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(-) Description

Title :  THE CRYSTAL STRUCTURE OF RNA1P: A NEW FOLD FOR A GTPASE-ACTIVATING PROTEIN
 
Authors :  R. C. Hillig, L. Renault, I. R. Vetter, T. Drell, A. Wittinghofer, J. Becker
Date :  29 Mar 99  (Deposition) - 29 Mar 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.66
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Gtpase-Activating Protein, Gap, Rna1P, Rangap, Lrr, Leucine- Rich Repeat Protein, Twinning, Hemihedral Twinning, Merohedral Twinning, Merohedry, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  R. C. Hillig, L. Renault, I. R. Vetter, T. Drell 4Th. , A. Wittinghofer, J. Becker
The Crystal Structure Of Rna1P: A New Fold For A Gtpase-Activating Protein.
Mol. Cell V. 3 781 1999
PubMed-ID: 10394366  |  Reference-DOI: 10.1016/S1097-2765(01)80010-1
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GTPASE-ACTIVATING PROTEIN RNA1_SCHPO
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21
    Expression System PlasmidPET3D
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    MutationYES
    Organism CommonFISSION YEAST
    Organism ScientificSCHIZOSACCHAROMYCES POMBE
    Organism Taxid4896
    Other DetailsSELENOMETHIONINE MUTANT EXPRESSED IN E.COLI B834
    SynonymRNA1P

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1HG1AUTHORCYS A:93COMMON HG-SITE IN ETHYLMERCURY(II)-CHLORIDE AND MERCURY(II)ACETATE (FRACT. COORD. AS REFINED BY MLPHARE): -0.109 -0.369 0.000 -0.353 -0.355 -0.150
2HG2AUTHORALA A:2ADDITIONAL HG-SITE IN MERCURY(II)ACETATE (FRACT. COORD. AS REFINED BY MLPHARE): -0.179 -0.112 -0.019 - 0.310 -0.156 -0.130
3HG3AUTHORCYS B:93NULL
4HG4AUTHORALA B:2NULL

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1YRG)

(-) Exons   (0, 0)

(no "Exon" information available for 1YRG)

(-) 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:343
 aligned with RNA1_SCHPO | P41391 from UniProtKB/Swiss-Prot  Length:386

    Alignment length:343
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341   
           RNA1_SCHPO     2 SRFSIEGKSLKLDAITTEDEKSVFAVLLEDDSVKEIVLSGNTIGTEAARWLSENIASKKDLEIAEFSDIFTGRVKDEIPEALRLLLQALLKCPKLHTVRLSDNAFGPTAQEPLIDFLSKHTPLEHLYLHNNGLGPQAGAKIARALQELAVNKKAKNAPPLRSIICGRNRLENGSMKEWAKTFQSHRLLHTVKMVQNGIRPEGIEHLLLEGLAYCQELKVLDLQDNTFTHLGSSALAIALKSWPNLRELGLNDCLLSARGAAAVVDAFSKLENIGLQTLRLQYNEIELDAVRTLKTVIDEKMPDLLFLELNGNRFSEEDDVVDEIREVFSTRGRGELDELDDME 344
               SCOP domains d1yrga_ A: Rna1p (RanGAP1), N-terminal domain                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains 1yrgA00 A:2-344 Ribonuclease Inhibitor                                                                                                                                                                                                                                                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee............hhhhh...hhhhh.....eee.......hhhhhhhhhhh.......eee.........hhhhhhhhhhhhhhhhh.....eee.......hhhhhhhhhhhhh.....eee......hhhhhhhhhhhhhhhhhhhhhh......eee........hhhhhhhhhhhh.....eee.......hhhhhhhhhh.hhh.....eee......hhhhhhhhhhhhhh.....eee.......hhhhhhhhhhhhh.......eee.......hhhhhhhhhhhhhh.....eee..........hhhhhhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yrg A   2 ARFSIEGKSLKLDAITTEDEKSVFAVLLEDDSVKEIVLSGNTIGTEAARWLSENIASKKDLEIAEFSDIFTGRVKDEIPEALRLLLQALLKCPKLHTVRLSDNAFGPTAQEPLIDFLSKHTPLEHLYLHNNGLGPQAGAKIARALQELAVNKKAKNAPPLRSIICGRNRLENGSMKEWAKTFQSHRLLHTVKMVQNGIRPEGIEHLLLEGLAYCQELKVLDLQDNTFTHLGSSALAIALKSWPNLRELGLNDCLLSARGAAAVVDAFSKLENIGLQTLRLQYNEIELDAVRTLKTVIDEKMPDLLFLELNGNRFSEEDDVVDEIREVFSTRGRGELDELDDME 344
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341   

Chain B from PDB  Type:PROTEIN  Length:343
 aligned with RNA1_SCHPO | P41391 from UniProtKB/Swiss-Prot  Length:386

    Alignment length:343
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341   
           RNA1_SCHPO     2 SRFSIEGKSLKLDAITTEDEKSVFAVLLEDDSVKEIVLSGNTIGTEAARWLSENIASKKDLEIAEFSDIFTGRVKDEIPEALRLLLQALLKCPKLHTVRLSDNAFGPTAQEPLIDFLSKHTPLEHLYLHNNGLGPQAGAKIARALQELAVNKKAKNAPPLRSIICGRNRLENGSMKEWAKTFQSHRLLHTVKMVQNGIRPEGIEHLLLEGLAYCQELKVLDLQDNTFTHLGSSALAIALKSWPNLRELGLNDCLLSARGAAAVVDAFSKLENIGLQTLRLQYNEIELDAVRTLKTVIDEKMPDLLFLELNGNRFSEEDDVVDEIREVFSTRGRGELDELDDME 344
               SCOP domains d1yrgb_ B: Rna1p (RanGAP1), N-terminal domain                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains 1yrgB00 B:2-344 Ribonuclease Inhibitor                                                                                                                                                                                                                                                                                                                  CATH domains
           Pfam domains (1) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------LRR_6-1yrgB01 B:215-238 ---------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------LRR_6-1yrgB02 B:215-238 ---------------------------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author .eee..............hhh...hhhhh.....eee.......hhhhhhhhhhhhh.....eee.........hhhhhhhhhhhhhhhhh.....eee.......hhhhhhhhhhhhh.....eee......hhhhhhhhhhhhhhhhhhhhhh......eee........hhhhhhhhhhhh.....eee.......hhhhhhhhhh.hhh.....eee......hhhhhhhhhhhhhh.....eee.......hhhhhhhhhhhhh.......eee.......hhhhhhhhhhhhhh.....eee..........hhhhhhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yrg B   2 ARFSIEGKSLKLDAITTEDEKSVFAVLLEDDSVKEIVLSGNTIGTEAARWLSENIASKKDLEIAEFSDIFTGRVKDEIPEALRLLLQALLKCPKLHTVRLSDNAFGPTAQEPLIDFLSKHTPLEHLYLHNNGLGPQAGAKIARALQELAVNKKAKNAPPLRSIICGRNRLENGSMKEWAKTFQSHRLLHTVKMVQNGIRPEGIEHLLLEGLAYCQELKVLDLQDNTFTHLGSSALAIALKSWPNLRELGLNDCLLSARGAAAVVDAFSKLENIGLQTLRLQYNEIELDAVRTLKTVIDEKMPDLLFLELNGNRFSEEDDVVDEIREVFSTRGRGELDELDDME 344
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341   

   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  (1, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: LRR (77)

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (RNA1_SCHPO | P41391)
molecular function
    GO:0005096    GTPase activator activity    Binds to and increases the activity of a GTPase, an enzyme that catalyzes the hydrolysis of GTP.
biological process
    GO:0030702    chromatin silencing at centromere    Repression of transcription of centromeric DNA by altering the structure of chromatin.
    GO:0051383    kinetochore organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the kinetochore, a multisubunit complex that is located at the centromeric region of DNA and provides an attachment point for the spindle microtubules.
    GO:0000070    mitotic sister chromatid segregation    The cell cycle process in which replicated homologous chromosomes are organized and then physically separated and apportioned to two sets during the mitotic cell cycle. Each replicated chromosome, composed of two sister chromatids, aligns at the cell equator, paired with its homologous partner. One homolog of each morphologic type goes into each of the resulting chromosome sets.
    GO:0006913    nucleocytoplasmic transport    The directed movement of molecules between the nucleus and the cytoplasm.
    GO:0043547    positive regulation of GTPase activity    Any process that activates or increases the activity of a GTPase.
    GO:0046827    positive regulation of protein export from nucleus    Any process that activates or increases the frequency, rate or extent of directed movement of proteins from the nucleus into the cytoplasm.
    GO:0043087    regulation of GTPase activity    Any process that modulates the rate of GTP hydrolysis by a GTPase.
cellular component
    GO:0000775    chromosome, centromeric region    The region of a chromosome that includes the centromeric DNA and associated proteins. In monocentric chromosomes, this region corresponds to a single area of the chromosome, whereas in holocentric chromosomes, it is evenly distributed along the chromosome.
    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.
    GO:0031965    nuclear membrane    Either of the lipid bilayers that surround the nucleus and form the nuclear envelope; excludes the intermembrane space.
    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:0048471    perinuclear region of cytoplasm    Cytoplasm situated near, or occurring around, the nucleus.

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 Related Entries

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        RNA1_SCHPO | P413911k5d 1k5g 2ca6

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