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(-) Description

Title :  CRYSTAL STRUCTURE OF THE FIRST DH/PH DOMAIN OF TRIO TO 1.7 A
 
Authors :  K. R. Skowronek, Y. Zheng, N. Nassar
Date :  30 Jan 03  (Deposition) - 29 Jun 04  (Release) - 16 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A
Keywords :  Dbl, Pleckstrin, Gef, Rho, Gtpase, Guanine-Nucleotide Releasing Factor, Phosphorylation, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. R. Skowronek, F. Guo, Y. Zheng, N. Nassar
The C-Terminal Basic Tail Of Rhog Assists The Guanine Nucleotide Exchange Factor Trio In Binding To Phospholipids
J. Biol. Chem. V. 279 37895 2004
PubMed-ID: 15199069  |  Reference-DOI: 10.1074/JBC.M312677200

(-) Compounds

Molecule 1 - TRIPLE FUNCTIONAL DOMAIN PROTEIN
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21
    Expression System PlasmidPET15B
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    FragmentN-TERMINAL DH/PH DOMAINS, RESIDUES 1225-1535
    GeneTRIO
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymPTPRF INTERACTING PROTEIN

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1NTY)

(-) Sites  (0, 0)

(no "Site" information available for 1NTY)

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:1313 -A:1313

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (3, 3)

Asymmetric/Biological Unit (3, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_069371D1368VTRIO_HUMANPolymorphism  ---AD1309V
2UniProtVAR_077096R1428QTRIO_HUMANDisease (MRD44)879255626AR1369Q
3UniProtVAR_077097P1461TTRIO_HUMANDisease (MRD44)879255627AP1402T

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

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DH_2PS50010 Dbl homology (DH) domain profile.TRIO_HUMAN1292-1467
1969-2145
  1A:1233-1408
-
2PH_DOMAINPS50003 PH domain profile.TRIO_HUMAN1479-1591
2157-2271
  1A:1420-1532
-

(-) Exons   (10, 10)

Asymmetric/Biological Unit (10, 10)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003442041ENSE00002146523chr5:14143811-14143991181TRIO_HUMAN1-53530--
1.3bENST000003442043bENSE00001365846chr5:14270934-1427100875TRIO_HUMAN53-78260--
1.4ENST000003442044ENSE00001737349chr5:14280431-14280545115TRIO_HUMAN78-116390--
1.5aENST000003442045aENSE00001133893chr5:14286980-14287172193TRIO_HUMAN116-180650--
1.6bENST000003442046bENSE00001133883chr5:14290825-14291337513TRIO_HUMAN181-3511710--
1.7aENST000003442047aENSE00001133874chr5:14293121-14293243123TRIO_HUMAN352-392410--
1.8aENST000003442048aENSE00001292823chr5:14297181-14297372192TRIO_HUMAN393-456640--
1.9ENST000003442049ENSE00001264084chr5:14304570-14304701132TRIO_HUMAN457-500440--
1.10ENST0000034420410ENSE00001082639chr5:14316622-14316852231TRIO_HUMAN501-577770--
1.11ENST0000034420411ENSE00000971019chr5:14330887-14331009123TRIO_HUMAN578-618410--
1.12ENST0000034420412ENSE00001697533chr5:14336645-14336836192TRIO_HUMAN619-682640--
1.13ENST0000034420413ENSE00001133823chr5:14358287-14358456170TRIO_HUMAN683-739570--
1.14ENST0000034420414ENSE00000846188chr5:14359466-14359640175TRIO_HUMAN739-797590--
1.15ENST0000034420415ENSE00000846186chr5:14363841-14364036196TRIO_HUMAN798-863660--
1.16ENST0000034420416ENSE00000728495chr5:14364759-14364925167TRIO_HUMAN863-918560--
1.17ENST0000034420417ENSE00000728487chr5:14366969-14367088120TRIO_HUMAN919-958400--
1.18ENST0000034420418ENSE00000846181chr5:14368817-14369008192TRIO_HUMAN959-1022640--
1.19ENST0000034420419ENSE00000728472chr5:14369483-14369632150TRIO_HUMAN1023-1072500--
1.20ENST0000034420420ENSE00000846177chr5:14374338-14374452115TRIO_HUMAN1073-1111390--
1.21ENST0000034420421ENSE00000728457chr5:14378121-14378236116TRIO_HUMAN1111-1149390--
1.22ENST0000034420422ENSE00000846173chr5:14381239-14381361123TRIO_HUMAN1150-1190410--
1.23bENST0000034420423bENSE00000728443chr5:14387547-14387741195TRIO_HUMAN1191-1255650--
1.24aENST0000034420424aENSE00001325217chr5:14387841-14387956116TRIO_HUMAN1256-1294391A:1231-12355
1.25ENST0000034420425ENSE00000846165chr5:14388722-1438878867TRIO_HUMAN1294-1316231A:1235-125723
1.26ENST0000034420426ENSE00001670384chr5:14389398-14389507110TRIO_HUMAN1317-1353371A:1258-129437
1.27ENST0000034420427ENSE00000846161chr5:14390340-1439040970TRIO_HUMAN1353-1376241A:1294-131724
1.29ENST0000034420429ENSE00000846158chr5:14391010-1439109990TRIO_HUMAN1377-1406301A:1318-134730
1.30ENST0000034420430ENSE00000846157chr5:14394147-1439423993TRIO_HUMAN1407-1437311A:1348-137831
1.31aENST0000034420431aENSE00001698500chr5:14397152-14397263112TRIO_HUMAN1438-1475381A:1379-141638
1.32aENST0000034420432aENSE00000846153chr5:14398989-14399179191TRIO_HUMAN1475-1538641A:1416-147964
1.33ENST0000034420433ENSE00000419579chr5:14401072-14401173102TRIO_HUMAN1539-1572341A:1480-151334
1.34ENST0000034420434ENSE00001082642chr5:14405957-14406099143TRIO_HUMAN1573-1620481A:1514-153522
1.35bENST0000034420435bENSE00001082641chr5:14406682-14406781100TRIO_HUMAN1620-1653340--
1.37bENST0000034420437bENSE00001325352chr5:14419887-14420130244TRIO_HUMAN1654-1735820--
1.40ENST0000034420440ENSE00001169289chr5:14461128-14461420293TRIO_HUMAN1735-1832980--
1.41ENST0000034420441ENSE00001123722chr5:14462864-14463034171TRIO_HUMAN1833-1889570--
1.42aENST0000034420442aENSE00001123717chr5:14465654-1446574996TRIO_HUMAN1890-1921320--
1.43ENST0000034420443ENSE00001188306chr5:14471427-14471575149TRIO_HUMAN1922-1971500--
1.44ENST0000034420444ENSE00001169316chr5:14472701-1447276767TRIO_HUMAN1971-1993230--
1.45aENST0000034420445aENSE00001014185chr5:14474103-14474206104TRIO_HUMAN1994-2028350--
1.46aENST0000034420446aENSE00001014225chr5:14477003-1447707270TRIO_HUMAN2028-2051240--
1.47aENST0000034420447aENSE00001014221chr5:14479370-1447945990TRIO_HUMAN2052-2081300--
1.48ENST0000034420448ENSE00001014201chr5:14480028-1448012093TRIO_HUMAN2082-2112310--
1.49ENST0000034420449ENSE00001014199chr5:14481343-1448139351TRIO_HUMAN2113-2129170--
1.50aENST0000034420450aENSE00001014186chr5:14481650-1448172778TRIO_HUMAN2130-2155260--
1.51bENST0000034420451bENSE00001014193chr5:14482691-14482882192TRIO_HUMAN2156-2219640--
1.52ENST0000034420452ENSE00001014202chr5:14485178-14485355178TRIO_HUMAN2220-2279600--
1.53cENST0000034420453cENSE00001188272chr5:14487573-14488369797TRIO_HUMAN2279-25442660--
1.54bENST0000034420454bENSE00001123707chr5:14492676-14492923248TRIO_HUMAN2545-2627830--
1.55bENST0000034420455bENSE00001264248chr5:14496988-14497126139TRIO_HUMAN2627-2673470--
1.56ENST0000034420456ENSE00001123693chr5:14497956-1449798328TRIO_HUMAN2674-2683100--
1.57aENST0000034420457aENSE00001014212chr5:14498198-14498360163TRIO_HUMAN2683-2737550--
1.58bENST0000034420458bENSE00001263926chr5:14498628-14498749122TRIO_HUMAN2737-2778420--
1.59ENST0000034420459ENSE00001123660chr5:14502688-1450276679TRIO_HUMAN2778-2804270--
1.60aENST0000034420460aENSE00001123652chr5:14504502-14504702201TRIO_HUMAN2804-2871680--
1.61ENST0000034420461ENSE00001014227chr5:14507231-14507369139TRIO_HUMAN2871-2917470--
1.62dENST0000034420462dENSE00001856401chr5:14507989-145103132325TRIO_HUMAN2918-30971800--

(-) 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:305
 aligned with TRIO_HUMAN | O75962 from UniProtKB/Swiss-Prot  Length:3097

    Alignment length:305
                                  1299      1309      1319      1329      1339      1349      1359      1369      1379      1389      1399      1409      1419      1429      1439      1449      1459      1469      1479      1489      1499      1509      1519      1529      1539      1549      1559      1569      1579      1589     
          TRIO_HUMAN   1290 ARRKEFIMAELIQTEKAYVRDLRECMDTYLWEMTSGVEEIPPGIVNKELIIFGNMQEIYEFHNNIFLKELEKYEQLPEDVGHCFVTWADKFQMYVTYCKNKPDSTQLILEHAGSYFDEIQQRHGLANSISSYLIKPVQRITKYQLLLKELLTCCEEGKGEIKDGLEVMLSVPKRANDAMHLSMLEGFDENIESQGELILQESFQVWDPKTLIRKGRERHLFLFEMSLVFSKEVKDSSGRSKYLYKSKLFTSELGVTEHVEGDPCKFALWVGRTPTSDNKIVLKASSIENKQDWIKHIREVIQERT 1594
               SCOP domains d1ntya1 A:1231-1414 Triple functional domain protein TRIO                                                                                                                               d1ntya2 A:1415-1535 Triple functional domain protein TRIO                                                                 SCOP domains
               CATH domains 1ntyA01 A:1231-1411 Dbl Homology Domain; Chain A                                                                                                                                     1ntyA02 A:1412-1535 Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)                              CATH domains
               Pfam domains ------RhoGEF-1ntyA01 A:1237-1407                                                                                                                                                 -------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh.ee.....hhhhh.eeeeeeeeee........eeeeeeeee..eeeeeeeee.....eeeeeeeeee...eeee........eeeeee.........eeee..hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------V-----------------------------------------------------------Q--------------------------------T------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --DH_2  PDB: A:1233-1408 UniProt: 1292-1467                                                                                                                                       -----------PH_DOMAIN  PDB: A:1420-1532 UniProt: 1479-1591                                                                   --- PROSITE
           Transcript 1 (1) 1.24a----------------------Exon 1.26  PDB: A:1258-1294          -----------------------Exon 1.29  PDB: A:1318-1347   Exon 1.30  PDB: A:1348-1378    Exon 1.31a  PDB: A:1379-1416          ---------------------------------------------------------------Exon 1.33  PDB: A:1480-1513       Exon 1.34 [INCOMPLETE] Transcript 1 (1)
           Transcript 1 (2) ----Exon 1.25              ------------------------------------Exon 1.27               --------------------------------------------------------------------------------------------------Exon 1.32a  PDB: A:1416-1479 UniProt: 1475-1538                 -------------------------------------------------------- Transcript 1 (2)
                1nty A 1231 ARRKEFIMAELIQTEKAYVRDLRECMDTYLWEMTSGVEEIPPGIVNKELIIFGNMQEIYEFHNNIFLKELEKYEQLPEDVGHCFVTWADKFQMYVTYCKNKPDSTQLILEHAGSYFDEIQQRHGLANSISSYLIKPVQRITKYQLLLKELLTCCEEGKGEIKDGLEVMLSVPKRANDAMHLSMLEGFDENIESQGELILQESFQVWDPKTLIRKGRERHLFLFEMSLVFSKEVKDSSGRSKYLYKSKLFTSELGVTEHVEGDPCKFALWVGRTPTSDNKIVLKASSIENKQDWIKHIREVIQERT 1535
                                  1240      1250      1260      1270      1280      1290      1300      1310      1320      1330      1340      1350      1360      1370      1380      1390      1400      1410      1420      1430      1440      1450      1460      1470      1480      1490      1500      1510      1520      1530     

   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  (2, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit

(-) Gene Ontology  (19, 19)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (TRIO_HUMAN | O75962)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0005089    Rho guanyl-nucleotide exchange factor activity    Stimulates the exchange of guanyl nucleotides associated with a GTPase of the Rho family. Under normal cellular physiological conditions, the concentration of GTP is higher than that of GDP, favoring the replacement of GDP by GTP in association with the GTPase.
    GO:0019899    enzyme binding    Interacting selectively and non-covalently with any enzyme.
    GO:0005085    guanyl-nucleotide exchange factor activity    Stimulates the exchange of guanyl nucleotides associated with a GTPase. Under normal cellular physiological conditions, the concentration of GTP is higher than that of GDP, favoring the replacement of GDP by GTP in association with the GTPase.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    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.
    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:0004672    protein kinase activity    Catalysis of the phosphorylation of an amino acid residue in a protein, usually according to the reaction: a protein + ATP = a phosphoprotein + ADP.
    GO:0004674    protein serine/threonine kinase activity    Catalysis of the reactions: ATP + protein serine = ADP + protein serine phosphate, and ATP + protein threonine = ADP + protein threonine phosphate.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
    GO:0043547    positive regulation of GTPase activity    Any process that activates or increases the activity of a GTPase.
    GO:0043065    positive regulation of apoptotic process    Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process.
    GO:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
    GO:0035023    regulation of Rho protein signal transduction    Any process that modulates the frequency, rate or extent of Rho protein signal transduction.
    GO:0051056    regulation of small GTPase mediated signal transduction    Any process that modulates the frequency, rate or extent of small GTPase mediated signal transduction.
    GO:0007185    transmembrane receptor protein tyrosine phosphatase signaling pathway    A series of molecular signals initiated by the binding of an extracellular ligand to a receptor on the surface of the target cell where the receptor possesses protein tyrosine phosphatase activity, and ending with regulation of a downstream cellular process, e.g. transcription.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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 Related Entries

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

UniProtKB/Swiss-Prot
        TRIO_HUMAN | O759622nz8

(-) Related Entries Specified in the PDB File

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