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(-) Description

Title :  S1 RNA BINDING DOMAIN, NMR, 20 STRUCTURES
 
Authors :  M. Bycroft
Date :  27 Nov 96  (Deposition) - 01 Apr 97  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  S1 Rna-Binding Domain, Polynucleotide Phosphorylase (Pnpase) (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Bycroft, T. J. Hubbard, M. Proctor, S. M. Freund, A. G. Murzin
The Solution Structure Of The S1 Rna Binding Domain: A Member Of An Ancient Nucleic Acid-Binding Fold.
Cell(Cambridge, Mass. ) V. 88 235 1997
PubMed-ID: 9008164  |  Reference-DOI: 10.1016/S0092-8674(00)81844-9
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PNPASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Gene: S1 RNA BINDING DOMAIN FROM ESCHERICHIA COLI PNPASE
    Expression System Plasmid: PGET2T
    Expression System Taxid: 562
    Fragment: S1 RNA BINDING DOMAIN
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: POLYRIBONUCLEOTIDE NUCLEOTIDYLTRANSFERASE, POLYNUCLEOTIDE PHOSPHORYLASE

 Structural Features

(-) Chains, Units

  
NMR Structure (20x): 

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 1SRO)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1S1PS50126 S1 domain profile.PNP_ECOLI622-690  1A:6-74

(-) Exons   (0, 0)

(no "Exon" information available for 1SRO)

(-) 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:PROTEIN  Length:76
 aligned with PNP_ECOLI | P05055 from UniProtKB/Swiss-Prot  Length:711

    Alignment length:76
                                   626       636       646       656       666       676       686      
            PNP_ECOLI   617 AEIEVGRVYTGKVTRIVDFGAFVAIGGGKEGLVHISQIADKRVEKVTDYLQMGQEVPVKVLEVDRQGRIRLSIKEA 692
               SCOP domains d1sroa_ A: S1 RNA-binding domain of polyribonucleotide phosphorylase, PNPase SCOP domains
               CATH domains 1sroA00 A:1-76 Nucleic acid-binding proteins                                 CATH domains
               Pfam domains ---------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeee..eee..eee.......................hhhh.....eeeeeeee.......eeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----S1  PDB: A:6-74 UniProt: 622-690                                     -- PROSITE
                 Transcript ---------------------------------------------------------------------------- Transcript
                 1sro A   1 AEIEVGRVYTGKVTRIVDFGAFVAIGGGKEGLVHISQIADKRVEKVTDYLQMGQEVPVKVLEVDRQGRIRLSIKEA  76
                                    10        20        30        40        50        60        70
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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  (1, 1)

NMR Structure
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1SRO)

(-) Gene Ontology  (18, 18)

NMR Structure(hide GO term definitions)
Chain A   (PNP_ECOLI | P05055)
molecular function
    GO:0000175    3'-5'-exoribonuclease activity    Catalysis of the sequential cleavage of mononucleotides from a free 3' terminus of an RNA molecule.
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0035438    cyclic-di-GMP binding    Interacting selectively and non-covalently with cyclic-di-GMP, cyclic dimeric guanosine monophosphate.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    GO:0016779    nucleotidyltransferase activity    Catalysis of the transfer of a nucleotidyl group to a reactant.
    GO:0004654    polyribonucleotide nucleotidyltransferase activity    Catalysis of the reaction: RNA(n+1) + phosphate <=> RNA(n) + a nucleoside diphosphate.
    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:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    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:0006396    RNA processing    Any process involved in the conversion of one or more primary RNA transcripts into one or more mature RNA molecules.
    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:0009408    response to heat    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a heat stimulus, a temperature stimulus above the optimal temperature for that organism.
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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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 Related Entries

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UniProtKB/Swiss-Prot
        PNP_ECOLI | P05055: 3cdi 3cdj 3gcm 3gll 3gme 3h1c

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