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(-) Description

Title :  CRYSTAL STRUCTURE OF THE RRM-DOMAIN OF THE POLY(A)-SPECIFIC RIBONUCLEASE PARN BOUND TO M7GTP
 
Authors :  T. Monecke, S. Schell, A. Dickmanns, R. Ficner
Date :  14 Apr 08  (Deposition) - 29 Jul 08  (Release) - 06 Nov 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (4x)
Keywords :  Parn, Protein-Rna-Complex, M7G-Cap, M7Gtp, Rna Recognition Motif, Rrm, Exonuclease, Hydrolase, Magnesium, Metal-Binding, Nonsense- Mediated Mrna Decay, Nuclease, Nucleus, Phosphoprotein, Rna-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Monecke, S. Schell, A. Dickmanns, R. Ficner
Crystal Structure Of The Rrm Domain Of Poly(A)-Specific Ribonuclease Reveals A Novel M(7)G-Cap-Binding Mode.
J. Mol. Biol. V. 382 827 2008
PubMed-ID: 18694759  |  Reference-DOI: 10.1016/J.JMB.2008.07.073

(-) Compounds

Molecule 1 - POLY(A)-SPECIFIC RIBONUCLEASE PARN
    Chains: A
    EC Number: 3.1.13.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX-6P-PARN3
    Expression System Strain: BL 21 (DE3)
    Expression System Vector Type: PLASMID
    Fragment: RNA-RECOGNITION-MOTIF OF PARN (RESIDUES 445-540)
    Gene: PARN, DAN
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: POLYADENYLATE-SPECIFIC RIBONUCLEASE, DEADENYLATING NUCLEASE, DEADENYLATION NUCLEASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (1x): A
Biological Unit 2 (4x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1MGP1Ligand/Ion7-METHYL-GUANOSINE-5'-TRIPHOSPHATE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1MGP1Ligand/Ion7-METHYL-GUANOSINE-5'-TRIPHOSPHATE
Biological Unit 2 (1, 4)
No.NameCountTypeFull Name
1MGP4Ligand/Ion7-METHYL-GUANOSINE-5'-TRIPHOSPHATE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:454 , TRP A:456 , LYS A:457 , GLN A:472 , TRP A:475 , ASP A:477 , ASP A:478 , HOH A:579 , HOH A:608BINDING SITE FOR RESIDUE MGP A 1

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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 Sequence-Structure Mapping

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(-) PROSITE Motifs  (0, 0)

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(-) Exons   (0, 0)

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(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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  UniProt sequence: complete  aligned part    
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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:75
 aligned with PARN_HUMAN | O95453 from UniProtKB/Swiss-Prot  Length:639

    Alignment length:78
                                   446       456       466       476       486       496       506        
           PARN_HUMAN   437 GPDLQPKRDHVLHVTFPKEWKTSDLYQLFSAFGNIQISWIDDTSAFVSLSQPEQVKIAVNTSKYAESYRIQTYAEYMG 514
               SCOP domains ------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..-.e--eeeeeeee.....hhhhhhhhh...eeeeeeeee..eeeeeeeeehhhhhhhhhhh........hhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------ Transcript
                 3ctr A 440 GP-LG--SDHVLHVTFPKEWKTSDLYQLFSAFGNIQISWIDDTSAFVSLSQPEQVKIAVNTSKYAESYRIQTYAEYMG 514
                             | ||  446       456       466       476       486       496       506        
                             | ||  |                                                                      
                           441 ||  |                                                                      
                             442|  |                                                                      
                              443  |                                                                      
                                 444
   Legend:   → Mismatch (orange background)
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  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 3CTR)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (23, 23)

Asymmetric Unit(hide GO term definitions)
Chain A   (PARN_HUMAN | O95453)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0004527    exonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' or 5' 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:0003730    mRNA 3'-UTR binding    Interacting selectively and non-covalently with the 3' untranslated region of an mRNA molecule.
    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: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:0004535    poly(A)-specific ribonuclease activity    Catalysis of the exonucleolytic cleavage of poly(A) to 5'-AMP.
    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:0019901    protein kinase binding    Interacting selectively and non-covalently with a protein kinase, any enzyme that catalyzes the transfer of a phosphate group, usually from ATP, to a protein substrate.
biological process
    GO:0009451    RNA modification    The covalent alteration of one or more nucleotides within an RNA molecule to produce an RNA molecule with a sequence that differs from that coded genetically.
    GO:0090503    RNA phosphodiester bond hydrolysis, exonucleolytic    The chemical reactions and pathways involving the hydrolysis of terminal 3',5'-phosphodiester bonds in one or two strands of ribonucleotides.
    GO:0007292    female gamete generation    Generation of the female gamete; specialised haploid cells produced by meiosis and along with a male gamete takes part in sexual reproduction.
    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: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:0000289    nuclear-transcribed mRNA poly(A) tail shortening    Shortening of the poly(A) tail of a nuclear-transcribed mRNA from full length to an oligo(A) length.
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
    GO:0043488    regulation of mRNA stability    Any process that modulates the propensity of mRNA molecules to degradation. Includes processes that both stabilize and destabilize mRNAs.
cellular component
    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:0005730    nucleolus    A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
    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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        PARN_HUMAN | O95453: 2a1r 2a1s

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