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(-) Description

Title :  CRYSTAL STRUCTURE OF DH-PH DOMAIN OF RHOGEF3(XPLN)
 
Authors :  K. Murayama, M. Kato-Murayama, T. Terada, M. Shirouzu, S. Yokoyama, Ri Structural Genomics/Proteomics Initiative (Rsgi)
Date :  07 May 07  (Deposition) - 13 May 08  (Release) - 12 Dec 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.79
Chains :  Asym./Biol. Unit :  A
Keywords :  Dh-Ph Domain, Guanine-Nucleotide Releasing Factor, Signaling Protein, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. Murayama, M. Kato-Murayama, R. Akasaka, T. Terada, S. Yokoyama, M. Shirouzu
Structure Of The Rho-Specific Guanine Nucleotide-Exchange Factor Xpln
Acta Crystallogr. , Sect. F V. 68 1455 2012
PubMed-ID: 23192023  |  Reference-DOI: 10.1107/S1744309112045265

(-) Compounds

Molecule 1 - RHO GUANINE NUCLEOTIDE EXCHANGE FACTOR 3
    ChainsA
    EngineeredYES
    Expression SystemCELL FREE PROTEIN SYNTHSIS
    Expression System PlasmidPX060725-06
    Expression System Vector TypePLASMID
    FragmentDH-PH DOMAIN
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    SynonymXPLN

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric/Biological Unit (2, 6)
No.NameCountTypeFull Name
1MSE2Mod. Amino AcidSELENOMETHIONINE
2SO44Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:161 , GLN A:185 , ASN A:234 , ARG A:305 , HOH A:507 , HOH A:521 , HOH A:532 , HOH A:707 , HOH A:838BINDING SITE FOR RESIDUE SO4 A 501
2AC2SOFTWAREARG A:235 , TYR A:265 , ARG A:266 , HOH A:659 , HOH A:753BINDING SITE FOR RESIDUE SO4 A 502
3AC3SOFTWARELEU A:158 , ARG A:266 , GLN A:315 , THR A:316 , HIS A:317 , HOH A:550 , HOH A:727BINDING SITE FOR RESIDUE SO4 A 503
4AC4SOFTWAREGLU A:212 , GLY A:213 , GLN A:214 , LYS A:215 , HOH A:602 , HOH A:864BINDING SITE FOR RESIDUE SO4 A 504

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Z0Q)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2Z0Q)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Z0Q)

(-) PROSITE Motifs  (3, 3)

Asymmetric/Biological Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DH_2PS50010 Dbl homology (DH) domain profile.ARHG3_MOUSE121-303  1A:12-194
2DH_1PS00741 Dbl homology (DH) domain signature.ARHG3_MOUSE251-276  1A:142-167
3PH_DOMAINPS50003 PH domain profile.ARHG3_MOUSE290-448  1A:181-339

(-) Exons   (0, 0)

(no "Exon" information available for 2Z0Q)

(-) 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
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Chain A from PDB  Type:PROTEIN  Length:321
 aligned with ARHG3_MOUSE | Q91X46 from UniProtKB/Swiss-Prot  Length:524

    Alignment length:336
                                   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       372       382       392       402       412       422       432       442      
          ARHG3_MOUSE   113 QVLTAKEIKRQEAIFELSQGEEDLIEDLKLAKKAYHDPMLKLSIMTEQELNQIFGTLDSLIPLHEELLSQLRDVRKPDGSTEHVGPILVGWLPCLSSYDSYCSNQVAAKALLDHKKQDHRVQDFLQRCLESPFSRKLDLWNFLDIPRSRLVKYPLLLREILRHTPNDNPDQQHLEEAINIIQGIVAEINTKTGESECRYYKERLLYLEEGQKDSLIDSSRVLCCHGELKNNRGVKLHVFLFQEVLVITRAVTHNEQLCYQLYRQPIPVKDLTLEDLQDGEVRLGGSLRGAFSNNERVKNFFRVSFKNGSQSQTHSLQANDTFNKQQWLNCIRQAKE 448
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------RhoGEF-2z0qA02 A:16-193                                                                                                                                                           ---------PH-2z0qA01 A:203-339                                                                                                                      Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh.-------------...hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhee.......hhhhhh...eeeeeeeee....eeeeeee..eeeeeeeeee..eeeeee....ee.hhheeee............--..hhhhhh..eeeeee.hhhhheeeeee..hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) --------DH_2  PDB: A:12-194 UniProt: 121-303                                                                                                                                                   ------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------------------------------------------------------------------DH_1  PDB: A:142-167      -------------PH_DOMAIN  PDB: A:181-339 UniProt: 290-448                                                                                                                      PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2z0q A   4 QVLTAKEIKRQEAIFELSQGEEDLIEDLKLAKKAYHDPmLKLSImTEQELNQIFGTLDSLIPLHEELLSQLRDVRKPDGSTEHVGPILVGWLPCLSSYDSYCSNQVAAKALLDHKKQDHRVQDF-------------DLWNFLDIPRSRLVKYPLLLREILRHTPNDNPDQQHLEEAINIIQGIVAEINTKTGESECRYYKERLLYLEEGQKDSLIDSSRVLCCHGELKNNRGVKLHVFLFQEVLVITRAVTHNEQLCYQLYRQPIPVKDLTLEDLQDGEVRLGGSL--AFSNNERVKNFFRVSFKNGSQSQTHSLQANDTFNKQQWLNCIRQAKE 339
                                    13        23        33        43    |   53        63        73        83        93       103       113       123   |     -       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283      |293       303       313       323       333      
                                                                 42-MSE |                                                                            127           141                                                                                                                                                  290  |                                              
                                                                       48-MSE                                                                                                                                                                                                                                              293                                              

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 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 2Z0Q)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2Z0Q)

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: PH (111)
(-)
Family: PH (71)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (ARHG3_MOUSE | Q91X46)
molecular function
    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: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.
biological process
    GO:0035556    intracellular signal transduction    The process in which a signal is passed on to downstream components within the cell, which become activated themselves to further propagate the signal and finally trigger a change in the function or state of the cell.
    GO:0043547    positive regulation of GTPase activity    Any process that activates or increases the activity of a GTPase.
    GO:0035023    regulation of Rho protein signal transduction    Any process that modulates the frequency, rate or extent of Rho protein signal transduction.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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.

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