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(-) Description

Title :  CRYSTAL STRUCTURE OF THE PH1877 PROTEIN
 
Authors :  H. Takagi, T. Numata, Y. Kakuta, M. Kimura
Date :  12 Dec 03  (Deposition) - 31 Aug 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Rnase P Protein, Tim-Barrel, Rna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. Takagi, M. Watanabe, Y. Kakuta, R. Kamachi, T. Numata, I. Tanaka, M. Kimura
Crystal Structure Of The Ribonuclease P Protein Ph1877P From Hyperthermophilic Archaeon Pyrococcus Horikoshii Ot3
Biochem. Biophys. Res. Commun. V. 319 787 2004
PubMed-ID: 15184052  |  Reference-DOI: 10.1016/J.BBRC.2004.05.055
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HYPOTHETICAL PROTEIN PH1877
    ChainsA
    EC Number3.1.26.5
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET22B
    Expression System StrainROSETTA-GAMI(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GenePH1877
    Organism ScientificPYROCOCCUS HORIKOSHII
    Organism Taxid53953
    SynonymPH1877P

 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 1V77)

(-) Sites  (0, 0)

(no "Site" information available for 1V77)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1V77)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1V77)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1V77)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1V77)

(-) Exons   (0, 0)

(no "Exon" information available for 1V77)

(-) 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:202
 aligned with RNP3_PYRHO | O59543 from UniProtKB/Swiss-Prot  Length:212

    Alignment length:202
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206  
           RNP3_PYRHO     7 VKFIEMDIRDKEAYELAKEWFDEVVVSIKFNEEVDKEKLREARKEYGKVAILLSNPKPSLVRDTVQKFKSYLIYVESNDLRVIRYSIEKGVDAIISPWVNRKDPGIDHVLAKLMVKKNVALGFSLRPLLYSNPYERANLLRFMMKAWKLVEKYKVRRFLTSSAQEKWDVRYPRDLISLGVVIGMEIPQAKASISMYPEIILK 208
               SCOP domains d1v77a_ A: Ribonuclease P protein component 3, Rnp3                                                                                                                                                        SCOP domains
               CATH domains 1v77A00 A:7-208 Metal-dependent hydrolases                                                                                                                                                                 CATH domains
               Pfam domains ---------------------------------------------RNase_P_p30-1v77A01 A:52-202                                                                                                                           ------ Pfam domains
         Sec.struct. author ...eeeee.hhhhhhhhhhhh.eeeeeeee....hhhhhhhhhhhhh.eeeeee..hhhhhhhhhhhh...eeeee..hhhhhhhhhhh...eee...........hhhhhhhhhhhh.eeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeee....hhhhh.hhhhhhhhhhhh..hhhhhhhh.hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1v77 A   7 VKFIEMDIRDKEAYELAKEWFDEVVVSIKFNEEVDKEKLREARKEYGKVAILLSNPKPSLVRDTVQKFKSYLIYVESNDLRVIRYSIEKGVDAIISPWVNRKDPGIDHVLAKLMVKKNVALGFSLRPLLYSNPYERANLLRFMMKAWKLVEKYKVRRFLTSSAQEKWDVRYPRDLISLGVVIGMEIPQAKASISMYPEIILK 208
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206  

   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  (1, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RNP3_PYRHO | O59543)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0004519    endonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
    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:0004518    nuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids.
    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:0004526    ribonuclease P activity    Catalysis of the endonucleolytic cleavage of RNA, removing 5' extra nucleotides from tRNA precursor.
    GO:0004540    ribonuclease activity    Catalysis of the hydrolysis of phosphodiester bonds in chains of RNA.
biological process
    GO:0090501    RNA phosphodiester bond hydrolysis    The RNA metabolic process in which the phosphodiester bonds between ribonucleotides are cleaved by hydrolysis.
    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:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
    GO:0001682    tRNA 5'-leader removal    Generation of the mature 5'-end of the tRNA, usually via an endonucleolytic cleavage by RNase P.
    GO:0008033    tRNA processing    The process in which a pre-tRNA molecule is converted to a mature tRNA, ready for addition of an aminoacyl group.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0030677    ribonuclease P complex    A ribonucleoprotein complex that catalyzes cleavage of the leader sequence of precursor tRNAs (pre-tRNAs), generating the mature 5' end of tRNAs.

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 Related Entries

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        RNP3_PYRHO | O595432czv

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