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(-) Description

Title :  INTERDOMAIN RRM PACKING CONTRIBUTES TO RNA RECOGNITION IN THE RNA15, HRP1, ANCHOR RNA 3' PROCESSING TERNARY COMPLEX
 
Authors :  T. C. Leeper, G. Varani
Date :  24 Jul 09  (Deposition) - 28 Jul 10  (Release) - 18 Aug 10  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B,C  (10x)
Keywords :  3' Processing, Rrm Domain, Rna15P, Hrp1P, Enhancer Element, Positioning Element, Rna Recognition, Mrna Processing, Nucleus, Rna- Binding, Nonsense-Mediated Mrna Decay, Phosphoprotein, Rna Binding Protein-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. C. Leeper, X. Qu, C. Lu, C. Moore, G. Varani
Novel Protein-Protein Contacts Facilitate Mrna 3'-Processin Signal Recognition By Rna15 And Hrp1.
J. Mol. Biol. V. 401 334 2010
PubMed-ID: 20600122  |  Reference-DOI: 10.1016/J.JMB.2010.06.032

(-) Compounds

Molecule 1 - 5'-R(P*UP*AP*UP*AP*UP*AP*UP*AP*AP*UP*AP*AP*U)-3'
    Chains: A
    Engineered: YES
    Synthetic: YES
 
Molecule 2 - MRNA 3'-END-PROCESSING PROTEIN RNA15
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: ROSETTA PLYS
    Expression System Taxid: 562
    Expression System Vector: PET32
    Fragment: UNP RESIDUES 14 TO 97
    Gene: 2.1, RNA15, YGL044C
    Organism Common: YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synonym: RNA15P
 
Molecule 3 - NUCLEAR POLYADENYLATED RNA-BINDING PROTEIN 4
    Chains: C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: ROSETTA PLYS
    Expression System Taxid: 562
    Expression System Vector: PET32
    Fragment: UNP RESIDUES 156 TO 322
    Gene: HRP1, NAB4, NAB5, YOL123W
    Organism Common: YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synonym: CLEAVAGE FACTOR IB, CFIB, HRP1P

 Structural Features

(-) Chains, Units

  
NMR Structure (10x): 

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2KM8)

(-) Sites  (0, 0)

(no "Site" information available for 2KM8)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2KM8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2KM8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2KM8)

(-) PROSITE Motifs  (1, 3)

NMR Structure (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RRMPS50102 Eukaryotic RNA Recognition Motif (RRM) profile.RNA15_YEAST18-96  1B:26-104
HRP1_YEAST159-241
243-320		  2C:159-241
C:243-320

(-) Exons   (1, 1)

NMR Structure (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YOL123W1YOL123W.1XV:87844-894481605HRP1_YEAST1-5345341C:156-322167

(-) Sequences/Alignments

NMR Structure
   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:RNA  Length:13
                                             
                 2km8 A   1 UAUAUAUAAUAAU  13
                                    10   


Chain B from PDB  Type:PROTEIN  Length:84
 aligned with RNA15_YEAST | P25299 from UniProtKB/Swiss-Prot  Length:296

    Alignment length:84
                                    23        33        43        53        63        73        83        93    
          RNA15_YEAST    14 NPPSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGYSSNS  97
               SCOP domains d2km8b_ B: automated matches                                                         SCOP domains
               CATH domains 2km8B00 B:22-105  [code=3.30.70.330, no name defined]                                CATH domains
               Pfam domains ------RRM_1-2km8B01 B:28-98                                                  ------- Pfam domains
         Sec.struct. author .....eeee.......hhhhhhhhh.....eeeeeee..........eeeeee.hhhhhhhhhhhh..........eee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----RRM  PDB: B:26-104 UniProt: 18-96                                              - PROSITE
                 Transcript ------------------------------------------------------------------------------------ Transcript
                 2km8 B  22 NPPSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGYSSNS 105
                                    31        41        51        61        71        81        91       101    


Chain C from PDB  Type:PROTEIN  Length:167
 aligned with HRP1_YEAST | Q99383 from UniProtKB/Swiss-Prot  Length:534

    Alignment length:167
                                   165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       
           HRP1_YEAST   156 KESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKTQHILDGKVIDPKRAIPRDEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQNKFIDFKDRKIEIKRAEPRH 322
               SCOP domains d2km8c1 C:156-241 automated matches                                                   d2km8c2 C:242-322 automated matches                                               SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----------------------------------------------------------------------------------------RRM_1-2km8C01 C:245-314                                               -------- Pfam domains (1)
           Pfam domains (2) -----------------------------------------------------------------------------------------RRM_1-2km8C02 C:245-314                                               -------- Pfam domains (2)
         Sec.struct. author ....eeeee......hhhhhhhhhh......eeee...........eeeee..hhhhhhhhhh................hhhhhhhheeeeee......hhhhhhhhhhh....................eeeeee..hhhhhhhhh..ee......eeeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---RRM  PDB: C:159-241 UniProt: 159-241                                               -RRM  PDB: C:243-320 UniProt: 243-320                                          -- PROSITE
               Transcript 1 Exon 1.1  PDB: C:156-322 UniProt: 1-534 [INCOMPLETE]                                                                                                                    Transcript 1
                 2km8 C 156 KESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKTQHILDGKVIDPKRAIPRDEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQNKFIDFKDRKIEIKRAEPRH 322
                                   165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315
   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, 3)

NMR Structure
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 3)

NMR Structure
(-)
Clan: RRM (206)

(-) Gene Ontology  (17, 28)

NMR Structure(hide GO term definitions)
Chain B   (RNA15_YEAST | P25299)
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.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    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:0046982    protein heterodimerization activity    Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
biological process
    GO:0031124    mRNA 3'-end processing    Any process involved in forming the mature 3' end of an mRNA molecule.
    GO:0006378    mRNA polyadenylation    The enzymatic addition of a sequence of 40-200 adenylyl residues at the 3' end of a eukaryotic mRNA primary transcript.
    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:0098789    pre-mRNA cleavage required for polyadenylation    The targeted, endonucleolytic cleavage of a pre-mRNA, required for polyadenylation of the 3' end. This cleavage is directed by binding sites near the 3' end of the mRNA and leaves a 3' hydoxyl end which then becomes a target for adenylation.
    GO:0072423    response to DNA damage checkpoint signaling    A process that occurs in response to signals generated as a result of DNA damage checkpoint signaling.
cellular component
    GO:0005847    mRNA cleavage and polyadenylation specificity factor complex    A multisubunit complex that binds to the canonical AAUAAA hexamer and to U-rich upstream sequence elements on the pre-mRNA, thereby stimulating the otherwise weakly active and nonspecific polymerase to elongate efficiently RNAs containing a poly(A) signal.
    GO:0005849    mRNA cleavage factor complex    Any macromolecular complex involved in cleavage or polyadenylation of mRNA molecules.
    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.

Chain C   (HRP1_YEAST | Q99383)
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.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    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).
biological process
    GO:0006378    mRNA polyadenylation    The enzymatic addition of a sequence of 40-200 adenylyl residues at the 3' end of a eukaryotic mRNA primary transcript.
    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:0000184    nuclear-transcribed mRNA catabolic process, nonsense-mediated decay    The nonsense-mediated decay pathway for nuclear-transcribed mRNAs degrades mRNAs in which an amino-acid codon has changed to a nonsense codon; this prevents the translation of such mRNAs into truncated, and potentially harmful, proteins.
    GO:0098789    pre-mRNA cleavage required for polyadenylation    The targeted, endonucleolytic cleavage of a pre-mRNA, required for polyadenylation of the 3' end. This cleavage is directed by binding sites near the 3' end of the mRNA and leaves a 3' hydoxyl end which then becomes a target for adenylation.
    GO:0072423    response to DNA damage checkpoint signaling    A process that occurs in response to signals generated as a result of DNA damage checkpoint signaling.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0010494    cytoplasmic stress granule    A dense aggregation in the cytosol composed of proteins and RNAs that appear when the cell is under stress.
    GO:0005849    mRNA cleavage factor complex    Any macromolecular complex involved in cleavage or polyadenylation of mRNA molecules.
    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
        HRP1_YEAST | Q99383: 2cjk
        RNA15_YEAST | P25299: 2l9b 2x1a 2x1b 2x1f

(-) Related Entries Specified in the PDB File

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