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- PDB-2lru: Solution Structure of the WNK1 Autoinhibitory Domain -

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Basic information

Entry
Database: PDB / ID: 2lru
TitleSolution Structure of the WNK1 Autoinhibitory Domain
ComponentsSerine/threonine-protein kinase WNK1
KeywordsTRANSFERASE / autoinhibitory domain / PF2 domain
Function / homology
Function and homology information


negative regulation of cell-cell adhesion mediated by integrin / lymphocyte migration into lymph node / chemokine (C-C motif) ligand 21 signaling pathway / monoatomic cation homeostasis / positive regulation of termination of RNA polymerase II transcription / negative regulation of pancreatic juice secretion / protein insertion into ER membrane by stop-transfer membrane-anchor sequence / negative regulation of small GTPase mediated signal transduction / monoatomic ion homeostasis / negative regulation of sodium ion transport ...negative regulation of cell-cell adhesion mediated by integrin / lymphocyte migration into lymph node / chemokine (C-C motif) ligand 21 signaling pathway / monoatomic cation homeostasis / positive regulation of termination of RNA polymerase II transcription / negative regulation of pancreatic juice secretion / protein insertion into ER membrane by stop-transfer membrane-anchor sequence / negative regulation of small GTPase mediated signal transduction / monoatomic ion homeostasis / negative regulation of sodium ion transport / positive regulation of mitotic cytokinesis / positive regulation of potassium ion import across plasma membrane / regulation of mRNA export from nucleus / negative regulation of heterotypic cell-cell adhesion / intracellular chloride ion homeostasis / positive regulation of T cell chemotaxis / regulation of sodium ion transmembrane transport / potassium channel inhibitor activity / cellular response to chemokine / potassium ion homeostasis / negative regulation of leukocyte cell-cell adhesion / cellular hyperosmotic response / membraneless organelle assembly / cell volume homeostasis / regulation of monoatomic cation transmembrane transport / intracellular membraneless organelle / positive regulation of systemic arterial blood pressure / protein serine/threonine kinase inhibitor activity / protein kinase activator activity / negative regulation of protein localization to plasma membrane / phosphatase binding / regulation of sodium ion transport / monoatomic ion transport / negative regulation of protein ubiquitination / sodium ion transmembrane transport / negative regulation of autophagy / cellular response to calcium ion / molecular condensate scaffold activity / modulation of chemical synaptic transmission / GABA-ergic synapse / regulation of blood pressure / positive regulation of angiogenesis / mitotic spindle / positive regulation of canonical Wnt signaling pathway / T cell receptor signaling pathway / heart development / protein phosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / protein serine kinase activity / protein serine/threonine kinase activity / protein kinase binding / magnesium ion binding / signal transduction / protein-containing complex / ATP binding / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
: / : / WNK CCTL2 domain / Serine/threonine-protein kinase OSR1/WNK, CCT domain / Oxidative-stress-responsive kinase 1 C-terminal domain / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain ...: / : / WNK CCTL2 domain / Serine/threonine-protein kinase OSR1/WNK, CCT domain / Oxidative-stress-responsive kinase 1 C-terminal domain / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Roll / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Alpha Beta
Similarity search - Domain/homology
Serine/threonine-protein kinase WNK1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing
Model detailsclosest to the average, model 1
AuthorsMoon, T.M. / Correa, F. / Gardner, K.H. / Goldsmith, E.J.
CitationJournal: J.Mol.Biol. / Year: 2013
Title: Solution Structure of the WNK1 Autoinhibitory Domain, a WNK-Specific PF2 Domain.
Authors: Moon, T.M. / Correa, F. / Kinch, L.N. / Piala, A.T. / Gardner, K.H. / Goldsmith, E.J.
History
DepositionApr 13, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 23, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2013Group: Database references
Revision 1.2Apr 24, 2013Group: Database references
Revision 1.3Jun 14, 2023Group: Database references / Other
Category: database_2 / pdbx_database_status / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _struct_ref_seq_dif.details
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine/threonine-protein kinase WNK1


Theoretical massNumber of molelcules
Total (without water)11,3591
Polymers11,3591
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 500structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Serine/threonine-protein kinase WNK1 / Protein kinase lysine-deficient 1 / Protein kinase with no lysine 1


Mass: 11358.877 Da / Num. of mol.: 1 / Fragment: UNP residues 480-572
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Wnk1, Hsn2, Prkwnk1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9JIH7, non-specific serine/threonine protein kinase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D (H)CCH-TOCSY
1313D CBCA(CO)NH
1413D HNCO
1513D HN(CA)CB
1613D H(CCO)NH
1713D C(CO)NH
1813D 1H-15N NOESY
1913D 1H-13C NOESY

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Sample preparation

DetailsContents: 0.65 mM [U-100% 13C; U-100% 15N] WNKAI, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
SampleConc.: 0.65 mM / Component: WNKAI-1 / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionsIonic strength: 0.01 / pH: 6.5 / Pressure: ambient / Temperature: 308 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
ARIALinge, O'Donoghue and Nilgesstructure solution
ARIALinge, O'Donoghue and Nilgesrefinement
RefinementMethod: torsion angle dynamics, simulated annealing / Software ordinal: 1
Details: The authors state that two protons (TYR516 hydroxyl, CYS 547 backbone amide) are clashing in 1 model of the 20, and are close in 6/20. While we have not been able to directly assign the ...Details: The authors state that two protons (TYR516 hydroxyl, CYS 547 backbone amide) are clashing in 1 model of the 20, and are close in 6/20. While we have not been able to directly assign the chemical shifts of that hydroxyl proton given the difficulties of exchange at this site, we believe that our existing NMR data are consistent with arrangement indicating a likely H-bond between the CYS 547 amide proton and TYR 516 hydroxyl oxygen.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 500 / Conformers submitted total number: 20

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