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(-) Description

Title :  CRYSTAL STRUCTURE OF THE S. POMBE RAI1
 
Authors :  S. Xiang, L. Tong
Date :  07 Jan 09  (Deposition) - 03 Feb 09  (Release) - 28 Apr 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase, Mrna Processing, Nucleus, Phosphoprotein, Rrna Processing, Transcription, Transcription Regulation, Transcription Termination, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Xiang, A. Cooper-Morgan, X. Jiao, M. Kiledjian, J. L. Manley, L. Tong
Structure And Function Of The 5'-->3' Exoribonuclease Rat1 And Its Activating Partner Rai1.
Nature V. 458 784 2009
PubMed-ID: 19194460  |  Reference-DOI: 10.1038/NATURE07731
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN DIN1
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET26B
    Expression System StrainROSETTA (DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneDIN1, RAI1, SPAC19D5.06C
    Organism CommonFISSION YEAST
    Organism ScientificSCHIZOSACCHAROMYCES POMBE
    Organism Taxid4896
    SynonymDHP1-INTERACTING PROTEIN 1

 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
1MG1Ligand/IonMAGNESIUM ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:150 , ASP A:201 , GLU A:239 , LEU A:240 , HOH A:376 , HOH A:383BINDING SITE FOR RESIDUE MG A1000

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Phe A:58 -Pro A:59

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3FQG)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3FQG)

(-) Exons   (0, 0)

(no "Exon" information available for 3FQG)

(-) 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:313
 aligned with DXO_SCHPO | O13836 from UniProtKB/Swiss-Prot  Length:352

    Alignment length:352
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350  
            DXO_SCHPO     1 MLREFSFYDVPPAHVPPVSEPLEIACYSLSRDRELLLDDSKLSYYYPPPLFSDLNTGFPNRFHPPKSDPDPISIVKDVLMTKGIQMNSSFLTWRGLITKIMCAPLDPRNHWETYLVMDPTSGIIMMEERTRSETSYANQDRMCYWGYKFEAISTLPEIWDACSRDQIEQRDNQDVVPDEQYCSIVKINIGKSKLILAGEVDCIWDKKPCSAKESDVHSDDGTIEEDASNAENPNLHYVELKTSKKYPLENYGMRKKLLKYWAQSFLLGIGRIIIGFRDDNGILIEMKELFTHQIPKMLRPYFKPNDWTPNRLLVVLEHALEWIKQTVKQHPPSTEFTLSYTGGSKLVLRQII 352
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.hhh...........eeeeeeee.....ee......eee..........................hhhhhhhhhhhh......eeeehhhhhhhhhh.......eeeeeee......eeee...-------..hhhhhhhhhhhhhheee.....-----------.......eeeeeeeeee..eeeeeeee..ee......---------------------..hhh.eeeeeee......hhhhhhhhhhhhhhhhhh...eeeeeee.....eeeeeeee.hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh......eeeeee....eeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fqg A   1 MLREFSFYDVPPAHVPPVSEPLEIACYSLSRDRELLLDDSKLSYYYPPPLFSDLNTGFPNRFHPPKSDPDPISIVKDVLMTKGIQMNSSFLTWRGLITKIMCAPLDPRNHWETYLVMDPTSGIIMMEERT-------NQDRMCYWGYKFEAISTLPEIWDA-----------QDVVPDEQYCSIVKINIGKSKLILAGEVDCIWDKKPC---------------------ENPNLHYVELKTSKKYPLENYGMRKKLLKYWAQSFLLGIGRIIIGFRDDNGILIEMKELFTHQIPKMLRPYFKPNDWTPNRLLVVLEHALEWIKQTVKQHPPSTEFTLSYTGGSKLVLRQII 352
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160|        -  |    180       190       200        |-         -         -|      240       250       260       270       280       290       300       310       320       330       340       350  
                                                                                                                                                           130     138                    161         173                                 209                   231                                                                                                                         

   Legend:   → Mismatch (orange background)
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    → 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 3FQG)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3FQG)

(-) Gene Ontology  (23, 23)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (DXO_SCHPO | O13836)
molecular function
    GO:0019003    GDP binding    Interacting selectively and non-covalently with GDP, guanosine 5'-diphosphate.
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0034353    RNA pyrophosphohydrolase activity    Catalysis of the removal of a 5' terminal pyrophosphate from the 5'-triphosphate end of an RNA, leaving a 5'-monophosphate end.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004518    nuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids.
    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:1990174    phosphodiesterase decapping endonuclease activity    Catalysis of the removal of the cap from an unmethylated 5'-end capped RNA resulting in the release of the entire cap structure (GpppN) and a 5' monophosphorylated RNA.
    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:0006353    DNA-templated transcription, termination    The cellular process that completes DNA-templated transcription; the formation of phosphodiester bonds ceases, the RNA-DNA hybrid dissociates, and RNA polymerase releases the DNA.
    GO:0090502    RNA phosphodiester bond hydrolysis, endonucleolytic    The chemical reactions and pathways involving the hydrolysis of internal 3',5'-phosphodiester bonds in one or two strands of ribonucleotides.
    GO:0006402    mRNA catabolic process    The chemical reactions and pathways resulting in the breakdown of mRNA, messenger RNA, which is responsible for carrying the coded genetic 'message', transcribed from DNA, to sites of protein assembly at the ribosomes.
    GO:0006397    mRNA processing    Any process involved in the conversion of a primary mRNA transcript into one or more mature mRNA(s) prior to translation into polypeptide.
    GO:0071035    nuclear polyadenylation-dependent rRNA catabolic process    The chemical reactions and pathways occurring in the nucleus and resulting in the breakdown of a ribosomal RNA (rRNA) molecule, including RNA fragments released as part of processing the primary transcript into multiple mature rRNA species, initiated by the enzymatic addition of a sequence of adenylyl residues (polyadenylation) at the 3' end the target rRNA.
    GO:0000956    nuclear-transcribed mRNA catabolic process    The chemical reactions and pathways resulting in the breakdown of nuclear-transcribed mRNAs in eukaryotic cells.
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
    GO:1901919    positive regulation of exoribonuclease activity    Any process that activates or increases the frequency, rate or extent of exoribonuclease activity.
    GO:0006364    rRNA processing    Any process involved in the conversion of a primary ribosomal RNA (rRNA) transcript into one or more mature rRNA molecules.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0030846    termination of RNA polymerase II transcription, poly(A)-coupled    The process in which transcription of polyadenylated RNA polymerase II transcripts is terminated; cleavage and polyadenylylation of the mRNA 3' end is coupled to transcription termination.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    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: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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        DXO_SCHPO | O138363fqd

(-) Related Entries Specified in the PDB File

3fqd 3fqi 3fqj