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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN MPS1 TPR DOMAIN
 
Authors :  D. Littler, E. Von Castelmur, V. De Marco, A. Perrakis
Date :  31 Aug 12  (Deposition) - 24 Apr 13  (Release) - 01 May 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Transferase, Kinetochore, Mitosis (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  W. Nijenhuis, E. Von Castelmur, D. Littler, V. De Marco, E. Tromer, M. Vleugel, M. H. Van Osch, B. Snel, A. Perrakis, G. J. Kops
A Tpr Domain-Containing N-Terminal Module Of Mps1 Is Required For Its Kinetochore Localization By Aurora B.
J. Cell Biol. V. 201 217 2013
PubMed-ID: 23569217  |  Reference-DOI: 10.1083/JCB.201210033

(-) Compounds

Molecule 1 - DUAL SPECIFICITY PROTEIN KINASE TTK
    ChainsA, B, C, D
    EC Number2.7.12.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPETNKI-HIS-3C-LIC-KAN
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VariantT1R
    Expression System Vector TypePLASMID
    FragmentTPR DOMAIN, RESIDUES 62-239
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymMPS1, PHOSPHOTYROSINE PICKED THREONINE-PROTEIN KINASE, PYT

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)A   
Biological Unit 2 (1x) B  
Biological Unit 3 (1x)  C 
Biological Unit 4 (1x)   D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 17)

Asymmetric Unit (5, 17)
No.NameCountTypeFull Name
1GOL10Ligand/IonGLYCEROL
2MLI2Ligand/IonMALONATE ION
3PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
4PG42Ligand/IonTETRAETHYLENE GLYCOL
5PGE2Ligand/IonTRIETHYLENE GLYCOL
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2MLI-1Ligand/IonMALONATE ION
3PEG-1Ligand/IonDI(HYDROXYETHYL)ETHER
4PG41Ligand/IonTETRAETHYLENE GLYCOL
5PGE-1Ligand/IonTRIETHYLENE GLYCOL
Biological Unit 2 (3, 7)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
2MLI2Ligand/IonMALONATE ION
3PEG-1Ligand/IonDI(HYDROXYETHYL)ETHER
4PG4-1Ligand/IonTETRAETHYLENE GLYCOL
5PGE1Ligand/IonTRIETHYLENE GLYCOL
Biological Unit 3 (3, 3)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2MLI-1Ligand/IonMALONATE ION
3PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
4PG4-1Ligand/IonTETRAETHYLENE GLYCOL
5PGE1Ligand/IonTRIETHYLENE GLYCOL
Biological Unit 4 (2, 4)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
2MLI-1Ligand/IonMALONATE ION
3PEG-1Ligand/IonDI(HYDROXYETHYL)ETHER
4PG41Ligand/IonTETRAETHYLENE GLYCOL
5PGE-1Ligand/IonTRIETHYLENE GLYCOL

(-) Sites  (17, 17)

Asymmetric Unit (17, 17)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPRO A:-1 , ASP A:64 , TRP A:65 , LEU A:68 , GLU C:96BINDING SITE FOR RESIDUE PG4 A1200
02AC2SOFTWARELYS A:140 , LYS A:141 , ARG A:172 , HOH A:2064BINDING SITE FOR RESIDUE GOL A1201
03AC3SOFTWAREGLU A:124 , ASP A:127 , TYR A:131 , HOH A:2048 , ARG C:136 , HIS C:146BINDING SITE FOR RESIDUE GOL A1202
04AC4SOFTWAREGLU B:96 , ALA B:97 , PRO B:99 , HOH B:2017 , HOH B:2058 , GLN D:93BINDING SITE FOR RESIDUE GOL B1196
05AC5SOFTWAREPRO B:-1 , ASP B:64 , ARG B:90BINDING SITE FOR RESIDUE PGE B1197
06AC6SOFTWAREASP B:101 , ALA B:137 , ASN B:138 , HOH B:2018 , HOH B:2048 , HOH B:2059 , ASN D:85 , LYS D:120 , GLN D:123BINDING SITE FOR RESIDUE GOL B1198
07AC7SOFTWAREARG B:136 , ALA B:137 , LYS B:140 , HIS B:146 , LYS B:168 , ARG B:172 , HOH B:2047 , GLU D:124 , ASP D:127 , TYR D:131BINDING SITE FOR RESIDUE MLI B1199
08AC8SOFTWARELYS B:140 , LYS B:141 , ARG B:172 , ALA B:174BINDING SITE FOR RESIDUE GOL B1200
09AC9SOFTWAREGLY B:0 , GLU B:63 , TYR B:103 , ASN B:106 , HOH B:2004 , LYS D:141BINDING SITE FOR RESIDUE GOL B1201
10BC1SOFTWARELYS B:102 , TYR B:103 , GLY B:104 , GLN B:105 , ASN B:106 , HOH B:2060 , LYS D:141 , HOH D:2022BINDING SITE FOR RESIDUE MLI B1202
11BC2SOFTWAREPRO C:-1 , ASP C:64 , LEU C:68 , ARG C:90BINDING SITE FOR RESIDUE PGE C1196
12BC3SOFTWARETYR A:103 , GLN A:105 , ASN A:106 , GLN C:105 , LYS C:141 , GOL C:1198 , HOH C:2044 , HOH C:2045BINDING SITE FOR RESIDUE PEG C1197
13BC4SOFTWAREGLY A:0 , PRO A:62 , GLU A:63 , TYR A:103 , ASN A:106 , LYS C:141 , PEG C:1197 , HOH C:2046BINDING SITE FOR RESIDUE GOL C1198
14BC5SOFTWAREGLU B:96 , PRO D:-1 , ASP D:64 , TRP D:65 , LEU D:68 , HOH D:2048BINDING SITE FOR RESIDUE PG4 D1200
15BC6SOFTWARELYS D:140 , HIS D:146 , ARG D:172 , HOH D:2044BINDING SITE FOR RESIDUE GOL D1201
16BC7SOFTWAREGLN B:105 , LYS B:141 , LYS D:102 , TYR D:103 , ASN D:106 , HOH D:2018 , HOH D:2023BINDING SITE FOR RESIDUE GOL D1202
17BC8SOFTWAREGLN D:133 , ARG D:136 , ALA D:137 , LYS D:140 , ARG D:172 , HOH D:2049BINDING SITE FOR RESIDUE GOL D1203

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4B94)

(-) Cis Peptide Bonds  (10, 10)

Asymmetric Unit
No.Residues
1Val A:77 -Pro A:78
2Val A:175 -Pro A:176
3Gly B:-2 -Pro B:-1
4Val B:77 -Pro B:78
5Val B:175 -Pro B:176
6Gly C:-2 -Pro C:-1
7Val C:77 -Pro C:78
8Val C:175 -Pro C:176
9Val D:77 -Pro D:78
10Val D:175 -Pro D:176

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 4)

Asymmetric Unit (1, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_037141A97VTTK_HUMANPolymorphism2230513A/B/C/DA97V

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_037141A97VTTK_HUMANPolymorphism2230513AA97V

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_037141A97VTTK_HUMANPolymorphism2230513BA97V

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 3 (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_037141A97VTTK_HUMANPolymorphism2230513CA97V

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 4 (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_037141A97VTTK_HUMANPolymorphism2230513DA97V

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4B94)

(-) Exons   (0, 0)

(no "Exon" information available for 4B94)

(-) 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:141
 aligned with TTK_HUMAN | P33981 from UniProtKB/Swiss-Prot  Length:857

    Alignment length:141
                                    68        78        88        98       108       118       128       138       148       158       168       178       188       198 
            TTK_HUMAN    59 ANNPEDWLSLLLKLEKNSVPLSDALLNKLIGRYSQAIEALPPDKYGQNESFARIQVRFAELKAIQEPDDARDYFQMARANCKKFAFVHISFAQFELSQGNVKKSKQLLQKAVERGAVPLEMLEIALRNLNLQKKQLLSEEE 199
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhh......hhhhhhhhhhhhhhhhh..hhhh...hhhhhhhhhhhhhhhhh.....hhhhhhhhhh....hhhhhhhhhhhhh...hhhhhhhhhhhhhh....hhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) --------------------------------------V------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4b94 A  -2 GPGPEDWLSLLLKLEKNSVPLSDALLNKLIGRYSQAIEALPPDKYGQNESFARIQVRFAELKAIQEPDDARDYFQMARANCKKFAFVHISFAQFELSQGNVKKSKQLLQKAVERGAVPLEMLEIALRNLNLQKKQLLSEEE 199
                              ||    68        78        88        98       108       118       128       138       148       158       168       178       188       198 
                              0|                                                                                                                                         
                              62                                                                                                                                         

Chain B from PDB  Type:PROTEIN  Length:137
 aligned with TTK_HUMAN | P33981 from UniProtKB/Swiss-Prot  Length:857

    Alignment length:137
                                    68        78        88        98       108       118       128       138       148       158       168       178       188       
            TTK_HUMAN    59 ANNPEDWLSLLLKLEKNSVPLSDALLNKLIGRYSQAIEALPPDKYGQNESFARIQVRFAELKAIQEPDDARDYFQMARANCKKFAFVHISFAQFELSQGNVKKSKQLLQKAVERGAVPLEMLEIALRNLNLQKKQLL 195
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhh......hhhhhhhhhhhhhhhhh..hhhh...hhhhhhhhhhhhhhhhh.....hhhhhhhhhhh...hhhhhhhhhhhhh...hhhhhhhhhhhhhh....hhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------V-------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4b94 B  -2 GPGPEDWLSLLLKLEKNSVPLSDALLNKLIGRYSQAIEALPPDKYGQNESFARIQVRFAELKAIQEPDDARDYFQMARANCKKFAFVHISFAQFELSQGNVKKSKQLLQKAVERGAVPLEMLEIALRNLNLQKKQLL 195
                              ||    68        78        88        98       108       118       128       138       148       158       168       178       188       
                              0|                                                                                                                                     
                              62                                                                                                                                     

Chain C from PDB  Type:PROTEIN  Length:137
 aligned with TTK_HUMAN | P33981 from UniProtKB/Swiss-Prot  Length:857

    Alignment length:137
                                    68        78        88        98       108       118       128       138       148       158       168       178       188       
            TTK_HUMAN    59 ANNPEDWLSLLLKLEKNSVPLSDALLNKLIGRYSQAIEALPPDKYGQNESFARIQVRFAELKAIQEPDDARDYFQMARANCKKFAFVHISFAQFELSQGNVKKSKQLLQKAVERGAVPLEMLEIALRNLNLQKKQLL 195
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhh......hhhhhhhhhhhhhhhhh..hhhh...hhhhhhhhhhhhhhhhh.....hhhhhhhhhhh...hhhhhhhhhhhhh...hhhhhhhhhhhhhh....hhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------V-------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4b94 C  -2 GPGPEDWLSLLLKLEKNSVPLSDALLNKLIGRYSQAIEALPPDKYGQNESFARIQVRFAELKAIQEPDDARDYFQMARANCKKFAFVHISFAQFELSQGNVKKSKQLLQKAVERGAVPLEMLEIALRNLNLQKKQLL 195
                              ||    68        78        88        98       108       118       128       138       148       158       168       178       188       
                              0|                                                                                                                                     
                              62                                                                                                                                     

Chain D from PDB  Type:PROTEIN  Length:141
 aligned with TTK_HUMAN | P33981 from UniProtKB/Swiss-Prot  Length:857

    Alignment length:141
                                    68        78        88        98       108       118       128       138       148       158       168       178       188       198 
            TTK_HUMAN    59 ANNPEDWLSLLLKLEKNSVPLSDALLNKLIGRYSQAIEALPPDKYGQNESFARIQVRFAELKAIQEPDDARDYFQMARANCKKFAFVHISFAQFELSQGNVKKSKQLLQKAVERGAVPLEMLEIALRNLNLQKKQLLSEEE 199
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhh......hhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhh.....hhhhhhhhhh....hhhhhhhhhhhhh...hhhhhhhhhhhhhh....hhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) --------------------------------------V------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4b94 D  -2 GPGPEDWLSLLLKLEKNSVPLSDALLNKLIGRYSQAIEALPPDKYGQNESFARIQVRFAELKAIQEPDDARDYFQMARANCKKFAFVHISFAQFELSQGNVKKSKQLLQKAVERGAVPLEMLEIALRNLNLQKKQLLSEEE 199
                              ||    68        78        88        98       108       118       128       138       148       158       168       178       188       198 
                              0|                                                                                                                                         
                              62                                                                                                                                         

   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  (0, 0)

(no "SCOP Domain" information available for 4B94)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4B94)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4B94)

(-) Gene Ontology  (21, 21)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (TTK_HUMAN | P33981)
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: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: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: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:0004712    protein serine/threonine/tyrosine kinase activity    Catalysis of the reactions: ATP + a protein serine = ADP + protein serine phosphate; ATP + a protein threonine = ADP + protein threonine phosphate; and ATP + a protein tyrosine = ADP + protein tyrosine 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:0051304    chromosome separation    The cell cycle process in which paired chromosomes are detached from each other. Chromosome separation begins with the release of cohesin complexes from chromosomes; in budding yeast, this includes the cleavage of cohesin complexes along the chromosome arms, followed by the separation of the centromeric regions. Chromosome separation also includes formation of chromatid axes mediated by condensins, and ends with the disentangling of inter-sister catenation catalyzed by topoisomerase II (topo II).
    GO:0007093    mitotic cell cycle checkpoint    A cell cycle checkpoint that ensures accurate chromosome replication and segregation by preventing progression through a mitotic cell cycle until conditions are suitable for the cell to proceed to the next stage.
    GO:0007094    mitotic spindle assembly checkpoint    A cell cycle checkpoint that delays the metaphase/anaphase transition of a mitotic nuclear division until the spindle is correctly assembled and chromosomes are attached to the spindle.
    GO:0007052    mitotic spindle organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the microtubule spindle during a mitotic cell cycle.
    GO:0018108    peptidyl-tyrosine phosphorylation    The phosphorylation of peptidyl-tyrosine to form peptidyl-O4'-phospho-L-tyrosine.
    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:0008284    positive regulation of cell proliferation    Any process that activates or increases the rate or extent of cell proliferation.
    GO:0010862    positive regulation of pathway-restricted SMAD protein phosphorylation    Any process that increases the rate, frequency or extent of pathway-restricted SMAD protein phosphorylation. Pathway-restricted SMAD proteins and common-partner SMAD proteins are involved in the transforming growth factor beta receptor signaling pathways.
    GO:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
    GO:0007051    spindle organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the spindle, the array of microtubules and associated molecules that forms between opposite poles of a eukaryotic cell during DNA segregation and serves to move the duplicated chromosomes apart.
cellular component
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005819    spindle    The array of microtubules and associated molecules that forms between opposite poles of a eukaryotic cell during mitosis or meiosis and serves to move the duplicated chromosomes apart.

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  TTK_HUMAN | P33981
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 Related Entries

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

UniProtKB/Swiss-Prot
        TTK_HUMAN | P339812x9e 2zmc 2zmd 3cek 3dbq 3gfw 3h9f 3hmn 3hmo 3hmp 3vqu 3w1f 3wyx 3wyy 3wzj 3wzk 4bhz 4bi0 4bi1 4bi2 4c4e 4c4f 4c4g 4c4h 4c4i 4c4j 4cv8 4cv9 4cva 4d2s 4h7x 4h7y 4js8 4jt3 4o6l 4zeg 5ap0 5ap1 5ap2 5ap3 5ap4 5ap5 5ap6 5ap7 5eh0 5ehl 5eho 5ehy 5ei2 5ei6 5ei8 5ljj 5n7v 5n84 5n87 5n93 5n9s 5na0 5nad

(-) Related Entries Specified in the PDB File

2x9e HUMAN MPS1 IN COMPLEX WITH NMS-P715