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(-) Description

Title :  BINARY COMPLEX OF CASEIN KINASE-1 FROM S. POMBE WITH AN ATP COMPETITIVE INHIBITOR, IC261
 
Authors :  N. Mashhoon, A. J. Demaggio, V. Tereshko, S. C. Bergmeier, M. Egli, M. F. Hoekstra, J. Kuret
Date :  18 Feb 00  (Deposition) - 19 Sep 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Protein Kinase, Casein Kinase-1, Protein-Inhibitor Binary Complex, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Mashhoon, A. J. Demaggio, V. Tereshko, S. C. Bergmeier, M. Egli, M. F. Hoekstra, J. Kuret
Crystal Structure Of A Conformation-Selective Casein Kinase-1 Inhibitor
J. Biol. Chem. V. 275 20052 2000
PubMed-ID: 10749871  |  Reference-DOI: 10.1074/JBC.M001713200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CASEIN KINASE-1
    Chains: A, B
    EC Number: 2.7.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PT7B
    Expression System Taxid: 562
    Fragment: CATALYTIC CORE RESIDUES 1 - 298
    Organism Common: FISSION YEAST
    Organism Scientific: SCHIZOSACCHAROMYCES POMBE
    Organism Taxid: 4896
    Other Details: A 298 RESIDUE TRUNCATION MUTANT OF CKI1
    Other Details - Source: SCHIZOSACCHAROMYCES POMBE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 13)

Asymmetric Unit (2, 13)
No.NameCountTypeFull Name
1IC12Ligand/Ion3-[(2,4,6-TRIMETHOXY-PHENYL)-METHYLENE]-INDOLIN-2-ONE
2SO411Ligand/IonSULFATE ION
Biological Unit 1 (2, 7)
No.NameCountTypeFull Name
1IC11Ligand/Ion3-[(2,4,6-TRIMETHOXY-PHENYL)-METHYLENE]-INDOLIN-2-ONE
2SO46Ligand/IonSULFATE ION
Biological Unit 2 (2, 6)
No.NameCountTypeFull Name
1IC11Ligand/Ion3-[(2,4,6-TRIMETHOXY-PHENYL)-METHYLENE]-INDOLIN-2-ONE
2SO45Ligand/IonSULFATE ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS A:159 , ARG A:173 , ASN A:177 , HOH A:424BINDING SITE FOR RESIDUE SO4 A 301
02AC2SOFTWAREARG A:183 , GLN A:219 , GLY A:220 , LYS A:229BINDING SITE FOR RESIDUE SO4 A 302
03AC3SOFTWAREARG A:162 , LYS A:167 , HIS A:169 , ARG A:197 , THR A:268 , SO4 A:304BINDING SITE FOR RESIDUE SO4 A 303
04AC4SOFTWAREGLU A:124 , ARG A:162 , LYS A:167 , SO4 A:303BINDING SITE FOR RESIDUE SO4 A 304
05AC5SOFTWAREPRO A:241 , LEU A:242 , ARG A:243 , TYR A:254 , ASN B:35BINDING SITE FOR RESIDUE SO4 A 305
06AC6SOFTWARELYS A:159 , ARG A:173 , GLU A:194 , GLN A:195BINDING SITE FOR RESIDUE SO4 A 306
07AC7SOFTWAREARG B:183 , GLN B:219 , GLY B:220 , LYS B:222 , LYS B:229BINDING SITE FOR RESIDUE SO4 B 308
08AC8SOFTWAREARG B:162 , HIS B:169 , ARG B:197 , THR B:268BINDING SITE FOR RESIDUE SO4 B 309
09AC9SOFTWAREGLU B:124 , ARG B:162BINDING SITE FOR RESIDUE SO4 B 310
10BC1SOFTWAREPRO B:241 , LEU B:242 , ARG B:243 , TYR B:254BINDING SITE FOR RESIDUE SO4 B 311
11BC2SOFTWAREILE A:18 , GLY A:21 , SER A:22 , ILE A:26 , LYS A:41 , GLU A:55 , TYR A:59 , ILE A:85 , ASP A:135 , ASN A:136 , LEU A:138 , VAL A:153 , ASP A:154BINDING SITE FOR RESIDUE IC1 A 300
12BC3SOFTWAREILE B:18 , GLU B:20 , GLY B:21 , SER B:22 , ILE B:26 , LYS B:41 , GLU B:55 , TYR B:59 , ILE B:85 , ASP B:86 , LEU B:88 , ASP B:135 , LEU B:138 , VAL B:153 , ASP B:154BINDING SITE FOR RESIDUE IC1 B 400

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1EH4)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1EH4)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1EH4)

(-) PROSITE Motifs  (2, 4)

Asymmetric Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.CKI1_SCHPO18-41
 		  2A:18-41
B:18-41
2PROTEIN_KINASE_STPS00108 Serine/Threonine protein kinases active-site signature.CKI1_SCHPO127-139
 		  2A:127-139
B:127-139
Biological Unit 1 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.CKI1_SCHPO18-41
 		  1A:18-41
-
2PROTEIN_KINASE_STPS00108 Serine/Threonine protein kinases active-site signature.CKI1_SCHPO127-139
 		  1A:127-139
-
Biological Unit 2 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.CKI1_SCHPO18-41
 		  1-
B:18-41
2PROTEIN_KINASE_STPS00108 Serine/Threonine protein kinases active-site signature.CKI1_SCHPO127-139
 		  1-
B:127-139

(-) Exons   (0, 0)

(no "Exon" information available for 1EH4)

(-) Sequences/Alignments

Asymmetric 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:293
 aligned with CKI1_SCHPO | P40233 from UniProtKB/Swiss-Prot  Length:446

    Alignment length:293
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295   
           CKI1_SCHPO     6 NVVGVHYKVGRRIGEGSFGVIFEGTNLLNNQQVAIKFEPRRSDAPQLRDEYRTYKLLAGCTGIPNVYYFGQEGLHNILVIDLLGPSLEDLLDLCGRKFSVKTVAMAAKQMLARVQSIHEKSLVYRDIKPDNFLIGRPNSKNANMIYVVDFGMVKFYRDPVTKQHIPYREKKNLSGTARYMSINTHLGREQSRRDDLEALGHVFMYFLRGSLPWQGLKAATNKQKYERIGEKKQSTPLRELCAGFPEEFYKYMHYARNLAFDATPDYDYLQGLFSKVLERLNTTEDENFDWNLL 298
               SCOP domains d1eh4a_ A: Casein kinase-1, CK1                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains 1eh4A01 A:6-87 Phosphorylase Kinase; domain 1                                     1eh4A02 A:88-298 Transferase(Phosphotransferase) domain 1                                                                                                                                                           CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee...ee...eee......ee..ee......eeeeeee......hhhhhhhhhhhh........eeeee....eeeeeee....hhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh..ee....hhh.eee..........eee......ee....................hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhh.hhhhhhh..hhhhhhhhhhhh........hhhhhhhhhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------PROTEIN_KINASE_ATP      -------------------------------------------------------------------------------------PROTEIN_KINAS--------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1eh4 A   6 NVVGVHYKVGRRIGEGSFGVIFEGTNLLNNQQVAIKFEPRRSDAPQLRDEYRTYKLLAGCTGIPNVYYFGQEGLHNVLVIDLLGPSLEDLLDLCGRKFSVKTVAMAAKQMLARVQSIHEKSLVYRDIKPDNFLIGRPNSKNANMIYVVDFGMVKFYRDPVTKQHIPYREKKNLSGTARYMSINTHLGREQSRRDDLEALGHVFMYFLRGSLPWQGLKAATNKQKYERIGEKKQSTPLRELCAGFPEEFYKYMHYARNLAFDATPDYDYLQGLFSKVLERLNTTEDENFDWNLL 298
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295   


Chain B from PDB  Type:PROTEIN  Length:293
 aligned with CKI1_SCHPO | P40233 from UniProtKB/Swiss-Prot  Length:446

    Alignment length:293
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295   
           CKI1_SCHPO     6 NVVGVHYKVGRRIGEGSFGVIFEGTNLLNNQQVAIKFEPRRSDAPQLRDEYRTYKLLAGCTGIPNVYYFGQEGLHNILVIDLLGPSLEDLLDLCGRKFSVKTVAMAAKQMLARVQSIHEKSLVYRDIKPDNFLIGRPNSKNANMIYVVDFGMVKFYRDPVTKQHIPYREKKNLSGTARYMSINTHLGREQSRRDDLEALGHVFMYFLRGSLPWQGLKAATNKQKYERIGEKKQSTPLRELCAGFPEEFYKYMHYARNLAFDATPDYDYLQGLFSKVLERLNTTEDENFDWNLL 298
               SCOP domains d1eh4b_ B: Casein kinase-1, CK1                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains 1eh4B01 B:6-87 Phosphorylase Kinase; domain 1                                     1eh4B02 B:88-298 Transferase(Phosphotransferase) domain 1                                                                                                                                                           CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee...eeeeeeeee....eeeeeee.....eeeeeee.......hhhhhhhhhhhhh.......eeeee.....eeeee.....hhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh..ee....hhh.eee..........eee......ee..........................hhhhhh...hhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhh.hhhhhh...hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------PROTEIN_KINASE_ATP      -------------------------------------------------------------------------------------PROTEIN_KINAS--------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1eh4 B   6 NVVGVHYKVGRRIGEGSFGVIFEGTNLLNNQQVAIKFEPRRSDAPQLRDEYRTYKLLAGCTGIPNVYYFGQEGLHNVLVIDLLGPSLEDLLDLCGRKFSVKTVAMAAKQMLARVQSIHEKSLVYRDIKPDNFLIGRPNSKNANMIYVVDFGMVKFYRDPVTKQHIPYREKKNLSGTARYMSINTHLGREQSRRDDLEALGHVFMYFLRGSLPWQGLKAATNKQKYERIGEKKQSTPLRELCAGFPEEFYKYMHYARNLAFDATPDYDYLQGLFSKVLERLNTTEDENFDWNLL 298
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295
   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 Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (2, 4)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1EH4)

(-) Gene Ontology  (20, 20)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (CKI1_SCHPO | P40233)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    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: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: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:0004713    protein tyrosine kinase activity    Catalysis of the reaction: ATP + a protein tyrosine = ADP + protein tyrosine phosphate.
    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:0018105    peptidyl-serine phosphorylation    The phosphorylation of peptidyl-serine to form peptidyl-O-phospho-L-serine.
    GO:0038083    peptidyl-tyrosine autophosphorylation    The phosphorylation by a protein of one or more of its own tyrosine amino acid residues, or a tyrosine residue on an identical protein.
    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:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
    GO:0090215    regulation of 1-phosphatidylinositol-4-phosphate 5-kinase activity    Any process that modulates the frequency, rate or extent of the catalysis of the reaction: ATP + 1-phosphatidyl-1D-myo-inositol 4-phosphate = ADP + 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate.
    GO:0008360    regulation of cell shape    Any process that modulates the surface configuration of a cell.
    GO:0030100    regulation of endocytosis    Any process that modulates the frequency, rate or extent of endocytosis.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
    GO:0005773    vacuole    A closed structure, found only in eukaryotic cells, that is completely surrounded by unit membrane and contains liquid material. Cells contain one or several vacuoles, that may have different functions from each other. Vacuoles have a diverse array of functions. They can act as a storage organelle for nutrients or waste products, as a degradative compartment, as a cost-effective way of increasing cell size, and as a homeostatic regulator controlling both turgor pressure and pH of the cytosol.

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  1eh4
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  CKI1_SCHPO | P40233
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 Related Entries

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

UniProtKB/Swiss-Prot
        CKI1_SCHPO | P40233: 1csn 2csn

(-) Related Entries Specified in the PDB File

1csn BINARY COMPLEX OF CASEIN KINASE-1 WITH MGATP
2csn BINARY COMPLEX OF CASEIN KINASE-1 WITH CKI7