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(-) Description

Title :  CRYSTAL STRUCTURE OF THE RNA BINDING DOMAIN OF PUF4 FROM SACCHAROMYCES CEREVISIAE
 
Authors :  M. T. Miller, J. J. Higgin, T. M. T. Hall
Date :  10 Jan 08  (Deposition) - 11 Mar 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.69
Chains :  Asym./Biol. Unit :  A
Keywords :  Puf4, Pumilio, Rna Binding, Ho Endonuclease, Transcription, Rna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. T. Miller, J. J. Higgin, T. M. T. Hall
Basis Of Altered Rna-Binding Specificity By Puf Proteins Revealed By Crystal Structures Of Yeast Puf4P
Nat. Struct. Mol. Biol. V. 15 397 2008
PubMed-ID: 18327269  |  Reference-DOI: 10.1038/NSMB.1390
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN PUF4
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentSINGLE STRANDED RNA BINDING DOMIN
    GenePUF4
    Organism CommonBAKER'S YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932

 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 3BWT)

(-) Sites  (0, 0)

(no "Site" information available for 3BWT)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Leu A:588 -Gly A:589

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 8)

Asymmetric/Biological Unit (1, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PUMPS50302 Pumilio RNA-binding repeat profile.PUF4_YEAST563-598
599-634
635-671
672-707
708-743
744-783
784-821
823-861
  8A:563-598
A:599-634
A:635-671
A:672-707
A:708-743
A:744-783
A:784-821
A:823-861

(-) Exons   (1, 1)

Asymmetric/Biological Unit (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YGL014W1YGL014W.1VII:466146-4688122667PUF4_YEAST1-8888881A:554-886333

(-) 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:333
 aligned with PUF4_YEAST | P25339 from UniProtKB/Swiss-Prot  Length:888

    Alignment length:333
                                   563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713       723       733       743       753       763       773       783       793       803       813       823       833       843       853       863       873       883   
           PUF4_YEAST   554 SRFADAVLDQYIGSIHSLCKDQHGCRFLQKQLDILGSKAADAIFEETKDYTVELMTDSFGNYLIQKLLEEVTTEQRIVLTKISSPHFVEISLNPHGTRALQKLIECIKTDEEAQIVVDSLRPYTVQLSKDLNGNHVIQKCLQRLKPENFQFIFDAISDSCIDIATHRHGCCVLQRCLDHGTTEQCDNLCDKLLALVDKLTLDPFGNYVVQYIITKEAEKNKYDYTHKIVHLLKPRAIELSIHKFGSNVIEKILKTAIVSEPMILEILNNGGETGIQSLLNDSYGNYVLQTALDISHKQNDYLYKRLSEIVAPLLVGPIRNTPHGKRIIGMLHL 886
               SCOP domains d3bwta_ A: automated matches                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhh..hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh.hhhhhhhhhhhhh.hhhhhhhhhhhhh.hhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh..hhhhhhhhhhh.hhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------PUM  PDB: A:563-598 UniProt: 563-598PUM  PDB: A:599-634 UniProt: 599-634PUM  PDB: A:635-671 UniProt: 635-671 PUM  PDB: A:672-707 UniProt: 672-707PUM  PDB: A:708-743 UniProt: 708-743PUM  PDB: A:744-783 UniProt: 744-783    PUM  PDB: A:784-821 UniProt: 784-821  -PUM  PDB: A:823-861 UniProt: 823-861   ------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:554-886 UniProt: 1-888 [INCOMPLETE]                                                                                                                                                                                                                                                                                          Transcript 1
                 3bwt A 554 SRFADAVLDQYIGSIHSLCKDQHGCRFLQKQLDILGSKAADAIFEETKDYTVELMTDSFGNYLIQKLLEEVTTEQRIVLTKISSPHFVEISLNPHGTRALQKLIECIKTDEEAQIVVDSLRPYTVQLSKDLNGNHVIQKCLQRLKPENFQFIFDAISDSCIDIATHRHGCCVLQRCLDHGTTEQCDNLCDKLLALVDKLTLDPFGNYVVQYIITKEAEKNKYDYTHKIVHLLKPRAIELSIHKFGSNVIEKILKTAIVSEPMILEILNNGGETGIQSLLNDSYGNYVLQTALDISHKQNDYLYKRLSEIVAPLLVGPIRNTPHGKRIIGMLHL 886
                                   563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713       723       733       743       753       763       773       783       793       803       813       823       833       843       853       863       873       883   

   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, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PUF4_YEAST | P25339)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0003729    mRNA binding    Interacting selectively and non-covalently with messenger RNA (mRNA), an intermediate molecule between DNA and protein. mRNA includes UTR and coding sequences, but does not contain introns.
biological process
    GO:0001308    negative regulation of chromatin silencing involved in replicative cell aging    The process, which occurs as a dividing cell ages, leading to expression of genes that are typically not expressed due to silencing by regulatory proteins.
    GO:0017148    negative regulation of translation    Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.
    GO:0000288    nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay    A major pathway of degradation of nuclear-transcribed mRNAs that proceeds through a series of ordered steps that includes poly(A) tail shortening and that can regulate mRNA stability.
    GO:0008104    protein localization    Any process in which a protein is transported to, or maintained in, a specific location.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.

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    Leu A:588 - Gly A:589   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        PUF4_YEAST | P253393bx2 3bx3 4dzs

(-) Related Entries Specified in the PDB File

1ib2 CRYSTAL STRUCTURE OF A PUMILIO-HOMOLOGY DOMAIN
1m6w CRYSTAL STRUCTURE OF THE PUMILIO-HOMOLOGY DOMAIN FROM HUMAN PUMILIO1 IN COMPLEX WITH NRE1-19 RNA
1m8x CRYSTAL STRUCTURE OF THE PUMILIO-HOMOLOGY DOMAIN FROM HUMAN PUMILIO1 IN COMPLEX WITH NRE1-14 RNA
1m8y CRYSTAL STRUCTURE OF THE PUMILIO-HOMOLOGY DOMAIN FROM HUMAN PUMILIO1 IN COMPLEX WITH NRE2-10 RNA
1m8z CRYSTAL STRUCTURE OF A PUMILIO-HOMOLOGY DOMAIN
3bx2
3bx3