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(-) Description

Title :  CRYSTAL STRUCTURE OF TRNA PSEUDOURIDINE SYNTHASE TRUB AND ITS RNA COMPLEX: RNA-PROTEIN RECOGNITION THROUGH A COMBINATION OF RIGID DOCKING AND INDUCED FIT
 
Authors :  H. Pan, S. Agarwalla, D. T. Moustakas, J. Finer-Moore, R. M. Stroud
Date :  01 Oct 03  (Deposition) - 04 Nov 03  (Release) - 16 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,C,D,E
Keywords :  Rna Modification, Pseudouridylation, Lyase-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Pan, S. Agarwalla, D. T. Moustakas, J. Finer-Moore, R. M. Stroud
Crystal Structure Of Trna Pseudouridine Synthase Trub And Its Rna Complex: Rna Recognition Through A Combination Of Rigid Docking And Induced Fit
Proc. Natl. Acad. Sci. Usa V. 100 12648 2003
PubMed-ID: 14566049  |  Reference-DOI: 10.1073/PNAS.2135585100

(-) Compounds

Molecule 1 - 5'-R(*CP*UP*GP*UP*GP*UP*(FHU) P*CP*GP*AP*UP*CP*CP*AP*CP*AP*G)-3'
    Chains: C
    Engineered: YES
    Synthetic: YES
 
Molecule 2 - 5'-R(*CP*UP*GP*UP*GP*UP*UP*CP*GP*AP*UP*CP*CP*AP*CP*AP*G)- 3'
    Chains: D, E
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - TRNA PSEUDOURIDINE SYNTHASE B
    Chains: A
    EC Number: 4.2.1.70
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET28B
    Expression System Strain: BL21DE3
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: TRUB
    Organism Scientific: THERMOTOGA MARITIMA
    Organism Taxid: 2336
    Synonym: TRNA PSEUDOURIDINE 55 SYNTHASE, PSI55 SYNTHASE, PSEUDOURIDYLATE SYNTHASE, URACIL HYDROLYASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ACDE

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1FHU1Mod. Nucleotide(5S,6R)-5-FLUORO-6-HYDROXY-PSEUDOURIDINE-5'-MONOPHOSPHATE

(-) Sites  (0, 0)

(no "Site" information available for 1R3E)

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:101 -A:193

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1R3E)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1R3E)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PUAPS50890 PUA domain profile.TRUB_THEMA229-306  1A:238-315

(-) Exons   (0, 0)

(no "Exon" information available for 1R3E)

(-) 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:305
 aligned with TRUB_THEMA | Q9WZW0 from UniProtKB/Swiss-Prot  Length:309

    Alignment length:309
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300         
           TRUB_THEMA     1 MKHGILVAYKPKGPTSHDVVDEVRKKLKTRKVGHGGTLDPFACGVLIIGVNQGTRILEFYKDLKKVYWVKMRLGLITETFDITGEVVEERECNVTEEEIREAIFSFVGEYDQVPPAYSAKKYKGERLYKLAREGKIINLPPKRVKIFKIWDVNIEGRDVSFRVEVSPGTYIRSLCMDIGYKLGCGATAVELVRESVGPHTIEESLNVFEAAPEEIENRIIPLEKCLEWLPRVVVHQESTKMILNGSQIHLEMLKEWDGFKKGEVVRVFNEEGRLLALAEAERNSSFLETLRKHERNERVLTLRKVFNTR 309
               SCOP domains d1r3ea2 A:10-237 Pseudouridine synthase II TruB                                                                                                                                                                                     d1r3ea1 A:238-318 Pseudouridine synthase II TruB, C-terminal dom    ain           SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -----------------------TruB_N-1r3eA02 A:33-180                                                                                                                             ----------------------------------------------------------PUA-1r3eA01 A:239-309                                                  --------- Pfam domains
         Sec.struct. author ...eeeeeee....hhhhhhhhhhhhh....eee........eeeeeeee.hhhhhhhhhh...eeeeeeeee.eee........eeee.....hhhhhhhhhhh..eeeee........ee..eehhhhhhh........eeeeeeeeeeeeee..eeeeeeee....hhhhhhhhhhhhh...eeeeeeeeeee..ee.hhh......hhhhhhhhhee.hhh.....eee....hhhhhh....ee.....ee.......eeeee.....eeeeeee............----.eeeeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PUA  PDB: A:238-315 UniProt: 229-306                                          --- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1r3e A  10 MKHGILVAYKPKGPTSHDVVDEVRKKLKTRKVGHGGTLDPFACGVLIIGVNQGTRILEFYKDLKKVYWVKMRLGLITETFDITGEVVEERECNVTEEEIREAIFSFVGEYDQVPPAYSAKKYKGERLYKLAREGKIINLPPKRVKIFKIWDVNIEGRDVSFRVEVSPGTYIRSLCMDIGYKLGCGATAVELVRESVGPHTIEESLNVFEAAPEEIENRIIPLEKCLEWLPRVVVHQESTKMILNGSQIHLEMLKEWDGFKKGEVVRVFNEEGRLLALAEAERNSSFLETLRK----ERVLTLRKVFNTR 318
                                    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       299 |    |309         
                                                                                                                                                                                                                                                                                                                             301  306            


Chain C from PDB  Type:RNA  Length:17
                                                 
                 1r3e C 404 CUGUGUuCGAUCCACAG 420
                                  |413       
                                410-FHU      


Chain D from PDB  Type:RNA  Length:17
                                                 
                 1r3e D 404 CUGUGUUCGAUCCACAG 420
                                   413       


Chain E from PDB  Type:RNA  Length:17
                                                 
                 1r3e E 404 CUGUGUUCGAUCCACAG 420
                                   413
   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)
  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  (2, 2)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1R3E)

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: PUA (42)
(-)
Family: PUA (12)
(-)
Clan: no clan defined [family: TruB_N] (12)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (TRUB_THEMA | Q9WZW0)
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:0006396    RNA processing    Any process involved in the conversion of one or more primary RNA transcripts into one or more mature RNA molecules.
    GO:1990481    mRNA pseudouridine synthesis    The intramolecular conversion of uridine to pseudouridine in an mRNA molecule.
    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:0006400    tRNA modification    The covalent alteration of one or more nucleotides within a tRNA molecule to produce a tRNA molecule with a sequence that differs from that coded genetically.
    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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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        TRUB_THEMA | Q9WZW0: 1ze1 1ze2 2ab4

(-) Related Entries Specified in the PDB File

1r3f CRYSTAL STRUCTURE OF TRNA PSEUDOURIDINE SYNTHASE TRUB AND ITS RNA COMPLEX: RNA-PROTEIN RECOGNITION THROUGH A COMBINATION OF RIGID DOCKING AND INDUCED FIT