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(-) Description

Title :  CRYSTAL STRUCTURE OF FULL LENGTH CENTAURIN ALPHA-1 BOUND WITH THE HEAD GROUP OF PIP3
 
Authors :  L. Shen, Y. Tong, W. Tempel, F. Mackenzie, C. H. Arrowsmith, A. M. Edward C. Bountra, J. Weigelt, A. Bochkarev, H. Park, Structural Genomics Consortium (Sgc)
Date :  26 Jan 10  (Deposition) - 24 Nov 10  (Release) - 15 Dec 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  X
Keywords :  Structural Genomics Consortium, Gap, Gtpase Activation, Sgc, Metal- Binding, Nucleus, Phosphoprotein, Zinc-Finger, Hydrolase Activator (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Tong, W. Tempel, H. Wang, K. Yamada, L. Shen, G. A. Senisterra, F. Mackenzie, A. H. Chishti, H. W. Park
Phosphorylation-Independent Dual-Site Binding Of The Fha Domain Of Kif13 Mediates Phosphoinositide Transport Via Centaurin Alpha1.
Proc. Natl. Acad. Sci. Usa V. 107 20346 2010
PubMed-ID: 21057110  |  Reference-DOI: 10.1073/PNAS.1009008107

(-) Compounds

Molecule 1 - ARF-GAP WITH DUAL PH DOMAIN-CONTAINING PROTEIN 1
    Chains: X
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21-CODONPLUS(DE3)-RIL
    Expression System Taxid: 562
    Gene: ADAP1, CENTA1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: CENTAURIN-ALPHA-1, CNT-A1, PUTATIVE MAPK-ACTIVATING PROTEIN PM25

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : X

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1IP92Ligand/Ion(2R)-3-{[(R)-{[(1S,2S,3R,4S,5S,6S)-2,6-DIHYDROXY-3,4,5-TRIS(PHOSPHONOOXY)CYCLOHEXYL]OXY}(HYDROXY)PHOSPHORYL]OXY}PROPANE-1,2-DIYL DIOCTANOATE
2ZN1Ligand/IonZINC ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS X:21 , CYS X:24 , CYS X:41 , CYS X:44BINDING SITE FOR RESIDUE ZN X 401
2AC2SOFTWARESER X:43 , LYS X:261 , THR X:262 , GLY X:263 , PRO X:264 , GLU X:268 , ARG X:271 , ARG X:273 , TYR X:284 , ARG X:332 , HOH X:463 , HOH X:470 , HOH X:498 , HOH X:541 , HOH X:573 , HOH X:580 , HOH X:603BINDING SITE FOR RESIDUE IP9 X 371
3AC3SOFTWARELYS X:138 , GLY X:140 , ARG X:141 , ARG X:149 , TYR X:162 , ASN X:164 , LYS X:172 , ARG X:206 , THR X:340 , GLU X:341 , SER X:342 , ARG X:345 , HOH X:423 , HOH X:442 , HOH X:471 , HOH X:506 , HOH X:531 , HOH X:637BINDING SITE FOR RESIDUE IP9 X 372

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3LJU)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3LJU)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric/Biological Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_047470G241SADAP1_HUMANPolymorphism10256887XS241S
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (2, 3)

Asymmetric/Biological Unit (2, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ARFGAPPS50115 ARF GTPase-activating proteins domain profile.ADAP1_HUMAN7-126  1X:7-126
2PH_DOMAINPS50003 PH domain profile.ADAP1_HUMAN129-230
252-356		  2X:129-230
X:252-356

(-) Exons   (0, 0)

(no "Exon" information available for 3LJU)

(-) 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 X from PDB  Type:PROTEIN  Length:373
 aligned with ADAP1_HUMAN | O75689 from UniProtKB/Swiss-Prot  Length:374

    Alignment length:378
                                    1                                                                                                                                                                                                                                                                                                                                                                                 
                                    |2        12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362        
          ADAP1_HUMAN     - --------MAKERRRAVLELLQRPGNARCADCGAPDPDWASYTLGVFICLSCSGIHRNIPQVSKVKSVRLDAWEEAQVEFMASHGNDAARARFESKVPSFYYRPTPSDCQLLREQWIRAKYERQEFIYPEKQEPYSAGYREGFLWKRGRDNGQFLSRKFVLTEREGALKYFNRNDAKEPKAVMKIEHLNATFQPAKIGHPHGLQVTYLKDNSTRNIFIYHEDGKEIVDWFNALRAARFHYLQVAFPGAGDADLVPKLSRNYLKEGYMEKTGPKQTEGFRKRWFTMDDRRLMYFKDPLDAFARGEVFIGSKESGYTVLHGFPPSTQGHHWPHGITIVTPDRKFLFACETESDQREWVAAFQKAVDRPMLPQEYAVEAHF 370
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains -------------ArfGap-3ljuX02 X:6-122                                                                                               ----------------------------------------------------------------------------------------------------------------------------------PH-3ljuX01 X:253-356                                                                                    -------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhh...........eee....eeehhhhhhhhhh......eee......hhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhh.....hhhhhhhhhh.eeeeeeeee......eeeeeeeee....eeeee.-----...eeee...eeeeehhhhhh....eeeeeee..eeeeeeee..hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhh.....eeeeeee.........eeeeeeee..eeeee.........eeee..hhhhh.eeee............eeeeee....eeeeee.hhhhhhhhhhhhhhhhhh....hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------S--------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------ARFGAP  PDB: X:7-126 UniProt: 7-126                                                                                     --PH_DOMAIN  PDB: X:129-230 UniProt: 129-230                                                            ---------------------PH_DOMAIN  PDB: X:252-356 UniProt: 252-356                                                               -------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3lju X  -7 SGRENLYFQGKERRRAVLELLQRPGNARCADCGAPDPDWASYTLGVFICLSCSGIHRNIPQVSKVKSVRLDAWEEAQVEFMASHGNDAARARFESKVPSFYYRPTPSDCQLLREQWIRAKYERQEFIYPEKQEPYSAGYREGFLWKRGRDNGQFLSRKFVLTEREGALKYFN-----EPKAVMKIEHLNATFQPAKIGHPHGLQVTYLKDNSTRNIFIYHEDGKEIVDWFNALRAARFHYLQVAFPGASDADLVPKLSRNYLKEGYMEKTGPKQTEGFRKRWFTMDDRRLMYFKDPLDAFARGEVFIGSKESGYTVLHGFPPSTQGHHWPHGITIVTPDRKFLFACETESDQREWVAAFQKAVDRPMLPQEYAVEAHF 370
                                     2        12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162 |     172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362        
                                                                                                                                                                                                     164   170
   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 3LJU)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3LJU)

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: PH (111)
(-)
Family: PH (71)
(-)
Clan: no clan defined [family: ArfGap] (6)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain X   (ADAP1_HUMAN | O75689)
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:0043533    inositol 1,3,4,5 tetrakisphosphate binding    Interacting selectively and non-covalently with inositol 1,3,4,5 tetrakisphosphate.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0007166    cell surface receptor signaling pathway    A series of molecular signals initiated by activation of a receptor on the surface of a cell. The pathway begins with binding of an extracellular ligand to a cell surface receptor, or for receptors that signal in the absence of a ligand, by ligand-withdrawal or the activity of a constitutively active receptor. The pathway ends with regulation of a downstream cellular process, e.g. transcription.
    GO:0043547    positive regulation of GTPase activity    Any process that activates or increases the activity of a GTPase.
    GO:0043087    regulation of GTPase activity    Any process that modulates the rate of GTP hydrolysis by a GTPase.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        ADAP1_HUMAN | O75689: 3feh 3fm8 3mdb

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