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(-) Description

Title :  THE CRYSTAL STRUCTURE OF THE MINIMAL FUNCTIONAL DOMAIN OF THE MICROTUBULE DESTABILIZER KIF2C COMPLEXED WITH MG-ADP
 
Authors :  T. Ogawa, R. Nitta, Y. Okada, N. Hirokawa
Date :  09 Jan 04  (Deposition) - 02 Mar 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.24
Chains :  Asym./Biol. Unit :  A
Keywords :  Kinesin-Like Protein, Microtubule Destabilizer, Structural Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. Ogawa, R. Nitta, Y. Okada, N. Hirokawa
A Common Mechanism For Microtubule Destabilizers-M Type Kinesins Stabilize Curling Of The Protofilament Using The Class-Specific Neck And Loops.
Cell(Cambridge, Mass. ) V. 116 591 2004
PubMed-ID: 14980225  |  Reference-DOI: 10.1016/S0092-8674(04)00129-1
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - KINESIN-LIKE PROTEIN KIF2C
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET21B
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentRESIDUES 1-403
    GeneKIF2C
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    SynonymMITOTIC CENTROMERE-ASSOCIATED KINESIN, MCAK

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2MG1Ligand/IonMAGNESIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:169 , ADP A:500BINDING SITE FOR RESIDUE MG A 501
2AC2SOFTWAREARG A:78 , THR A:164 , GLY A:165 , SER A:166 , GLY A:167 , LYS A:168 , THR A:169 , HIS A:170 , MG A:501 , HOH A:621BINDING SITE FOR RESIDUE ADP A 500

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:59 -A:101

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1V8J)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1V8J)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1KINESIN_MOTOR_2PS50067 Kinesin motor domain profile.KIF2C_MOUSE254-584  1A:72-402
2KINESIN_MOTOR_1PS00411 Kinesin motor domain signature.KIF2C_MOUSE482-493  1A:300-311

(-) Exons   (0, 0)

(no "Exon" information available for 1V8J)

(-) 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:337
 aligned with KIF2C_MOUSE | Q922S8 from UniProtKB/Swiss-Prot  Length:721

    Alignment length:364
                                   233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583    
          KIF2C_MOUSE   224 PNWEFARMIKEFRVTMECSPLTVTDPIEEHRICVCVRKRPLNKQELAKKEIDVISVPSKCLLLVHEPKLKVDLTKYLENQAFCFDFAFDETASNEVVYRFTARPLVQTIFEGGKATCFAYGQTGSGKTHTMGGDLSGKSQNASKGIYAMASRDVFLLKNQPRYRNLNLEVYVTFFEIYNGKVFDLLNKKAKLRVLEDSRQQVQVVGLQEYLVTCADDVIKMINMGSACRTSGQTFANSNSSRSHACFQILLRTKGRLHGKFSLVDLAGNERGADTSSADRQTRMEGAEINKSLLALKECIRALGQNKAHTPFRESKLTQVLRDSFIGENSRTCMIAMISPGISSCEYTLNTLRYADRVKELSPH 587
               SCOP domains d1v8ja_ A: Kinesin                                                                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains 1v8jA00 A:42-404 Kines   in                                                                                                                                                                                                                                                                                                                                                  CATH domains
               Pfam domains ----------------------   -----------Kinesin-1v8jA01 A:78-402                                                                                                                                                                                                                                                                                                             - - Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh....---......eeeeeee...hhhhhhh.....ee.....eeeeeeeee.....eeeeeeeee..eee....hhhhhhhh.hhhhhhhhhh..eeeeeee.....hhhhhhh..-----.....hhhhhhhhhhhhhhhhhhhhh...eeeeeeeee....eee......eeeeee.....eeee....eee.hhhhhhhhhhhhhhh....----..hhhhheeeeeeeee....eeeeeeeee......--------..hhhhhhhhhhhhhhhhhhhhhhh.------...hhhhhhhhhhhhh..eeeeeeeee..hhhhhhhhhhhhhhhhhhhh..-. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------------------------------KINESIN_MOTOR_2  PDB: A:72-402 UniProt: 254-584                                                                                                                                                                                                                                                                                            --- PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------KINESIN_MOTO---------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1v8j A  42 PNWEFARMIKEFRVTMECSPLT---PIEEHRICVCVRKRPLNKQELAKKEIDVISVPSKCLLLVHEPKLKVDLTKYLENQAFCFDFAFDETASNEVVYRFTARPLVQTIFEGGKATCFAYGQTGSGKTHTMGGD-----QNASKGIYAMASRDVFLLKNQPRYRNLNLEVYVTFFEIYNGKVFDLLNKKAKLRVLEDSRQQVQVVGLQEYLVTCADDVIKMINMGSACRTSG----NSNSSRSHACFQILLRTKGRLHGKFSLVDLAGNER--------RQTRMEGAEINKSLLALKECIRALGQ------FRESKLTQVLRDSFIGENSRTCMIAMISPGISSCEYTLNTLRYADRVKELS-H 404
                                    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       301       311|      321       331       341    |    - |     361       371       381       391       401 | |
                                                63  67                                                                                                         175   181                                                                                         273  278                               312      321                      346    353                                               403 |
                                                                                                                                                                                                                                                                                                                                                                                                     404

   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, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit

(-) Gene Ontology  (27, 27)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (KIF2C_MOUSE | Q922S8)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0016887    ATPase activity    Catalysis of the reaction: ATP + H2O = ADP + phosphate + 2 H+. May or may not be coupled to another reaction.
    GO:0008017    microtubule binding    Interacting selectively and non-covalently with microtubules, filaments composed of tubulin monomers.
    GO:0003777    microtubule motor activity    Catalysis of movement along a microtubule, coupled to the hydrolysis of a nucleoside triphosphate (usually ATP).
    GO:0051010    microtubule plus-end binding    Interacting selectively and non-covalently with the plus end of a microtubule.
    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.
biological process
    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:0007059    chromosome segregation    The process in which genetic material, in the form of chromosomes, is organized into specific structures and then physically separated and apportioned to two or more sets. In eukaryotes, chromosome segregation begins with the condensation of chromosomes, includes chromosome separation, and ends when chromosomes have completed movement to the spindle poles.
    GO:0030951    establishment or maintenance of microtubule cytoskeleton polarity    Any cellular process that results in the specification, formation or maintenance of polarized microtubule-based cytoskeletal structures.
    GO:0007019    microtubule depolymerization    The removal of tubulin heterodimers from one or both ends of a microtubule.
    GO:0007018    microtubule-based movement    A microtubule-based process that results in the movement of organelles, other microtubules, or other cellular components. Examples include motor-driven movement along microtubules and movement driven by polymerization or depolymerization of microtubules.
    GO:0007080    mitotic metaphase plate congression    The cell cycle process in which chromosomes are aligned at the metaphase plate, a plane halfway between the poles of the mitotic spindle, during mitosis.
    GO:0051983    regulation of chromosome segregation    Any process that modulates the frequency, rate or extent of chromosome segregation, the process in which genetic material, in the form of chromosomes, is organized and then physically separated and apportioned to two or more sets.
cellular component
    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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005881    cytoplasmic microtubule    Any microtubule in the cytoplasm of a cell.
    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:0005871    kinesin complex    Any complex that includes a dimer of molecules from the kinesin superfamily, a group of related proteins that contain an extended region of predicted alpha-helical coiled coil in the main chain that likely produces dimerization. The native complexes of several kinesin family members have also been shown to contain additional peptides, often designated light chains as all of the noncatalytic subunits that are currently known are smaller than the chain that contains the motor unit. Kinesin complexes generally possess a force-generating enzymatic activity, or motor, which converts the free energy of the gamma phosphate bond of ATP into mechanical work.
    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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005874    microtubule    Any of the long, generally straight, hollow tubes of internal diameter 12-15 nm and external diameter 24 nm found in a wide variety of eukaryotic cells; each consists (usually) of 13 protofilaments of polymeric tubulin, staggered in such a manner that the tubulin monomers are arranged in a helical pattern on the microtubular surface, and with the alpha/beta axes of the tubulin subunits parallel to the long axis of the tubule; exist in equilibrium with pool of tubulin monomers and can be rapidly assembled or disassembled in response to physiological stimuli; concerned with force generation, e.g. in the spindle.
    GO:0015630    microtubule cytoskeleton    The part of the cytoskeleton (the internal framework of a cell) composed of microtubules and associated proteins.
    GO:0035371    microtubule plus-end    The growing (plus) end of a microtubule. In vitro, microtubules polymerize more quickly at the plus end than at the minus end. In vivo, microtubule growth occurs only at the plus end, and the plus end switches between periods of growth and shortening, a behavior known as dynamic instability.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        KIF2C_MOUSE | Q922S81v8k

(-) Related Entries Specified in the PDB File

1v8k COMPLEXED WITH MG-AMPPNP