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(-) Description

Title :  STRUCTURAL AND MUTATIONAL ANALYSIS OF TRNA-INTRON SPLICING ENDONUCLEASE FROM THERMOPLASMA ACIDOPHILUM DSM 1728
 
Authors :  Y. K. Kim, K. Mizutani, K. H. Rhee, W. H. Lee, S. Y. Park, K. Y. Hwang
Date :  10 Jan 07  (Deposition) - 27 Nov 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Trna, Intron, Splicing, Endonuclease, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. K. Kim, K. Mizutani, K. H. Rhee, K. H. Nam, W. H. Lee, E. H. Lee, E. E. Kim S. Y. Park, K. Y. Hwang
Structural And Mutational Analysis Of Trna Intron-Splicing Endonuclease From Thermoplasma Acidophilum Dsm 1728: Catalytic Mechanism Of Trna Intron-Splicing Endonucleases
J. Bacteriol. V. 189 8339 2007
PubMed-ID: 17827289  |  Reference-DOI: 10.1128/JB.00713-07

(-) Compounds

Molecule 1 - TRNA-SPLICING ENDONUCLEASE
    Chains: A
    EC Number: 3.1.27.9
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET28A
    Expression System Strain: BL 21 DE3
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: ENDA
    Organism Scientific: THERMOPLASMA ACIDOPHILUM
    Organism Taxid: 273075
    Strain: DSM 1728
    Synonym: TRNA-INTRON SPLICING ENDONUCLEASE, TRNA-INTRON ENDONUCLEASE

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 2OHE)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2OHE)

(-) Exons   (0, 0)

(no "Exon" information available for 2OHE)

(-) Sequences/Alignments

Asymmetric 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:290
 aligned with ENDA_THEAC | Q9HIY5 from UniProtKB/Swiss-Prot  Length:289

    Alignment length:290
                             1                                                                                                                                                                                                                                                                                                
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289
           ENDA_THEAC     - -MEQGICGSHVFFIEDGKSKNYIIGKYKIGYLSGDNLILDPYECLYLYFKGRISFQNSDSFRDLFDTVTFDRYVAYEILKNKGYRVKEDSGLIYFRKGTEKPLSLRVMREYDRIQFSDLVENPVDYYFTVDEEGDPTVYSSQEIFPAGRNLVSPVSAPVVRMGGRSFGAGDLEWWIGTAFHGFRLLTENEANYISGNHSASQVDMVYSDLVGRGCIVKTGFKYGANFRVYLGRDSQHAEYLVSVMPEEERWYSISRGVRVASSVRKTMIYASIYKNEVRYVALKRVKDII 289
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------tRNA_int_endo-2oheA01 A:204-279                                             ---------- Pfam domains
         Sec.struct. author ...eee....eeee.hhhhhhhhhhhhh..eee..eee.hhhhhhhhhhh..eee..hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeee..eeeee......eeeee.....eehhhhhhh....eeeee.....eeeeeeeee...............eee..eeeee........eee..eee.hhhhhhhhh.....hhhhhhhhhhhhh..eeee.hhhh..eeee.........eeeee....eehhhhhhhhhhhhhh..eeeeeeee..eeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ohe A   0 HMEQGICGSHVFFIEDGKSKNYIIGKYKIGYLSGDNLILDPYECLYLYFKGRISFQNSDSFRDLFDTVTFDRYVAYEILKNKGYRVKEDSGLIYFRKGTEKPLSLRVMREYDRIQFSDLVENPVDYYFTVDEEGDPTVYSSQEIFPGGRNLVSPVSAPVVRMGGRSFGAGDLEWWIGTAFHGFRLLTENEANYISGNHSASQVDMVYSDLVGRGCIVKTGFKYGANFRVYLGRDSQHAEYLVSVMPEEERWYSISRGVRVASSVRKTMIYASIYKNEVRYVALKRVKDII 289
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289
   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)
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  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 2OHE)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2OHE)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: tRNA-IECD (4)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A   (ENDA_THEAC | Q9HIY5)
molecular function
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
    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:0000213    tRNA-intron endonuclease activity    Catalysis of the endonucleolytic cleavage of pre-tRNA, producing 5'-hydroxyl and 2',3'-cyclic phosphate termini, and specifically removing the intron.
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:0008033    tRNA processing    The process in which a pre-tRNA molecule is converted to a mature tRNA, ready for addition of an aminoacyl group.
    GO:0006388    tRNA splicing, via endonucleolytic cleavage and ligation    Splicing of tRNA substrates via recognition of the folded RNA structure that brings the 5' and 3' splice sites into proximity and cleavage of the RNA at both the 3' and 5' splice sites by an endonucleolytic mechanism, followed by ligation of the exons.

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  2ohe
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 Related Entries

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        ENDA_THEAC | Q9HIY5: 2ohc

(-) Related Entries Specified in the PDB File

2ohc