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(-) Description

Title :  CRYSTAL STRUCTURE OF THE N-TERMINAL DOMAIN OF BUBR1
 
Authors :  S. D'Arcy, O. R. Davies, T. L. Blundell, V. M. Bolanos-Garcia
Date :  16 Oct 09  (Deposition) - 09 Mar 10  (Release) - 07 Jul 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Tumor Suppressor, Mitotic Checkpoint, Tpr, Kinase, Apoptosis, Serine/Threonine-Protein Kinase, Cell Division, Cell Cycle, Kinetochore, Transferase, Cytoskeleton (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. D'Arcy, O. R. Davies, T. L. Blundell, V. M. Bolanos-Garcia
Defining The Molecular Basis Of Bubr1 Kinetochore Interactions And Anaphase-Promoting Complex/Cyclosome (Apc/C)-Cdc20 Inhibition
J. Biol. Chem. V. 285 14764 2010
PubMed-ID: 20220147  |  Reference-DOI: 10.1074/JBC.M109.082016

(-) Compounds

Molecule 1 - MITOTIC CHECKPOINT SERINE/THREONINE-PROTEIN KINASE BUB1 BETA
    ChainsA
    EC Number2.7.11.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPHAT4
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    FragmentN-TERMINAL TPR DOMAIN, RESIDUES 57-220
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymMAD3/BUB1-RELATED PROTEIN KINASE, HBUBR1, MITOTIC CHECKPOINT KINASE MAD3L, PROTEIN SSK1, BUBR1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2EDO2Ligand/Ion1,2-ETHANEDIOL
3PR2Ligand/IonPRASEODYMIUM ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:134 , ASP A:137 , GLU A:214 , GLU A:215 , GLU A:218 , ACT A:1223BINDING SITE FOR RESIDUE PR A1221
2AC2SOFTWAREGLU A:134 , GLU A:187 , GLN A:190 , GLU A:215 , ACT A:1223 , HOH A:2046 , HOH A:2114BINDING SITE FOR RESIDUE PR A1222
3AC3SOFTWAREGLU A:134 , PRO A:135 , LEU A:136 , ASP A:137 , ARG A:165 , GLU A:215 , GLU A:218 , PR A:1221 , PR A:1222 , HOH A:2046 , HOH A:2114BINDING SITE FOR RESIDUE ACT A1223
4AC4SOFTWAREALA A:164 , ARG A:165 , GLU A:184 , PRO A:185 , LEU A:186 , GLU A:187 , HOH A:2115 , HOH A:2116BINDING SITE FOR RESIDUE EDO A1224
5AC5SOFTWAREGLU A:134 , ARG A:194 , GLU A:211 , GLU A:214 , GLU A:215 , HOH A:2117BINDING SITE FOR RESIDUE EDO A1225

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2WVI)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2WVI)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2WVI)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BUB1_NPS51489 BUB1 N-terminal domain profile.BUB1B_HUMAN62-226  1A:62-220

(-) Exons   (0, 0)

(no "Exon" information available for 2WVI)

(-) 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:160
 aligned with BUB1B_HUMAN | O60566 from UniProtKB/Swiss-Prot  Length:1050

    Alignment length:164
                                    66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216    
          BUB1B_HUMAN    57 QQKRAFEYEIRFYTGNDPLDVWDRYISWTEQNYPQGGKESNMSTLLERAVEALQGEKRYYSDPRFLNLWLKLGRLCNEPLDMYSYLHNQGIGVSLAQFYISWAEEYEARENFRKADAIFQEGIQQKAEPLERLQSQHRQFQARVSRQTLLALEKEEEEEVFESS 220
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains Mad3_BUB1_I-2wviA01 A:57-179                                                                                               ----------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhh.......hhhhhhhhhhhhhhhh..----.hhhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhh.hhhhhhhhhhhh.....hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----BUB1_N  PDB: A:62-220 UniProt: 62-226                                                                                                                           PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wvi A  57 QQKRAFEYEIRFYTGNDPLDVWDRYISWTEQNYPQ----SNMSTLLERAVEALQGEKRYYSDPRFLNLWLKLGRLCNEPLDMYSYLHNQGIGVSLAQFYISWAEEYEARENFRKADAIFQEGIQQKAEPLERLQSQHRQFQARVSRQTLLALEKEEEEEVFESS 220
                                    66        76        86    |   96       106       116       126       136       146       156       166       176       186       196       206       216    
                                                             91   96                                                                                                                            

   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 2WVI)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2WVI)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit

(-) Gene Ontology  (38, 38)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (BUB1B_HUMAN | O60566)
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: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:0031145    anaphase-promoting complex-dependent catabolic process    The chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent attachment of ubiquitin, with ubiquitin-protein ligation catalyzed by the anaphase-promoting complex, and mediated by the proteasome.
    GO:0006915    apoptotic process    A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
    GO:0007049    cell cycle    The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
    GO:0051301    cell division    The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.
    GO:0008283    cell proliferation    The multiplication or reproduction of cells, resulting in the expansion of a cell population.
    GO:0007091    metaphase/anaphase transition of mitotic cell cycle    The cell cycle process in which a cell progresses from metaphase to anaphase during mitosis, triggered by the activation of the anaphase promoting complex by Cdc20/Sleepy homolog which results in the degradation of Securin.
    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:0051436    negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle    Any process that stops, prevents, or reduces the frequency, rate or extent of ubiquitin ligase activity that contributes to the mitotic cell cycle.
    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:0051437    positive regulation of ubiquitin-protein ligase activity involved in regulation of mitotic cell cycle transition    Any process that activates, maintains or increases the rate of ubiquitin ligase activity that contributes to the regulation of the mitotic cell cycle phase transition.
    GO:0043161    proteasome-mediated ubiquitin-dependent protein catabolic process    The chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent attachment of ubiquitin, and mediated by the proteasome.
    GO:0071459    protein localization to chromosome, centromeric region    Any process in which a protein is transported to, or maintained at, the centromeric region of a chromosome.
    GO:0034501    protein localization to kinetochore    Any process in which a protein is transported to, or maintained at, the kinetochore.
    GO:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
    GO:0042787    protein ubiquitination involved in ubiquitin-dependent protein catabolic process    The process in which a ubiquitin group, or multiple groups, are covalently attached to the target protein, thereby initiating the degradation of that protein.
    GO:0007062    sister chromatid cohesion    The cell cycle process in which the sister chromatids of a replicated chromosome become tethered to each other.
cellular component
    GO:0005680    anaphase-promoting complex    A ubiquitin ligase complex that degrades mitotic cyclins and anaphase inhibitory protein, thereby triggering sister chromatid separation and exit from mitosis. Substrate recognition by APC occurs through degradation signals, the most common of which is termed the Dbox degradation motif, originally discovered in cyclin B.
    GO:0005694    chromosome    A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
    GO:0000775    chromosome, centromeric region    The region of a chromosome that includes the centromeric DNA and associated proteins. In monocentric chromosomes, this region corresponds to a single area of the chromosome, whereas in holocentric chromosomes, it is evenly distributed along the chromosome.
    GO:0000777    condensed chromosome kinetochore    A multisubunit complex that is located at the centromeric region of a condensed chromosome and provides an attachment point for the spindle microtubules.
    GO:0000940    condensed chromosome outer kinetochore    The region of a condensed chromosome kinetochore most external to centromeric DNA; this outer region mediates kinetochore-microtubule interactions.
    GO:0000778    condensed nuclear chromosome kinetochore    A multisubunit complex that is located at the centromeric region of a condensed nuclear chromosome and provides an attachment point for the spindle microtubules.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005856    cytoskeleton    Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0000776    kinetochore    A multisubunit complex that is located at the centromeric region of DNA and provides an attachment point for the spindle microtubules.
    GO:0005815    microtubule organizing center    An intracellular structure that can catalyze gamma-tubulin-dependent microtubule nucleation and that can anchor microtubules by interacting with their minus ends, plus ends or sides.
    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:0048471    perinuclear region of cytoplasm    Cytoplasm situated near, or occurring around, the nucleus.
    GO:0051233    spindle midzone    The area in the center of the spindle where the spindle microtubules from opposite poles overlap.

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 Related Entries

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

UniProtKB/Swiss-Prot
        BUB1B_HUMAN | O605663si5 4ggd 5jja 5k6s 5khu 5lcw 5swf

(-) Related Entries Specified in the PDB File

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