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- PDB-2ojx: Molecular and structural basis of polo-like kinase 1 substrate re... -

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Basic information

Entry
Database: PDB / ID: 2ojx
TitleMolecular and structural basis of polo-like kinase 1 substrate recognition: Implications in centrosomal localization
Components
  • Serine/threonine-protein kinase PLK1
  • Synthetic peptide
KeywordsTRANSFERASE / POLO BOX DOMAIN / KINASE / centrosome
Function / homology
Function and homology information


positive regulation of G2/MI transition of meiotic cell cycle / Mitotic Telophase/Cytokinesis / regulation of protein localization to cell cortex / Mitotic Metaphase/Anaphase Transition / synaptonemal complex disassembly / Golgi inheritance / regulation of protein binding / Activation of NIMA Kinases NEK9, NEK6, NEK7 / nuclear membrane disassembly / homologous chromosome segregation ...positive regulation of G2/MI transition of meiotic cell cycle / Mitotic Telophase/Cytokinesis / regulation of protein localization to cell cortex / Mitotic Metaphase/Anaphase Transition / synaptonemal complex disassembly / Golgi inheritance / regulation of protein binding / Activation of NIMA Kinases NEK9, NEK6, NEK7 / nuclear membrane disassembly / homologous chromosome segregation / polo kinase / mitotic nuclear membrane disassembly / Phosphorylation of Emi1 / protein localization to nuclear envelope / metaphase/anaphase transition of mitotic cell cycle / synaptonemal complex / female meiosis chromosome segregation / anaphase-promoting complex binding / Phosphorylation of the APC/C / outer kinetochore / negative regulation of cyclin-dependent protein serine/threonine kinase activity / positive regulation of ubiquitin protein ligase activity / regulation of mitotic spindle assembly / double-strand break repair via alternative nonhomologous end joining / microtubule bundle formation / mitotic chromosome condensation / Polo-like kinase mediated events / Golgi Cisternae Pericentriolar Stack Reorganization / centrosome cycle / regulation of mitotic metaphase/anaphase transition / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / positive regulation of ubiquitin-protein transferase activity / sister chromatid cohesion / regulation of mitotic cell cycle phase transition / regulation of mitotic nuclear division / WW domain binding / regulation of cyclin-dependent protein serine/threonine kinase activity / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / mitotic spindle assembly checkpoint signaling / mitotic spindle pole / regulation of anaphase-promoting complex-dependent catabolic process / mitotic G2 DNA damage checkpoint signaling / establishment of mitotic spindle orientation / mitotic sister chromatid segregation / positive regulation of proteolysis / phosphoprotein phosphatase activity / mitotic cytokinesis / centriolar satellite / spindle midzone / negative regulation of double-strand break repair via homologous recombination / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / Activation of ATR in response to replication stress / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Cyclin A/B1/B2 associated events during G2/M transition / RHO GTPases activate PKNs / Mitotic Prometaphase / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / EML4 and NUDC in mitotic spindle formation / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes / protein localization to chromatin / Anchoring of the basal body to the plasma membrane / regulation of mitotic cell cycle / positive regulation of G2/M transition of mitotic cell cycle / Resolution of Sister Chromatid Cohesion / centriole / AURKA Activation by TPX2 / protein-tyrosine-phosphatase / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / mitotic spindle organization / Condensation of Prophase Chromosomes / regulation of cytokinesis / protein tyrosine phosphatase activity / positive regulation of peptidyl-threonine phosphorylation / RHO GTPases Activate Formins / protein destabilization / establishment of protein localization / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / mitochondrial intermembrane space / kinetochore / spindle pole / positive regulation of protein localization to nucleus / spindle / Separation of Sister Chromatids / G2/M transition of mitotic cell cycle / The role of GTSE1 in G2/M progression after G2 checkpoint / microtubule cytoskeleton / Regulation of PLK1 Activity at G2/M Transition / double-strand break repair / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / mitotic cell cycle / midbody / peptidyl-serine phosphorylation / spermatogenesis / microtubule binding / cell population proliferation / regulation of cell cycle / protein kinase activity
Similarity search - Function
M-phase inducer phosphatase / M-phase inducer phosphatase / POLO box domain / Polo-like kinase 1, catalytic domain / Second polo-box domain / First polo-box domain / POLO box domain superfamily / POLO box duplicated region / POLO box domain / POLO box domain profile. ...M-phase inducer phosphatase / M-phase inducer phosphatase / POLO box domain / Polo-like kinase 1, catalytic domain / Second polo-box domain / First polo-box domain / POLO box domain superfamily / POLO box duplicated region / POLO box domain / POLO box domain profile. / Arylsulfatase, C-terminal domain / Rhodanese Homology Domain / Rhodanese-like domain / Rhodanese domain profile. / Rhodanese-like domain superfamily / Rhodanese-like domain / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
M-phase inducer phosphatase 3 / Serine/threonine-protein kinase PLK1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsGarcia-Alvarez, B. / de Carcer, G. / Ibanez, S. / Bragado-Nilsson, E. / Montoya, G.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: Molecular and structural basis of polo-like kinase 1 substrate recognition: Implications in centrosomal localization.
Authors: Garcia-Alvarez, B. / de Carcer, G. / Ibanez, S. / Bragado-Nilsson, E. / Montoya, G.
History
DepositionJan 15, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2007Provider: repository / Type: Initial release
Revision 1.1Oct 29, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 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: Serine/threonine-protein kinase PLK1
E: Synthetic peptide


Theoretical massNumber of molelcules
Total (without water)28,4192
Polymers28,4192
Non-polymers00
Water18010
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.186, 49.178, 56.234
Angle α, β, γ (deg.)90.00, 109.48, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Serine/threonine-protein kinase PLK1 / Polo-like kinase 1 / PLK-1 / Serine/threonine-protein kinase 13 / STPK13


Mass: 27502.334 Da / Num. of mol.: 1 / Fragment: residues 365-603
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLK1, PLK / Plasmid: PGEX-6P-2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-pLys / References: UniProt: P53350, polo kinase
#2: Protein/peptide Synthetic peptide


Mass: 917.082 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic peptide / References: UniProt: P30307*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 1.84 Å3/Da / Density % sol: 33.25 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20 % PEG 10000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 1, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.85→50 Å / Num. obs: 4971 / % possible obs: 96.3 % / Observed criterion σ(I): 1 / Redundancy: 2.6 % / Rsym value: 0.09 / Net I/σ(I): 4.8
Reflection shellResolution: 2.85→3 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 1.9 / Num. unique all: 618 / Rsym value: 0.31 / % possible all: 96.3

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Processing

Software
NameVersionClassification
REFMAC5refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UMW

1umw


Resolution: 2.85→18.94 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(I): 1
RfactorNum. reflection% reflection
Rfree0.27 --
Rwork0.23 --
obs0.23 4225 96.3 %
Refinement stepCycle: LAST / Resolution: 2.85→18.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1725 0 0 10 1735

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