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- PDB-3p71: Crystal structure of the complex of LCMT-1 and PP2A -

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Basic information

Entry
Database: PDB / ID: 3p71
TitleCrystal structure of the complex of LCMT-1 and PP2A
Components
  • Leucine carboxyl methyltransferase 1
  • Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform
KeywordsTRANSFERASE/HYDROLASE / LEUCINE CARBOXYMETHYLTRANSFERASE-1 / SERINE/THREONINE PROTEIN KEYWDS 2 PHOSPHATASE 2A / METHYLTRANSFERASE / S-ADENOSYL-L-METHIONINE / TRANSFERASE-HYDROLASE complex
Function / homology
Function and homology information


protein C-terminal carboxyl O-methyltransferase activity / [phosphatase 2A protein]-leucine-carboxy methyltransferase / protein C-terminal leucine carboxyl O-methyltransferase activity / C-terminal protein methylation / Integration of energy metabolism / PP2A-mediated dephosphorylation of key metabolic factors / regulation of microtubule binding / MASTL Facilitates Mitotic Progression / protein phosphatase type 2A complex / regulation of mitotic cell cycle spindle assembly checkpoint ...protein C-terminal carboxyl O-methyltransferase activity / [phosphatase 2A protein]-leucine-carboxy methyltransferase / protein C-terminal leucine carboxyl O-methyltransferase activity / C-terminal protein methylation / Integration of energy metabolism / PP2A-mediated dephosphorylation of key metabolic factors / regulation of microtubule binding / MASTL Facilitates Mitotic Progression / protein phosphatase type 2A complex / regulation of mitotic cell cycle spindle assembly checkpoint / peptidyl-serine dephosphorylation / peptidyl-threonine dephosphorylation / positive regulation of microtubule binding / Regulation of glycolysis by fructose 2,6-bisphosphate metabolism / Inhibition of replication initiation of damaged DNA by RB1/E2F1 / GABA receptor binding / protein methylation / APC truncation mutants have impaired AXIN binding / AXIN missense mutants destabilize the destruction complex / Truncations of AMER1 destabilize the destruction complex / Initiation of Nuclear Envelope (NE) Reformation / S-adenosylmethionine-dependent methyltransferase activity / ERKs are inactivated / Beta-catenin phosphorylation cascade / Signaling by GSK3beta mutants / CTNNB1 S33 mutants aren't phosphorylated / CTNNB1 S37 mutants aren't phosphorylated / CTNNB1 S45 mutants aren't phosphorylated / CTNNB1 T41 mutants aren't phosphorylated / negative regulation of epithelial to mesenchymal transition / Disassembly of the destruction complex and recruitment of AXIN to the membrane / regulation of growth / negative regulation of glycolytic process through fructose-6-phosphate / positive regulation of NLRP3 inflammasome complex assembly / myosin phosphatase activity / CTLA4 inhibitory signaling / protein serine/threonine phosphatase activity / Platelet sensitization by LDL / protein-serine/threonine phosphatase / regulation of cell differentiation / ERK/MAPK targets / T cell homeostasis / regulation of G1/S transition of mitotic cell cycle / mesoderm development / phosphoprotein phosphatase activity / chromosome, centromeric region / DARPP-32 events / regulation of glucose metabolic process / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / negative regulation of protein-containing complex assembly / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Cyclin A/B1/B2 associated events during G2/M transition / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / protein dephosphorylation / meiotic cell cycle / protein tyrosine phosphatase activity / RHO GTPases Activate Formins / response to lead ion / RAF activation / regulation of protein phosphorylation / Spry regulation of FGF signaling / Degradation of beta-catenin by the destruction complex / protein modification process / tau protein binding / PKR-mediated signaling / positive regulation of protein serine/threonine kinase activity / spindle pole / Negative regulation of MAPK pathway / Separation of Sister Chromatids / G2/M transition of mitotic cell cycle / Cyclin D associated events in G1 / microtubule cytoskeleton / Regulation of TP53 Degradation / mitotic cell cycle / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / regulation of apoptotic process / intracellular signal transduction / membrane raft / protein heterodimerization activity / synapse / mitochondrion / extracellular exosome / nucleoplasm / membrane / nucleus / metal ion binding / plasma membrane / cytosol
Similarity search - Function
Leucine carboxyl methyltransferase 1 / Methyltransferase Ppm1/Ppm2/Tcmp / Leucine carboxyl methyltransferase / : / Serine/threonine specific protein phosphatases signature. / Protein phosphatase 2A homologues, catalytic domain. / Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase / Metallo-dependent phosphatases / Purple Acid Phosphatase; chain A, domain 2 / Calcineurin-like phosphoesterase domain, ApaH type ...Leucine carboxyl methyltransferase 1 / Methyltransferase Ppm1/Ppm2/Tcmp / Leucine carboxyl methyltransferase / : / Serine/threonine specific protein phosphatases signature. / Protein phosphatase 2A homologues, catalytic domain. / Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase / Metallo-dependent phosphatases / Purple Acid Phosphatase; chain A, domain 2 / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like / Vaccinia Virus protein VP39 / 4-Layer Sandwich / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-AN6 / : / DI(HYDROXYETHYL)ETHER / Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform / Leucine carboxyl methyltransferase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsXing, Y. / Stanevich, V. / Satyshur, K.A. / Jiang, L.
CitationJournal: Mol.Cell / Year: 2011
Title: The Structural Basis for Tight Control of PP2A Methylation and Function by LCMT-1.
Authors: Stanevich, V. / Jiang, L. / Satyshur, K.A. / Li, Y. / Jeffrey, P.D. / Li, Z. / Menden, P. / Semmelhack, M.F. / Xing, Y.
History
DepositionOct 11, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 16, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 8, 2014Group: Database references
Revision 1.3Oct 15, 2014Group: Structure summary
Revision 1.4Sep 6, 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 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id / _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
T: Leucine carboxyl methyltransferase 1
C: Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,1546
Polymers73,5432
Non-polymers6114
Water2,162120
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4160 Å2
ΔGint-19 kcal/mol
Surface area24630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.802, 65.305, 193.092
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 2 molecules TC

#1: Protein Leucine carboxyl methyltransferase 1 / Protein-leucine O-methyltransferase


Mass: 38504.211 Da / Num. of mol.: 1 / Mutation: C19M, A21E, D22N, P115S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CGI-68, LCMT, LCMT1 / Plasmid: PET15B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9UIC8, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Protein Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform / PP2A-alpha / Replication protein C / RP-C


Mass: 35038.480 Da / Num. of mol.: 1 / Fragment: CATALYTIC SUBUNIT ALPHA ISOFORM
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPP2CA / Plasmid: BACULOVIRUS / Cell line (production host): HI5 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P67775, protein-serine/threonine phosphatase

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Non-polymers , 4 types, 124 molecules

#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-AN6 / 5'-{[(3S)-3-amino-3-carboxypropyl](ethyl)amino}-5'-deoxyadenosine


Type: L-peptide linking / Mass: 395.414 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H25N7O5
#5: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsAUTHORS STATE THAT RESIDUES 294-298 IN ENTITY 2 (MOLECULE C) HAVE BEEN DELETED FOR PURPOSE OF ...AUTHORS STATE THAT RESIDUES 294-298 IN ENTITY 2 (MOLECULE C) HAVE BEEN DELETED FOR PURPOSE OF PROPER DIMERIZATION OF THE C AND T MOLECULES

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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: 2.09 Å3/Da / Density % sol: 41.2 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.2
Details: PROTEIN COMPLEX (~5 MG/ML), 100MM TRIS-HCL, 22-26% V/V PEG 4000, 200 MM SODIUM ACETATE, 5 MM DTT, pH 8.2, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 5, 2009
Details: MERIDIONALLY-BENT FUSED SILICA MIRROR WITH PALLADIUM AND UNCOATED STRIPES VERTICALLY-FOCUSING AT 6.6:1 DEMAGNIFICATION.
RadiationMonochromator: DOUBLE SI(111) CRYSTAL WITH CRYOGENICALLY-COOLED FIRST CRYSTAL AND SAGITALLY-BENT SECOND CRYSTAl HORIZONTALLY-FOCUSING AT 3.3:1 DEMAGNIFICATION.
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 17595 / Num. obs: 16691 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.5 % / Rsym value: 0.137 / Net I/σ(I): 7.45
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 5.2 % / Mean I/σ(I) obs: 4.39 / Rsym value: 0.29 / % possible all: 92.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 3IEI, 2IE3

3iei

2ie3


Resolution: 2.7→48.27 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.909 / SU B: 30.789 / SU ML: 0.286 / Cross valid method: THROUGHOUT / ESU R Free: 0.385 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24939 902 5.2 %RANDOM
Rwork0.19157 ---
obs0.19454 16510 98.4 %-
all-16510 --
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: 43.535 Å2
Baniso -1Baniso -2Baniso -3
1-1.14 Å20 Å20 Å2
2--0.56 Å20 Å2
3----1.71 Å2
Refinement stepCycle: LAST / Resolution: 2.7→48.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5002 0 37 120 5159
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0225150
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0281.9656956
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.455616
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.34923.938259
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.43615908
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.361539
X-RAY DIFFRACTIONr_chiral_restr0.070.2752
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0213921
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2611.53073
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.50624957
X-RAY DIFFRACTIONr_scbond_it0.7132077
X-RAY DIFFRACTIONr_scangle_it1.2274.51999
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 54 -
Rwork0.196 1123 -
obs--93.71 %
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)
11.0889-0.2077-0.64321.6455-0.31782.8136-0.0970.0551-0.1527-0.0798-0.0145-0.01470.3648-0.11060.11150.3625-0.06560.06740.2306-0.03950.0634-13.75594.6332-10.4231
21.22040.1175-0.56862.2295-0.57924.0958-0.06570.29690.0580.00850.04890.0198-0.2389-0.45870.01680.29090.04620.04030.29880.02440.0119-6.316934.303-38.2191
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1T20 - 800
2X-RAY DIFFRACTION1C303 - 310
3X-RAY DIFFRACTION2C2 - 293
4X-RAY DIFFRACTION2C299 - 302
5X-RAY DIFFRACTION2C501 - 708

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