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(-) Description

Title :  CRYSTAL STRUCTURE OF THE ARF-GAP DOMAIN AND ANKYRIN REPEATS OF PAPBETA.
 
Authors :  V. Mandiyan, J. Andreev, J. Schlessinger, S. R. Hubbard
Date :  05 Nov 99  (Deposition) - 22 Dec 99  (Release) - 14 Dec 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A
Keywords :  Zinc-Binding Module, Ankyrin Repeats, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  V. Mandiyan, J. Andreev, J. Schlessinger, S. R. Hubbard
Crystal Structure Of The Arf-Gap Domain And Ankyrin Repeats Of Pyk2-Associated Protein Beta.
Embo J. V. 18 6890 1999
PubMed-ID: 10601011  |  Reference-DOI: 10.1093/EMBOJ/18.24.6890
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PYK2-ASSOCIATED PROTEIN BETA
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET21A
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentARF-GAP DOMAIN
    OrganBRAIN
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090

 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
1ZN1Ligand/IonZINC ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:264 , CYS A:267 , CYS A:284 , CYS A:287 , ARG A:350BINDING SITE FOR RESIDUE ZN A 600

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:332 -A:332

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (3, 3)

Asymmetric/Biological Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ARFGAPPS50115 ARF GTPase-activating proteins domain profile.ASAP2_MOUSE424-546  1A:249-371
2ANK_REP_REGIONPS50297 Ankyrin repeat region circular profile.ASAP2_MOUSE587-678  1A:412-503
3ANK_REPEATPS50088 Ankyrin repeat profile.ASAP2_MOUSE623-655  1A:448-480

(-) Exons   (0, 0)

(no "Exon" information available for 1DCQ)

(-) 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:276
 aligned with ASAP2_MOUSE | Q7SIG6 from UniProtKB/Swiss-Prot  Length:958

    Alignment length:276
                                   431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681       691      
          ASAP2_MOUSE   422 LTKEIISEVQRMTGNDVCCDCGAPDPTWLSTNLGILTCIECSGIHRELGVHYSRMQSLTLDVLGTSELLLAKNIGNAGFNEIMECCLPSEDPVKPNPGSDMIARKDYITAKYMERRYARKKHADTAAKLHSLCEAVKTRDIFGLLQAYADGVDLTEKIPLANGHEPDETALHLAVRSVDRTSLHIVDFLVQNSGNLDKQTGKGSTALHYCCLTDNAECLKLLLRGKASIEIANESGETPLDIAKRLKHEHCEELLTQALSGRFNSHVHVEYEWRLL 697
               SCOP domains d1dcqa2 A:247-368 Pyk2-associated protein beta ARF-GAP domain                                                             d1dcqa1 A:369-522 Pyk2-associated protein beta                                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhh...............eee.....eehhhhhhhhhhhh.....eee......hhhhhhhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhh..........hhhhhhhhhhhhhhh.hhhhhhhhhhh..................hhhhhhhhhh...hhhhhhhhhhhh...........hhhhhhhhh.hhhhhhhhhhh............hhhhhhhhh.hhhhhhhhhhhhh................ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) --ARFGAP  PDB: A:249-371 UniProt: 424-546                                                                                    ----------------------------------------ANK_REP_REGION  PDB: A:412-503 UniProt: 587-678                                             ------------------- PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ANK_REPEAT  PDB: A:448-480       ------------------------------------------ PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1dcq A 247 LTKEIISEVQRMTGNDVCCDCGAPDPTWLSTNLGILTCIECSGIHRELGVHYSRMQSLTLDVLGTSELLLAKNIGNAGFNEIMECCLPSEDPVKPNPGSDMIARKDYITAKYMERRYARKKHADTAAKLHSLCEAVKTRDIFGLLQAYADGVDLTEKIPLANGHEPDETALHLAVRSVDRTSLHIVDFLVQNSGNLDKQTGKGSTALHYCCLTDNAECLKLLLRGKASIEIANESGETPLDIAKRLKHEHCEELLTQALSGRFNSHVHVEYEWRLL 522
                                   256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516      

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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (2, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1DCQ)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (ASAP2_MOUSE | Q7SIG6)
molecular function
    GO:0005096    GTPase activator activity    Binds to and increases the activity of a GTPase, an enzyme that catalyzes the hydrolysis of GTP.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0003674    molecular_function    Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.
biological process
    GO:0008150    biological_process    Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.
    GO:0043547    positive regulation of GTPase activity    Any process that activates or increases the activity of a GTPase.
cellular component
    GO:0005794    Golgi apparatus    A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
    GO:0032580    Golgi cisterna membrane    The lipid bilayer surrounding any of the thin, flattened compartments that form the central portion of the Golgi complex.
    GO:0005575    cellular_component    The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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.

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