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(-) Description

Title :  CRYSTAL STRUCTURE OF THE TRNA PSEUDOURIDINE SYNTHASE TRUA FROM THERMUS THERMOPHILUS HB8
 
Authors :  X. Dong, Y. Bessho, M. Shirouzu, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  28 Jun 06  (Deposition) - 12 Dec 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.25
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Trua, Pseudouridine Synthase, Trna Modification, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. Dong, Y. Bessho, R. Shibata, M. Nishimoto, M. Shirouzu, S. Kuramitsu, S. Yokoyama
Crystal Structure Of Trna Pseudouridine Synthase Trua From Thermus Thermophilus Hb8
Rna Biol. V. 3 115 2006
PubMed-ID: 17114947

(-) Compounds

Molecule 1 - TRNA PSEUDOURIDINE SYNTHASE A
    Chains: A, B
    EC Number: 5.4.99.12
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET11A
    Expression System Strain: HMS174(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 1-249
    Gene: TRUA
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 300852
    Strain: HB8
    Synonym: TRNA-URIDINE ISOMERASE I, TRNA PSEUDOURIDYLATE SYNTHASE I

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1VS3)

(-) Sites  (0, 0)

(no "Site" information available for 1VS3)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1VS3)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1VS3)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1VS3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1VS3)

(-) Exons   (0, 0)

(no "Exon" information available for 1VS3)

(-) 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:249
 aligned with TRUA_THET8 | Q5SHU9 from UniProtKB/Swiss-Prot  Length:253

    Alignment length:249
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240         
           TRUA_THET8     1 MRRLLLLCEYDGTLFAGLQRQGRGLRTVQGELERALPGIGALPKAVAAGRTDAGVHALAMPFHVDVESAIPVEKVPEALNRLLPEDLKVVGAREVAPDFHARKDALWRAYRYRILVRPHPSPLLRHRALWVRRPLDLEAMEEALSLLLGRHNFLGFAKEETRPGERELLEARLQVAEGEAGLEVRLYFRGKSFLRGQVRGMVGTLLEVGLGKRPPESLKAILKTADRRLAGPTAPAHGLYFVEAAYPEE 249
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 1vs3A01 A:1-105  [code=3.30.70.580, no name defined]                                                     ------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeee.hhhh...........hhhhhhhhhhhhhh.....ee........eeeeeeeeeee....hhhhhhhhhhhhh...eeeeeeeee...........eeeeeeeeee............eee....hhhhhhhhhhhhheeee.hhhh.......eeeeeeeeeeeee....eeeeeeeee.....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh....hhh.eeeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vs3 A   1 MRRLLLLCEYDGTLFAGLQRQGRGLRTVQGELERALPGIGALPKAVAAGRTDAGVHALAMPFHVDVESAIPVEKVPEALNRLLPEDLKVVGAREVAPDFHARKDALWRAYRYRILVRPHPSPLLRHRALWVRRPLDLEAMEEALSLLLGRHNFLGFAKEETRPGERELLEARLQVAEGEAGLEVRLYFRGKSFLRGQVRGMVGTLLEVGLGKRPPESLKAILKTADRRLAGPTAPAHGLYFVEAAYPEE 249
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240         


Chain B from PDB  Type:PROTEIN  Length:249
 aligned with TRUA_THET8 | Q5SHU9 from UniProtKB/Swiss-Prot  Length:253

    Alignment length:249
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240         
           TRUA_THET8     1 MRRLLLLCEYDGTLFAGLQRQGRGLRTVQGELERALPGIGALPKAVAAGRTDAGVHALAMPFHVDVESAIPVEKVPEALNRLLPEDLKVVGAREVAPDFHARKDALWRAYRYRILVRPHPSPLLRHRALWVRRPLDLEAMEEALSLLLGRHNFLGFAKEETRPGERELLEARLQVAEGEAGLEVRLYFRGKSFLRGQVRGMVGTLLEVGLGKRPPESLKAILKTADRRLAGPTAPAHGLYFVEAAYPEE 249
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 1vs3B01 B:1-105  [code=3.30.70.580, no name defined]                                                     ------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) ----------------------------------------------------------------------------------------------------------------------------------------------PseudoU_synth_1-1vs3B01 B:143-247                                                                        -- Pfam domains (1)
           Pfam domains (2) ----------------------------------------------------------------------------------------------------------------------------------------------PseudoU_synth_1-1vs3B02 B:143-247                                                                        -- Pfam domains (2)
           Pfam domains (3) ----------------------------------------------------------------------------------------------------------------------------------------------PseudoU_synth_1-1vs3B03 B:143-247                                                                        -- Pfam domains (3)
           Pfam domains (4) ----------------------------------------------------------------------------------------------------------------------------------------------PseudoU_synth_1-1vs3B04 B:143-247                                                                        -- Pfam domains (4)
         Sec.struct. author .eeeeeeeee................hhhhhhhhhhhhhh.....ee........eeeeeeeeeee....hhhhhhhhhhhhh...eeeeeeeee...........eeeeeeeeee............eee....hhhhhhhhhhhhheeee.hhhh.......eeeeeeeeeeeee....eeeeeeeee.....hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh....hhh.eeeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vs3 B   1 MRRLLLLCEYDGTLFAGLQRQGRGLRTVQGELERALPGIGALPKAVAAGRTDAGVHALAMPFHVDVESAIPVEKVPEALNRLLPEDLKVVGAREVAPDFHARKDALWRAYRYRILVRPHPSPLLRHRALWVRRPLDLEAMEEALSLLLGRHNFLGFAKEETRPGERELLEARLQVAEGEAGLEVRLYFRGKSFLRGQVRGMVGTLLEVGLGKRPPESLKAILKTADRRLAGPTAPAHGLYFVEAAYPEE 249
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240
   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 1VS3)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: PseudoU_synth_1] (4)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (TRUA_THET8 | Q5SHU9)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0016853    isomerase activity    Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
    GO:0009982    pseudouridine synthase activity    Catalysis of the reaction: RNA uridine = RNA pseudouridine. Conversion of uridine in an RNA molecule to pseudouridine by rotation of the C1'-N-1 glycosidic bond of uridine in RNA to a C1'-C5.
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:0001522    pseudouridine synthesis    The intramolecular conversion of uridine to pseudouridine within an RNA molecule. This posttranscriptional base modification occurs in tRNA, rRNA, and snRNAs.
    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:0031119    tRNA pseudouridine synthesis    The intramolecular conversion of uridine to pseudouridine in a tRNA molecule.

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