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- PDB-2q8y: Structural insight into the enzymatic mechanism of the phophothre... -

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Basic information

Entry
Database: PDB / ID: 2q8y
TitleStructural insight into the enzymatic mechanism of the phophothreonine lyase
Components
  • 27.5 kDa virulence protein
  • Mitogen-activated protein kinase 7
KeywordsLYASE/TRANSFERASE / alpha/beta fold / LYASE-TRANSFERASE COMPLEX
Function / homology
Function and homology information


Signalling to ERK5 / Lyases; Carbon-oxygen lyases; Acting on phosphates / negative regulation of response to cytokine stimulus / negative regulation of heterotypic cell-cell adhesion / calcineurin-NFAT signaling cascade / cellular response to laminar fluid shear stress / Gastrin-CREB signalling pathway via PKC and MAPK / ERKs are inactivated / mitogen-activated protein kinase binding / negative regulation of calcineurin-NFAT signaling cascade ...Signalling to ERK5 / Lyases; Carbon-oxygen lyases; Acting on phosphates / negative regulation of response to cytokine stimulus / negative regulation of heterotypic cell-cell adhesion / calcineurin-NFAT signaling cascade / cellular response to laminar fluid shear stress / Gastrin-CREB signalling pathway via PKC and MAPK / ERKs are inactivated / mitogen-activated protein kinase binding / negative regulation of calcineurin-NFAT signaling cascade / ERK/MAPK targets / negative regulation of smooth muscle cell apoptotic process / enzyme inhibitor activity / positive regulation of protein metabolic process / RET signaling / MAP kinase activity / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / JUN kinase activity / mitogen-activated protein kinase / regulation of angiogenesis / negative regulation of endothelial cell apoptotic process / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / cellular response to transforming growth factor beta stimulus / cellular response to growth factor stimulus / PML body / negative regulation of inflammatory response / cellular response to hydrogen peroxide / adenylate cyclase-activating G protein-coupled receptor signaling pathway / MAPK cascade / Senescence-Associated Secretory Phenotype (SASP) / cell differentiation / intracellular signal transduction / lyase activity / protein serine kinase activity / protein serine/threonine kinase activity / signal transduction / positive regulation of transcription by RNA polymerase II / extracellular region / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Phosphothreonine lyase fold / phosphothreonine lyase / OspF/SpvC / OspF/SpvC superfamily / Salmonella virulence-associated 28kDa protein / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / : / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. ...Phosphothreonine lyase fold / phosphothreonine lyase / OspF/SpvC / OspF/SpvC superfamily / Salmonella virulence-associated 28kDa protein / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / : / 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
MAPK phosphothreonine lyase / Mitogen-activated protein kinase 7
Similarity search - Component
Biological speciesSalmonella enteritidis (bacteria)
Homo Sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsZhu, Y.-Q. / Wang, D.-C. / Shao, F.
CitationJournal: Mol.Cell / Year: 2007
Title: Structural insights into the enzymatic mechanism of the pathogenic MAPK phosphothreonine lyase
Authors: Zhu, Y. / Li, H. / Long, C. / Hu, L. / Xu, H. / Liu, L. / Chen, S. / Wang, D.C. / Shao, F.
History
DepositionJun 12, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations / Source and taxonomy
Category: database_2 / pdbx_entity_src_syn ...database_2 / pdbx_entity_src_syn / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entity_src_syn.details / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_common_name / _pdbx_entity_src_syn.organism_scientific / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 27.5 kDa virulence protein
B: Mitogen-activated protein kinase 7


Theoretical massNumber of molelcules
Total (without water)28,9342
Polymers28,9342
Non-polymers00
Water4,053225
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1200 Å2
ΔGint-10 kcal/mol
Surface area10910 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)37.367, 71.842, 96.060
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein 27.5 kDa virulence protein


Mass: 27623.037 Da / Num. of mol.: 1 / Mutation: K136A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enteritidis (bacteria) / Gene: mkaD, spvC, vsdD / Plasmid: pGEX-6p-2 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Bl21(DE3) / References: UniProt: P0A2N1, Lyases; Carbon-oxygen lyases
#2: Protein/peptide Mitogen-activated protein kinase 7 / Extracellular signal-regulated kinase 5 / ERK-5 / ERK4 / BMK1 kinase


Mass: 1311.246 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo Sapiens (human)
References: UniProt: Q13164, mitogen-activated protein kinase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 225 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.23 Å3/Da / Density % sol: 44.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 12% PEG3350,0.1M MES pH6.0,0.1 M NaKTartrate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 5, 2007
RadiationMonochromator: Cu / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→25.9 Å / Num. obs: 18132 / % possible obs: 99.8 % / Observed criterion σ(F): 10.4 / Observed criterion σ(I): 107.8 / Redundancy: 6.5 % / Biso Wilson estimate: 19.484 Å2 / Rmerge(I) obs: 0.076 / Rsym value: 0.083 / Net I/σ(I): 21
Reflection shellResolution: 2→2.11 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.304 / Mean I/σ(I) obs: 5.4 / Num. unique all: 2578 / Rsym value: 0.331 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CrystalCleardata collection
MOSFLMdata reduction
SCALAdata scaling
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2P1W

2p1w


Resolution: 2→25.9 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.922 / SU B: 3.388 / SU ML: 0.097 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.187 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21669 1846 10.2 %RANDOM
Rwork0.1813 ---
all0.18491 16331 --
obs0.18491 16284 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.817 Å2
Baniso -1Baniso -2Baniso -3
1--0.7 Å20 Å20 Å2
2---0.81 Å20 Å2
3---1.52 Å2
Refinement stepCycle: LAST / Resolution: 2→25.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1800 0 0 225 2025
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0211845
X-RAY DIFFRACTIONr_angle_refined_deg1.0591.9432486
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6295219
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.1923.861101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.36315312
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1791514
X-RAY DIFFRACTIONr_chiral_restr0.0670.2250
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021443
X-RAY DIFFRACTIONr_nbd_refined0.1740.2854
X-RAY DIFFRACTIONr_nbtor_refined0.2930.21261
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1130.2199
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.180.249
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.160.222
X-RAY DIFFRACTIONr_mcbond_it0.531.51138
X-RAY DIFFRACTIONr_mcangle_it0.89321765
X-RAY DIFFRACTIONr_scbond_it1.1983800
X-RAY DIFFRACTIONr_scangle_it1.8944.5721
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 153 -
Rwork0.209 1159 -
obs--99.92 %

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