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(-) Description

Title :  CRYSTAL STRUCTURE OF THE CDC25B PHOSPHATASE CATALYTIC DOMAIN IN THE APO FORM
 
Authors :  G. K. Buhrman, B. Parker, J. Sohn, J. Rudolph, C. Mattos
Date :  21 Jan 05  (Deposition) - 12 Apr 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A
Keywords :  Apo Enzyme, Hydrolase, Cell Cycle (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  G. K. Buhrman, B. Parker, J. Sohn, J. Rudolph, C. Mattos
Structural Mechanism Of Oxidative Regulation Of The Phosphatase Cdc25B Via An Intramolecular Disulfide Bond
Biochemistry V. 44 5307 2005
PubMed-ID: 15807524  |  Reference-DOI: 10.1021/BI047449FS0006-2960(04)07449-5
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - M-PHASE INDUCER PHOSPHATASE 2
    ChainsA
    EC Number3.1.3.48
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentCATALYTIC DOMAIN
    GeneCDC25B, CDC25HU2
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymCDC25B PHOSPHATASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:446 , ARG A:548BINDING SITE FOR RESIDUE CL A 1001

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Tyr A:497 -Pro A:498
2Glu A:524 -Pro A:525

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric/Biological Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_020933E548KMPIP2_HUMANPolymorphism11570019AE534K

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RHODANESE_3PS50206 Rhodanese domain profile.MPIP2_HUMAN431-538  1A:417-524

(-) Exons   (6, 6)

Asymmetric/Biological Unit (6, 6)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000002459601bENSE00001353605chr20:3776482-3777378897MPIP2_HUMAN1-67670--
1.2aENST000002459602aENSE00000858842chr20:3778269-3778396128MPIP2_HUMAN67-110440--
1.3ENST000002459603ENSE00000858844chr20:3779059-377911052MPIP2_HUMAN110-127180--
1.4ENST000002459604ENSE00000858846chr20:3780935-378097642MPIP2_HUMAN127-141150--
1.5ENST000002459605ENSE00000858850chr20:3781109-378114537MPIP2_HUMAN141-153130--
1.6aENST000002459606aENSE00000657911chr20:3781390-3781512123MPIP2_HUMAN154-194410--
1.6cENST000002459606cENSE00000858854chr20:3781618-3781740123MPIP2_HUMAN195-235410--
1.7ENST000002459607ENSE00000657912chr20:3781901-3782035135MPIP2_HUMAN236-280450--
1.8bENST000002459608bENSE00000858860chr20:3782369-378244981MPIP2_HUMAN281-307270--
1.9ENST000002459609ENSE00001482099chr20:3782571-3782747177MPIP2_HUMAN308-366590--
1.10ENST0000024596010ENSE00001190140chr20:3782928-378302396MPIP2_HUMAN367-398321A:376-3849
1.11cENST0000024596011cENSE00001658249chr20:3783557-378361963MPIP2_HUMAN399-419211A:385-40521
1.12bENST0000024596012bENSE00001645639chr20:3783755-378385399MPIP2_HUMAN420-452331A:406-43833
1.13cENST0000024596013cENSE00001714978chr20:3784051-3784184134MPIP2_HUMAN453-497451A:439-483 (gaps)45
1.14ENST0000024596014ENSE00001664388chr20:3785216-3785327112MPIP2_HUMAN497-534381A:483-52038
1.15dENST0000024596015dENSE00001869849chr20:3785468-37867621295MPIP2_HUMAN535-580461A:521-55030

(-) 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:171
 aligned with MPIP2_HUMAN | P30305 from UniProtKB/Swiss-Prot  Length:580

    Alignment length:175
                                   399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559     
          MPIP2_HUMAN   390 RELIGDYSKAFLLQTVDGKHQDLKYISPETMVALLTGKFSNIVDKFVIVDCRYPYEYEGGHIKTAVNLPLERDAESFLLKSPIAPCSLDKRVILIFHCEFSSERGPRMCRFIRERDRAVNDYPSLYYPEMYILKGGYKEFFPQHPNFCEPQDYRPMNHEAFKDELKTFRLKTRSW 564
               SCOP domains d1ymka_ A: CDC25b                                                                                                                                                               SCOP domains
               CATH domains 1ymkA00 A:376-550 Oxidized Rhodanese, domain 1                                                                                                                                  CATH domains
               Pfam domains -----------------------------------Rhodanese-1ymkA01 A:411-518                                                                                 -------------------------------- Pfam domains
         Sec.struct. author ........................eehhhhhhhhhh......eeeeeeee..hhhhhhh.ee...ee..hhhhhhhhhhh.....----.eeeeeee.....hhhhhhhhhhhhhhhhh..........eeee.hhhhhhh..hhh.ee........hhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------K---------------- SAPs(SNPs)
                    PROSITE -----------------------------------------RHODANESE_3  PDB: A:417-524 UniProt: 431-538                                                                -------------------------- PROSITE
           Transcript 1 (1) Exon 1.10Exon 1.11c           Exon 1.12b  PDB: A:406-438       Exon 1.13c  PDB: A:439-483 (gaps)            -------------------------------------Exon 1.15d  PDB: A:521-550     Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------------------------------------------------------Exon 1.14  PDB: A:483-520             ------------------------------ Transcript 1 (2)
                 1ymk A 376 MELIGDYSKAFLLQTVDGKHQDLKYISPETMVALLTGKFSNIVDKFVIVDCRYPYEYEGGHIKTAVNLPLERDAESFLLKSPIAP----KRVILIFHCEFSSERGPRMCRFIRERDRAVNDYPSLYYPEMYILKGGYKEFFPQHPNFCEPQDYRPMNHEAFKDELKTFRLKTRSW 550
                                   385       395       405       415       425       435       445       455    |  465       475       485       495       505       515       525       535       545     
                                                                                                              460  465                                                                                     

   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   (MPIP2_HUMAN | P30305)
molecular function
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0004721    phosphoprotein phosphatase activity    Catalysis of the reaction: a phosphoprotein + H2O = a protein + phosphate. Together with protein kinases, these enzymes control the state of phosphorylation of cell proteins and thereby provide an important mechanism for regulating cellular activity.
    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: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:0004725    protein tyrosine phosphatase activity    Catalysis of the reaction: protein tyrosine phosphate + H2O = protein tyrosine + phosphate.
biological process
    GO:0000086    G2/M transition of mitotic cell cycle    The mitotic cell cycle transition by which a cell in G2 commits to M phase. The process begins when the kinase activity of M cyclin/CDK complex reaches a threshold high enough for the cell cycle to proceed. This is accomplished by activating a positive feedback loop that results in the accumulation of unphosphorylated and active M cyclin/CDK complex.
    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:0007144    female meiosis I    The cell cycle process in which the first meiotic division occurs in the female germline.
    GO:0000278    mitotic cell cycle    Progression through the phases of the mitotic cell cycle, the most common eukaryotic cell cycle, which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells. In some variant cell cycles nuclear replication or nuclear division may not be followed by cell division, or G1 and G2 phases may be absent.
    GO:0001556    oocyte maturation    A developmental process, independent of morphogenetic (shape) change, that is required for an oocyte to attain its fully functional state. Oocyte maturation commences after reinitiation of meiosis commonly starting with germinal vesicle breakdown, and continues up to the second meiotic arrest prior to fertilization.
    GO:0035335    peptidyl-tyrosine dephosphorylation    The removal of phosphoric residues from peptidyl-O-phospho-tyrosine to form peptidyl-tyrosine.
    GO:0008284    positive regulation of cell proliferation    Any process that activates or increases the rate or extent of cell proliferation.
    GO:0032467    positive regulation of cytokinesis    Any process that activates or increases the frequency, rate or extent of the division of the cytoplasm of a cell, and its separation into two daughter cells.
    GO:0045931    positive regulation of mitotic cell cycle    Any process that activates or increases the rate or extent of progression through the mitotic cell cycle.
    GO:0045860    positive regulation of protein kinase activity    Any process that activates or increases the frequency, rate or extent of protein kinase activity.
    GO:0006470    protein dephosphorylation    The process of removing one or more phosphoric residues from a protein.
    GO:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
cellular component
    GO:0005813    centrosome    A structure comprised of a core structure (in most organisms, a pair of centrioles) and peripheral material from which a microtubule-based structure, such as a spindle apparatus, is organized. Centrosomes occur close to the nucleus during interphase in many eukaryotic cells, though in animal cells it changes continually during the cell-division cycle.
    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:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
    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:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    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:0000922    spindle pole    Either of the ends of a spindle, where spindle microtubules are organized; usually contains a microtubule organizing center and accessory molecules, spindle microtubules and astral microtubules.

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 Related Entries

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

UniProtKB/Swiss-Prot
        MPIP2_HUMAN | P303051cwr 1cws 1cwt 1qb0 1ym9 1ymd 1yml 1ys0 2a2k 2ifd 2ifv 2uzq 3fqt 3fqu 4wh7 4wh9

(-) Related Entries Specified in the PDB File

1ym9 CRYSTAL STRUCTURE OF THE CDC25B PHOSPHATASE CATALYTIC DOMAIN WITH THE ACTIVE SITE CYSTEINE IN THE SULFINIC FORM
1ymd CRYSTAL STRUCTURE OF THE CDC25B PHOSPHATASE CATALYTIC DOMAIN WITH THE ACTIVE SITE CYSTEINE IN THE SULFONIC FORM
1yml CRYSTAL STRUCTURE OF THE CDC25B PHOSPHATASE CATALYTIC DOMAIN WITH THE ACTIVE SITE CYSTEINE IN THE SULFENIC FORM
1ys0 CRYSTAL STRUCTURE OF THE CDC25B PHOSPHATASE CATALYTIC DOMAIN WITH THE ACTIVE SITE CYSTEINE IN THE DISULFIDE FORM