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- PDB-3iec: Helicobacter pylori CagA Inhibits PAR1/MARK Family Kinases by Mim... -

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Basic information

Entry
Database: PDB / ID: 3iec
TitleHelicobacter pylori CagA Inhibits PAR1/MARK Family Kinases by Mimicking Host Substrates
Components
  • Cytotoxicity-associated immunodominant antigen
  • Serine/threonine-protein kinase MARK2
KeywordsSIGNALING PROTEIN/TOXIN / Protein-protein complex / kinase / virulence factor / Alternative promoter usage / ATP-binding / Cell membrane / Developmental protein / Differentiation / Magnesium / Membrane / Metal-binding / Nucleotide-binding / Phosphoprotein / Serine/threonine-protein kinase / Transferase / SIGNALING PROTEIN-TOXIN COMPLEX
Function / homology
Function and homology information


: / establishment or maintenance of cell polarity regulating cell shape / microtubule bundle / toxin transmembrane transporter activity / mitochondrion localization / establishment or maintenance of epithelial cell apical/basal polarity / autophagy of mitochondrion / tau-protein kinase / tau-protein kinase activity / regulation of axonogenesis ...: / establishment or maintenance of cell polarity regulating cell shape / microtubule bundle / toxin transmembrane transporter activity / mitochondrion localization / establishment or maintenance of epithelial cell apical/basal polarity / autophagy of mitochondrion / tau-protein kinase / tau-protein kinase activity / regulation of axonogenesis / establishment of cell polarity / axon development / regulation of cytoskeleton organization / protein kinase activator activity / lateral plasma membrane / regulation of microtubule cytoskeleton organization / actin filament / positive regulation of neuron projection development / tau protein binding / microtubule cytoskeleton organization / Wnt signaling pathway / neuron migration / peptidyl-serine phosphorylation / protein autophosphorylation / molecular adaptor activity / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / intracellular signal transduction / protein phosphorylation / cadherin binding / protein serine kinase activity / protein serine/threonine kinase activity / lipid binding / dendrite / magnesium ion binding / mitochondrion / RNA binding / nucleoplasm / ATP binding / membrane / plasma membrane / cytoplasm
Similarity search - Function
Type IV secretion system CagA exotoxin / CagA exotoxin, phosphopeptide substrate mimic region / CagA, N-terminal / CagA exotoxin phosphopeptide substrate mimic region / CagA protein / : / Kinase associated domain 1 (KA1) / Kinase associated domain 1 / Kinase associated domain 1 (KA1) profile. / KA1 domain/Ssp2, C-terminal ...Type IV secretion system CagA exotoxin / CagA exotoxin, phosphopeptide substrate mimic region / CagA, N-terminal / CagA exotoxin phosphopeptide substrate mimic region / CagA protein / : / Kinase associated domain 1 (KA1) / Kinase associated domain 1 / Kinase associated domain 1 (KA1) profile. / KA1 domain/Ssp2, C-terminal / Ubiquitin-associated (UBA) domain / UBA/TS-N domain / Ubiquitin associated domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / Helicase, Ruva Protein; domain 3 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / 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 / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Cytotoxicity-associated immunodominant antigen / Serine/threonine-protein kinase MARK2
Similarity search - Component
Biological speciesHomo sapiens (human)
Helicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsStebbins, C.E. / Nesic, D. / Miller, M.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2010
Title: Helicobacter pylori CagA inhibits PAR1-MARK family kinases by mimicking host substrates.
Authors: Nesic, D. / Miller, M.C. / Quinkert, Z.T. / Stein, M. / Chait, B.T. / Stebbins, C.E.
History
DepositionJul 22, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 8, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Oct 13, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine/threonine-protein kinase MARK2
B: Serine/threonine-protein kinase MARK2
C: Serine/threonine-protein kinase MARK2
D: Serine/threonine-protein kinase MARK2
E: Cytotoxicity-associated immunodominant antigen
F: Cytotoxicity-associated immunodominant antigen
G: Cytotoxicity-associated immunodominant antigen
H: Cytotoxicity-associated immunodominant antigen


Theoretical massNumber of molelcules
Total (without water)201,3718
Polymers201,3718
Non-polymers00
Water12,376687
1
A: Serine/threonine-protein kinase MARK2
E: Cytotoxicity-associated immunodominant antigen


Theoretical massNumber of molelcules
Total (without water)50,3432
Polymers50,3432
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1880 Å2
ΔGint-7 kcal/mol
Surface area16200 Å2
MethodPISA
2
B: Serine/threonine-protein kinase MARK2
F: Cytotoxicity-associated immunodominant antigen


Theoretical massNumber of molelcules
Total (without water)50,3432
Polymers50,3432
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1970 Å2
ΔGint-7 kcal/mol
Surface area16340 Å2
MethodPISA
3
C: Serine/threonine-protein kinase MARK2
G: Cytotoxicity-associated immunodominant antigen


Theoretical massNumber of molelcules
Total (without water)50,3432
Polymers50,3432
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1900 Å2
ΔGint-6 kcal/mol
Surface area16200 Å2
MethodPISA
4
D: Serine/threonine-protein kinase MARK2
H: Cytotoxicity-associated immunodominant antigen


Theoretical massNumber of molelcules
Total (without water)50,3432
Polymers50,3432
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1920 Å2
ΔGint-5 kcal/mol
Surface area16060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.466, 93.256, 113.955
Angle α, β, γ (deg.)90.000, 100.940, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Serine/threonine-protein kinase MARK2 / MAP/microtubule affinity-regulating kinase 2 / ELKL motif kinase / EMK1 / PAR1 homolog


Mass: 36919.777 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 49-363
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CagA, EMK1, MARK2 / Production host: Escherichia coli (E. coli)
References: UniProt: Q7KZI7, non-specific serine/threonine protein kinase
#2: Protein
Cytotoxicity-associated immunodominant antigen / 120 kDa protein


Mass: 13423.082 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 885-1005
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: strain 26695 / Gene: cagA, cai / Production host: Escherichia coli (E. coli) / References: UniProt: P55980
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 687 / 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: 2.42 Å3/Da / Density % sol: 49.2 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop
Details: Initial crystals were grown by vapor diffusion using hanging drops formed from mixing a 2:1 volume ratio of the protein complex with an equilibration buffer consisting of 22.5-25% ...Details: Initial crystals were grown by vapor diffusion using hanging drops formed from mixing a 2:1 volume ratio of the protein complex with an equilibration buffer consisting of 22.5-25% polyethylene glycol (PEG) molecular weight 3350 Da, 300 mM Li2SO4, and 100 mM Bis-Tris pH 5.8-6.2, at 23 C. Higher quality crystals were obtained by micro-seeding and addition of 5% PEG 400 as an additive. For cryoprotection crystals where transferred directly into a buffer with a 25% PEG 3350 Da, 5-10% PEG 400 Da, 300mM Li2SO4, 100mM Bis-Tris pH 5.8-6.2, 7.5% glycerol, and flash-cooled immediately afterward to -160 C. , VAPOR DIFFUSION, HANGING DROP, temperature 296K
PH range: 5.8 - 6.2

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.0809 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 8, 2008
Details: Beamline X29 features high-flux radiation derived from a 54-pole harmonic emission undulator, a vertically focusing mirror and a horizontally focusing monochromator. A Cryomech AL300 is ...Details: Beamline X29 features high-flux radiation derived from a 54-pole harmonic emission undulator, a vertically focusing mirror and a horizontally focusing monochromator. A Cryomech AL300 is utilized to produce extremely stable cooling on a Si(111) crystal. The beamline is capable of delivering an energy range of 7-15 kev
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0809 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 97843 / % possible obs: 99.9 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.089 / Χ2: 1.04 / Net I/σ(I): 10.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.2-2.286.20.70697841.1711100
2.28-2.376.20.5296870.991100
2.37-2.486.30.39397501.0621100
2.48-2.616.30.29697751.0671100
2.61-2.776.30.19497551.1241100
2.77-2.996.30.13797621.0711100
2.99-3.296.30.09897731.021100
3.29-3.766.30.07398090.9861100
3.76-4.746.10.05998530.9871100
4.74-505.90.04898950.913199.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→40.96 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.927 / WRfactor Rfree: 0.256 / WRfactor Rwork: 0.21 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.82 / SU B: 12.78 / SU ML: 0.145 / SU R Cruickshank DPI: 0.224 / SU Rfree: 0.195 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.223 / ESU R Free: 0.195 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.248 4890 5 %RANDOM
Rwork0.204 ---
obs0.206 97422 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 76.53 Å2 / Biso mean: 26.151 Å2 / Biso min: 5.02 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å20 Å20.28 Å2
2---0.38 Å20 Å2
3---0.21 Å2
Refinement stepCycle: LAST / Resolution: 2.2→40.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10625 0 0 687 11312
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02210845
X-RAY DIFFRACTIONr_bond_other_d0.0010.027657
X-RAY DIFFRACTIONr_angle_refined_deg1.5071.97714596
X-RAY DIFFRACTIONr_angle_other_deg0.914318644
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.23751290
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.81523.858508
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.087152060
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.51572
X-RAY DIFFRACTIONr_chiral_restr0.0990.21593
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02111758
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022206
X-RAY DIFFRACTIONr_mcbond_it0.7681.56469
X-RAY DIFFRACTIONr_mcbond_other0.1711.52625
X-RAY DIFFRACTIONr_mcangle_it1.442210453
X-RAY DIFFRACTIONr_scbond_it2.2334376
X-RAY DIFFRACTIONr_scangle_it3.5334.54143
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 349 -
Rwork0.254 6779 -
all-7128 -
obs--99.73 %
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)
10.89240.3522-0.73611.9761-1.39862.3349-0.09140.09890.03540.05140.18440.0666-0.0117-0.1828-0.09290.059-0.02170.030.074-0.02830.059424.796-22.29452.483
22.64980.6533-1.86510.8977-0.72152.41920.2529-0.12020.04760.1475-0.14220.0104-0.24330.1242-0.11080.0613-0.03070.00840.1295-0.03310.059155.596-13.4083.398
32.1239-0.5642.01271.117-0.94812.70590.2398-0.0802-0.0955-0.1813-0.06060.11410.2891-0.0532-0.17910.08980.02680.04110.1328-0.02310.12819.243-35.301-3.699
41.01491.09330.80163.43252.34172.2509-0.14170.1977-0.1134-0.12640.3362-0.1114-0.05130.2692-0.19460.1215-0.04610.05890.12110.01350.0967-0.184-50.5452.651
58.86333.3494-2.58842.26350.57444.50320.311-0.27330.69230.1849-0.09970.4521-0.3992-0.5924-0.21140.20150.16930.13070.35590.13020.293516.874-6.62749.26
63.6753.33240.801910.7918-3.193.37570.19090.10080.9784-0.04610.10391.2856-0.6111-0.2274-0.29480.49420.12790.24130.24570.02180.381939.97-5.2256.668
72.7734-2.3824-1.36448.8737-3.72934.5263-0.1667-0.2145-0.8146-0.00580.69821.73970.6869-0.4337-0.53140.5952-0.2479-0.28670.38870.17950.6233-6.437-43.358-7.055
80.63270.4050.97811.6929-0.19852.03440.21690.1303-0.47380.1780.2649-0.71510.37370.1331-0.48190.12510.0895-0.15770.0854-0.13440.48228.174-66.32849.033
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A49 - 363
2X-RAY DIFFRACTION2B49 - 363
3X-RAY DIFFRACTION3C49 - 363
4X-RAY DIFFRACTION4D49 - 363
5X-RAY DIFFRACTION5E948 - 961
6X-RAY DIFFRACTION6F948 - 961
7X-RAY DIFFRACTION7G948 - 961
8X-RAY DIFFRACTION8H948 - 961

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