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(-) Description

Title :  CRYSTAL STRUCTURE OF TRNA-INTRON ENDONUCLEASE FROM SULFOLOBUS TOKODAII
 
Authors :  M. Kato-Murayama, Y. Bessho, M. Shirouzu, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  01 Jun 05  (Deposition) - 01 Dec 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A,B  (2x)
Keywords :  Trna-Intron Endonuclease, Trna Splicing, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Kato-Murayama, Y. Bessho, M. Shirouzu, S. Yokoyama
Crystal Structure Of Trna-Intron Endonuclease From Sulfolobus Tokodaii
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TRNA-SPLICING ENDONUCLEASE
    Chains: A, B
    EC Number: 3.1.27.9
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET11A
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: SULFOLOBUS TOKODAII
    Organism Taxid: 111955
    Synonym: TRNA-INTRON ENDONUCLEASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): AB
Biological Unit 2 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 10)

Asymmetric Unit (2, 10)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2MSE8Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 8)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2MSE8Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 16)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2MSE16Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER B:49BINDING SITE FOR RESIDUE CL B 1001

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2CV8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2CV8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2CV8)

(-) PROSITE Motifs  (0, 0)

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(-) Exons   (0, 0)

(no "Exon" information available for 2CV8)

(-) 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:160
 aligned with ENDA_SULTO | Q975R3 from UniProtKB/Swiss-Prot  Length:180

    Alignment length:180
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180
           ENDA_SULTO     1 MIGELVKDKILIKNIEDARLIYKMGYYGKPIGISKPKSAEEINSELILSLIEGVYLVKKGKLEIVSNGERLDFERLYQIGVTQIPRFRILYSVYEDLREKGYVVRSGIKYGADFAVYTIGPGIEHAPYLVIALDENSQISSNEILGFGRVSHSTRKELILGIVNLTNGKIRYIMFKWLKM 180
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee..eeee.hhhhhhhhhhhhh..ee..-----------..eeeehhhhhhhhhh...eeee..eeehhhhhhhhhhhhh.hhhhhhhhhhhhhhh..eeee.hhhh..eeee....-----.eeeeeee...eeehhhhh......----.eeeeeee......eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2cv8 A   1 mIGELVKDKILIKNIEDARLIYKmGYYGKPIG-----------SELILSLIEGVYLVKKGKLEIVSNGERLDFERLYQIGVTQIPRFRILYSVYEDLREKGYVVRSGIKYGADFAVYTIGP-----PYLVIALDENSQISSNEILGFGRVS----KELILGIVNLTNGKIRYImFKWLKm 180
                            |       10        20   |    30 |       -   |    50        60        70        80        90       100       110       120|     |130       140       150|    | 160       170   |   180
                            |                     24-MSE  32          44                                                                          121   127                     151  156               174-MSE |
                            1-MSE                                                                                                                                                                            180-MSE


Chain B from PDB  Type:PROTEIN  Length:180
 aligned with ENDA_SULTO | Q975R3 from UniProtKB/Swiss-Prot  Length:180

    Alignment length:180
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180
           ENDA_SULTO     1 MIGELVKDKILIKNIEDARLIYKMGYYGKPIGISKPKSAEEINSELILSLIEGVYLVKKGKLEIVSNGERLDFERLYQIGVTQIPRFRILYSVYEDLREKGYVVRSGIKYGADFAVYTIGPGIEHAPYLVIALDENSQISSNEILGFGRVSHSTRKELILGIVNLTNGKIRYIMFKWLKM 180
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee..eeee.hhhhhhhhhhhhh..ee.......hhhhh...eeeehhhhhhhhhh...eeee..eeehhhhhhhhhhhhh.hhhhhhhhhhhhhhh..eeee.hhhh..eeee..........eeeeeee...eeehhhhhhhhhhhh....eeeeeee......eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2cv8 B   1 mIGELVKDKILIKNIEDARLIYKmGYYGKPIGISKPKSAEEINSELILSLIEGVYLVKKGKLEIVSNGERLDFERLYQIGVTQIPRFRILYSVYEDLREKGYVVRSGIKYGADFAVYTIGPGIEHAPYLVIALDENSQISSNEILGFGRVSHSTRKELILGIVNLTNGKIRYImFKWLKm 180
                            |       10        20   |    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170   |   180
                            |                     24-MSE                                                                                                                                               174-MSE |
                            1-MSE                                                                                                                                                                            180-MSE
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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 2CV8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2CV8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2CV8)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (ENDA_SULTO | Q975R3)
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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