5 biphosphate carboxylase/oxygenase large subunit N-methyltransferase
B: Ribulose-1,5 biphosphate carboxylase/oxygenase large subunit N-methyltransferase
C: Ribulose-1,5 biphosphate carboxylase/oxygenase large subunit N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)307,51118
Polymers303,7756
Non-polymers3,73612
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
MethodPQS
Unit cell
Length a, b, c (Å)132.160, 156.680, 268.440
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Ribulose-1,5 biphosphate carboxylase/oxygenase large subunit N-methyltransferase / [Ribulose-biphosphate-carboxylase]-lysine N-methyltransferase / RuBisCO methyltransferase / Rubisco ...[Ribulose-biphosphate-carboxylase]-lysine N-methyltransferase / RuBisCO methyltransferase / Rubisco LSMT / rbcMT


Mass: 50629.160 Da / Num. of mol.: 3 / Fragment: Residues 46-482
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pisum sativum (garden pea) / Plasmid: pDEST14 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q43088, [ribulose-bisphosphate carboxylase]-lysine N-methyltransferase
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 666 / 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: 4.57 Å3/Da / Density % sol: 73.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 100 mM HEPES pH 6.8, 1.2-1.35 M Sodium Acetate, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 25 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
2100 mMHEPES1reservoirpH6.8
31.2-1.35 Msodium acetate1reservoir

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 2, 2002 / Details: Osmic Confocal Maxflux Optics
RadiationMonochromator: Osmic Confocal Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→35 Å / Num. all: 83954 / Num. obs: 83954 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 37.3 Å2 / Rsym value: 0.047 / Net I/σ(I): 31.6
Reflection shellResolution: 2.6→2.69 Å / Mean I/σ(I) obs: 2.3 / Rsym value: 0.508 / % possible all: 98.1
Reflection
*PLUS
Lowest resolution: 35 Å / Rmerge(I) obs: 0.047
Reflection shell
*PLUS
% possible obs: 98.1 % / Num. unique obs: 8294 / Rmerge(I) obs: 0.508 / Mean I/σ(I) obs: 2.31

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
SHARPphasing
CNS1.1refinement
RefinementMethod to determine structure: SAD / Resolution: 2.6→30.78 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 706590.6 / Data cutoff high rms absF: 706590.6 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.277 3836 5.1 %RANDOM
Rwork0.232 ---
all0.234 83954 --
obs-74865 87.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.7129 Å2 / ksol: 0.339644 e/Å3
Displacement parametersBiso mean: 69.5 Å2
Baniso -1Baniso -2Baniso -3
1--20.21 Å20 Å20 Å2
2--27.92 Å20 Å2
3----7.71 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.4 Å
Luzzati d res low-5 Å
Luzzati sigma a0.73 Å0.66 Å
Refinement stepCycle: LAST / Resolution: 2.6→30.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10481 0 123 666 11270
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d21.3
X-RAY DIFFRACTIONc_improper_angle_d0.78
X-RAY DIFFRACTIONc_mcbond_it1.271.5
X-RAY DIFFRACTIONc_mcangle_it2.242
X-RAY DIFFRACTIONc_scbond_it1.622
X-RAY DIFFRACTIONc_scangle_it2.622.5
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.426 568 5.3 %
Rwork0.394 10077 -
obs--75.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2SAH.PARSAH.TOP
X-RAY DIFFRACTION3HEPES.PARHEPES.TOP
X-RAY DIFFRACTION4WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 35 Å / Rfactor all: 0.234 / Rfactor Rfree: 0.278 / Rfactor Rwork: 0.232
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.79
LS refinement shell
*PLUS
Rfactor Rfree: 0.426 / Rfactor Rwork: 0.394

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