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(-) Description

Title :  CRYSTAL STRUCTURE OF THE KINASE DOMAIN OF WNK1
 
Authors :  X. Min, B. H. Lee, M. H. Cobb, E. J. Goldsmith
Date :  06 Jan 09  (Deposition) - 13 Jan 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Wnk1, Protein Serine/Threonine Kinase, Transferase, Atp-Binding, Kinase, Nucleotide-Binding, Phosphoprotein, Protein Kinase Inhibitor, Serine/Threonine-Protein Kinase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  X. Min, B. H. Lee, M. H. Cobb, E. J. Goldsmith
Crystal Structure Of The Kinase Domain Of Wnk1, A Kinase That Causes A Hereditary Form Of Hypertension.
Structure V. 12 1303 2004
PubMed-ID: 15242606  |  Reference-DOI: 10.1016/J.STR.2004.04.014

(-) Compounds

Molecule 1 - SERINE/THREONINE-PROTEIN KINASE WNK1
    ChainsA, B
    EC Number2.7.11.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPHIS PARALLEL
    Expression System StrainBL21
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentKINASE DOMAIN (UNP RESIDUES 194 TO 483)
    GenePRKWNK1, WNK1
    MutationYES
    Organism CommonBROWN RAT,RAT,RATS
    Organism ScientificRATTUS NORVEGICUS
    Organism Taxid10116
    SynonymPROTEIN KINASE WITH NO LYSINE 1, PROTEIN KINASE, LYSINE- DEFICIENT 1

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 27)

Asymmetric/Biological Unit (3, 27)
No.NameCountTypeFull Name
1GOL8Ligand/IonGLYCEROL
2MSE18Mod. Amino AcidSELENOMETHIONINE
3SO41Ligand/IonSULFATE ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:45 , CYS A:62 , THR A:113 , ASP A:180 , LEU A:183 , HOH A:1005 , HOH A:1041 , HOH A:1049BINDING SITE FOR RESIDUE GOL A 501
2AC2SOFTWARETYR A:218 , TYR A:234 , VAL A:247 , GLY A:250 , ILE A:272 , GLN A:274 , HOH A:1171BINDING SITE FOR RESIDUE GOL A 502
3AC3SOFTWAREARG A:273 , TYR A:280 , HOH A:1057 , HOH A:1063 , GLN B:88 , HOH B:1020BINDING SITE FOR RESIDUE GOL A 503
4AC4SOFTWARELYS B:163 , CYS B:164 , PHE B:201 , MSE B:222 , CYS B:223 , GLU B:226 , PRO B:233 , HOH B:1118BINDING SITE FOR RESIDUE GOL B 501
5AC5SOFTWAREALA B:60 , CYS B:62 , VAL B:93 , THR B:113 , GLU B:114 , MSE B:116 , PHE B:168 , ASP B:180 , GOL B:505BINDING SITE FOR RESIDUE GOL B 502
6AC6SOFTWARELYS B:78 , SER B:98 , HOH B:1104BINDING SITE FOR RESIDUE GOL B 503
7AC7SOFTWAREPHE A:191 , ALA A:240 , THR B:102 , VAL B:103 , LYS B:104BINDING SITE FOR RESIDUE GOL B 504
8AC8SOFTWAREVAL B:93 , PHE B:95 , LEU B:111 , THR B:113 , ILE B:178 , GLY B:179 , ASP B:180 , LEU B:181 , GOL B:502 , HOH B:1130BINDING SITE FOR RESIDUE GOL B 505
9AC9SOFTWAREARG B:127 , PRO B:156 , ILE B:158 , ARG B:160 , HOH B:1029 , HOH B:1110BINDING SITE FOR RESIDUE SO4 B 506

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3FPQ)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Thr A:154 -Pro A:155
2Thr B:154 -Pro B:155

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3FPQ)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_STPS00108 Serine/Threonine protein kinases active-site signature.WNK1_RAT345-357
 
  2A:157-169
B:157-169

(-) Exons   (0, 0)

(no "Exon" information available for 3FPQ)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:271
 aligned with WNK1_RAT | Q9JIH7 from UniProtKB/Swiss-Prot  Length:2126

    Alignment length:271
                                   219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479 
             WNK1_RAT   210 KAVGMSNDGRFLKFDIEIGRGSFKTVYKGLDTETTVEVAWCELQDRKLTKSERQRFKEEAEMLKGLQHPNIVRFYDSWESTVKGKKCIVLVTELMTSGTLKTYLKRFKVMKIKVLRSWCRQILKGLQFLHTRTPPIIHRDLKCDNIFITGPTGSVKIGDLGLATLKRASFAKSVIGTPEFMAPEMYEEKYDESVDVYAFGMCMLEMATSEYPYSECQNAAQIYRRVTSGVKPASFDKVAIPEVKEIIEGCIRQNKDERYSIKDLLNHAFFQ 480
               SCOP domains d3fpqa_ A: Protein kinase wnk1                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 3fpqA01 A:22-114 Phosphorylase Kinase; domain 1                                              3fpqA02 A:115-292 Transferase(Phosphotransferase) domain 1                                                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee.....eeeeeeeeee...eeeeeeee.....eeeeeeee.hhhhhhhhhhhhhhhhhhhh........eeeeeeeee..eeeeeeeee.....hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh..........hhh.eee......eee...hhhhhh.....ee........hhhhhhh...hhhhhhhhhhhhhhhhhh........hhhhhhhhhh....hhhhhhh.hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------PROTEIN_KINAS--------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fpq A  22 KAVGmSNDGRFLKFDIEIGRGSFKTVYKGLDTETTVEVAWCELQDRKLTKSERQRFKEEAEmLKGLQHPNIVRFYDSWESTVKGKKCIVLVTELmTSGTLKTYLKRFKVmKIKVLRSWCRQILKGLQFLHTRTPPIIHRDLKCDNIFITGPTGSVKIGDLGLATLKRASFAKAVIGTPEFmAPEmYEEKYDESVDVYAFGmCmLEmATSEYPYSECQNAAQIYRRVTSGVKPASFDKVAIPEVKEIIEGCIRQNKDERYSIKDLLNHAFFQ 292
                                |   31        41        51        61        71        81 |      91       101       111    |  121       131       141       151       161       171       181       191       201|   |  211       221| |  | 231       241       251       261       271       281       291 
                                |                                                       83-MSE                          116-MSE        131-MSE                                                                202-MSE             222-MSE|                                                                 
                               26-MSE                                                                                                                                                                             206-MSE           224-MSE                                                                
                                                                                                                                                                                                                                       227-MSE                                                             

Chain B from PDB  Type:PROTEIN  Length:272
 aligned with WNK1_RAT | Q9JIH7 from UniProtKB/Swiss-Prot  Length:2126

    Alignment length:272
                                   219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479  
             WNK1_RAT   210 KAVGMSNDGRFLKFDIEIGRGSFKTVYKGLDTETTVEVAWCELQDRKLTKSERQRFKEEAEMLKGLQHPNIVRFYDSWESTVKGKKCIVLVTELMTSGTLKTYLKRFKVMKIKVLRSWCRQILKGLQFLHTRTPPIIHRDLKCDNIFITGPTGSVKIGDLGLATLKRASFAKSVIGTPEFMAPEMYEEKYDESVDVYAFGMCMLEMATSEYPYSECQNAAQIYRRVTSGVKPASFDKVAIPEVKEIIEGCIRQNKDERYSIKDLLNHAFFQE 481
               SCOP domains d3fpqb_ B: Protein kinase wnk1                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 3fpqB01 B:22-114 Phosphorylase Kinase; domain 1                                              3fpqB02 B:115-293 Transferase(Phosphotransferase) domain 1                                                                                                                          CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee.....eeeeeeeeee...eeeeeeee....eeeeeeeee....hhhhhhhhhhhhhhhhh........eeeeeeeee..eeeeeeeee.....hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh..........hhh.eee......eee...hhhhhhh..............hhhhhh....hhhhhhhhhhhhhhhhhh........hhhhhhhhhh....hhhhhhh.hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------PROTEIN_KINAS---------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fpq B  22 KAVGmSNDGRFLKFDIEIGRGSFKTVYKGLDTETTVEVAWCELQDRKLTKSERQRFKEEAEmLKGLQHPNIVRFYDSWESTVKGKKCIVLVTELmTSGTLKTYLKRFKVmKIKVLRSWCRQILKGLQFLHTRTPPIIHRDLKCDNIFITGPTGSVKIGDLGLATLKRASFAKAVIGTPEFmAPEmYEEKYDESVDVYAFGmCmLEmATSEYPYSECQNAAQIYRRVTSGVKPASFDKVAIPEVKEIIEGCIRQNKDERYSIKDLLNHAFFQE 293
                                |   31        41        51        61        71        81 |      91       101       111    |  121       131       141       151       161       171       181       191       201|   |  211       221| |  | 231       241       251       261       271       281       291  
                               26-MSE                                                   83-MSE                          116-MSE        131-MSE                                                                202-MSE             222-MSE|                                                                  
                                                                                                                                                                                                                  206-MSE           224-MSE                                                                 
                                                                                                                                                                                                                                       227-MSE                                                              

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3FPQ)

(-) Gene Ontology  (30, 30)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (WNK1_RAT | Q9JIH7)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0019869    chloride channel inhibitor activity    Stops, prevents, or reduces the activity of a chloride channel.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0019902    phosphatase binding    Interacting selectively and non-covalently with any phosphatase.
    GO:0019870    potassium channel inhibitor activity    Stops, prevents, or reduces the activity of a potassium channel.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0004672    protein kinase activity    Catalysis of the phosphorylation of an amino acid residue in a protein, usually according to the reaction: a protein + ATP = a phosphoprotein + ADP.
    GO:0019901    protein kinase binding    Interacting selectively and non-covalently with a protein kinase, any enzyme that catalyzes the transfer of a phosphate group, usually from ATP, to a protein substrate.
    GO:0004860    protein kinase inhibitor activity    Stops, prevents or reduces the activity of a protein kinase, an enzyme which phosphorylates a protein.
    GO:0004674    protein serine/threonine kinase activity    Catalysis of the reactions: ATP + protein serine = ADP + protein serine phosphate, and ATP + protein threonine = ADP + protein threonine phosphate.
    GO:0030291    protein serine/threonine kinase inhibitor activity    Stops, prevents or reduces the activity of a protein serine/threonine kinase.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0035556    intracellular signal transduction    The process in which a signal is passed on to downstream components within the cell, which become activated themselves to further propagate the signal and finally trigger a change in the function or state of the cell.
    GO:0006811    ion transport    The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0033673    negative regulation of kinase activity    Any process that stops, prevents, or reduces the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0090188    negative regulation of pancreatic juice secretion    Any process that decreases the rate, frequency or extent of pancreatic juice secretion, the regulated release of pancreatic juice by the exocrine pancreas into the upper part of the intestine.
    GO:0010923    negative regulation of phosphatase activity    Any process that decreases the rate or frequency of phosphatase activity. Phosphatases catalyze the hydrolysis of phosphoric monoesters, releasing inorganic phosphate.
    GO:0006469    negative regulation of protein kinase activity    Any process that stops, prevents, or reduces the frequency, rate or extent of protein kinase activity.
    GO:0071901    negative regulation of protein serine/threonine kinase activity    Any process that decreases the rate, frequency, or extent of protein serine/threonine kinase activity.
    GO:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
    GO:0032414    positive regulation of ion transmembrane transporter activity    Any process that activates or increases the activity of an ion transporter.
    GO:0003084    positive regulation of systemic arterial blood pressure    The process that increases the force with which blood travels through the systemic arterial circulatory system.
    GO:0046777    protein autophosphorylation    The phosphorylation by a protein of one or more of its own amino acid residues (cis-autophosphorylation), or residues on an identical protein (trans-autophosphorylation).
    GO:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
    GO:0050794    regulation of cellular process    Any process that modulates the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level.
    GO:2000021    regulation of ion homeostasis    Any process that modulates the frequency, rate or extent of ion homeostasis.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        WNK1_RAT | Q9JIH72lru 4q2a 5drb

(-) Related Entries Specified in the PDB File

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