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(-) Description

Title :  CRYSTAL STRUCTURE OF THE PHOSPHOINOSITOL (3,4)-BISPHOSPHATE BINDING PH DOMAIN OF TAPP1 FROM HUMAN.
 
Authors :  C. C. Thomas, S. Dowler, M. Deak, D. R. Alessi, D. M. F. Van Aalten
Date :  17 Jul 01  (Deposition) - 11 Jul 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
Chains :  Asym./Biol. Unit :  A
Keywords :  Lipid-Binding Protein, Lipid Degradation, Ph Domain, Phosphatidylinositol (3, 4)-Bisphosphate, Signalling (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. C. Thomas, S. Dowler, M. Deak, D. R. Alessi, D. M. F. Van Aalten
Crystal Structure Of The Phosphatidylinositol 3, 4-Bisphosphate-Binding Pleckstrin Homology (Ph) Domain Of Tandem Ph-Domain-Containing Protein 1 (Tapp1): Molecular Basis Of Lipid Specificity
Biochem. J. V. 358 287 2001
PubMed-ID: 11513726  |  Reference-DOI: 10.1042/0264-6021:3580287
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TANDEM PH DOMAIN CONTAINING PROTEIN-1
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPGEX
    Expression System StrainBL21
    Expression System Taxid511693
    FragmentPLECKSTRIN HOMOLOGY DOMAIN RESIDUES 182-303
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsORDERED CITRATE MOLECULE IN LIPID BINDING POCKET
    SynonymTAPP1 N-TERMINAL PH DOMAIN

 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
1CIT1Ligand/IonCITRIC ACID

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:200 , GLY A:202 , ALA A:203 , ARG A:211 , TYR A:222 , LEU A:232 , ARG A:233 , ARG A:265BINDING SITE FOR RESIDUE CIT A3001

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PH_DOMAINPS50003 PH domain profile.PKHA1_HUMAN7-112
191-289
  1-
A:191-289

(-) Exons   (0, 0)

(no "Exon" information available for 1EAZ)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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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:104
 aligned with PKHA1_HUMAN | Q9HB21 from UniProtKB/Swiss-Prot  Length:404

    Alignment length:104
                                   199       209       219       229       239       249       259       269       279       289    
          PKHA1_HUMAN   190 SAVIKAGYCVKQGAVMKNWKRRYFQLDENTIGYFKSELEKEPLRVIPLKEVHKVQECKQSDIMMRDNLFEIVTTSRTFYVQADSPEEMHSWIKAVSGAIVAQRG 293
               SCOP domains d1eaza_ A: Tapp1                                                                                         SCOP domains
               CATH domains 1eazA00 A:190-293 Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)            CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeee......eeeeeeee...eeeee.........eeee.hhh.eeee..hhhhhh...eeeee....eeeee..hhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -PH_DOMAIN  PDB: A:191-289 UniProt: 191-289                                                         ---- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------- Transcript
                 1eaz A 190 SAVIKAGYCVKQGAVMKNWKRRYFQLDENTIGYFKSELEKEPLRVIPLKEVHKVQECKQSDIMMRDNLFEIVTTSRTFYVQADSPEEMHSWIKAVSGAIVAQRG 293
                                   199       209       219       229       239       249       259       269       279       289    

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  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: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (29, 29)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PKHA1_HUMAN | Q9HB21)
molecular function
    GO:0030165    PDZ domain binding    Interacting selectively and non-covalently with a PDZ domain of a protein, a domain found in diverse signaling proteins.
    GO:0008289    lipid binding    Interacting selectively and non-covalently with a lipid.
    GO:0043325    phosphatidylinositol-3,4-bisphosphate binding    Interacting selectively and non-covalently with phosphatidylinositol-3,4-bisphosphate, a derivative of phosphatidylinositol in which the inositol ring is phosphorylated at the 3' and 4' positions.
    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).
biological process
    GO:0050853    B cell receptor signaling pathway    A series of molecular signals initiated by the cross-linking of an antigen receptor on a B cell.
    GO:0033327    Leydig cell differentiation    The process in which a relatively unspecialized cell acquires specialized structural and/or functional features of a Leydig cell. A Leydig cell is a testosterone-secreting cell in the interstitial area, between the seminiferous tubules, in the testis.
    GO:0008209    androgen metabolic process    The chemical reactions and pathways involving androgens, C19 steroid hormones that can stimulate the development of male sexual characteristics.
    GO:0070301    cellular response to hydrogen peroxide    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a hydrogen peroxide (H2O2) stimulus.
    GO:0045184    establishment of protein localization    The directed movement of a protein to a specific location.
    GO:0008210    estrogen metabolic process    The chemical reactions and pathways involving estrogens, C18 steroid hormones that can stimulate the development of female sexual characteristics. Also found in plants.
    GO:0060325    face morphogenesis    The process in which the anatomical structures of the face are generated and organized. The face is the ventral division of the head.
    GO:0008585    female gonad development    The process whose specific outcome is the progression of the female gonad over time, from its formation to the mature structure.
    GO:0001553    luteinization    The set of processes resulting in differentiation of theca and granulosa cells into luteal cells and in the formation of a corpus luteum after ovulation.
    GO:0035264    multicellular organism growth    The increase in size or mass of an entire multicellular organism, as opposed to cell growth.
    GO:0051898    negative regulation of protein kinase B signaling    Any process that stops, prevents, or reduces the frequency, rate or extent of protein kinase B signaling, a series of reactions mediated by the intracellular serine/threonine kinase protein kinase B.
    GO:0060021    palate development    The biological process whose specific outcome is the progression of the palate from an initial condition to its mature state. This process begins with the formation of the structure and ends with the mature structure. The palate is the partition that separates the nasal and oral cavities.
    GO:0014065    phosphatidylinositol 3-kinase signaling    A series of reactions within the signal-receiving cell, mediated by the intracellular phosphatidylinositol 3-kinase (PI3K). Many cell surface receptor linked signaling pathways signal through PI3K to regulate numerous cellular functions.
    GO:0048008    platelet-derived growth factor receptor signaling pathway    The series of molecular signals generated as a consequence of a platelet-derived growth factor receptor binding to one of its physiological ligands.
    GO:0009791    post-embryonic development    The process whose specific outcome is the progression of the organism over time, from the completion of embryonic development to the mature structure. See embryonic development.
    GO:0031529    ruffle organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a ruffle, a projection at the leading edge of a crawling cell.
    GO:0048705    skeletal system morphogenesis    The process in which the anatomical structures of the skeleton are generated and organized.
    GO:0007283    spermatogenesis    The process of formation of spermatozoa, including spermatocytogenesis and spermiogenesis.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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: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.
    GO:0032587    ruffle membrane    The portion of the plasma membrane surrounding a ruffle.

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