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(-) Description

Title :  STRUCTURE OF A FUNCTIONAL RIBONUCLEOPROTEIN PSEUDOURIDINE SYNTHASE BOUND TO A SUBSTRATE RNA
 
Authors :  B. Liang, J. Zhou, E. Kahen, R. M. Terns, M. P. Terns, H. Li
Date :  22 May 09  (Deposition) - 23 Jun 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.65
Chains :  Asym./Biol. Unit :  A,B,C,D,E
Keywords :  Protein-Rna Complex, Box H/Aca, Ribonucleoprotein Particles, Rnp, Pseudouridine Synthase, Pseudouridylase, Pseudouridylation, Rna Editing, Post-Transcriptional Modification, Isomerase, Trna Processing, Ribonucleoprotein, Ribosome Biogenesis, Rrna Processing, Isomerase-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Liang, J. Zhou, E. Kahen, R. M. Terns, M. P. Terns, H. Li
Structure Of A Functional Ribonucleoprotein Pseudouridine Synthase Bound To A Substrate Rna
Nat. Struct. Mol. Biol. V. 16 740 2009
PubMed-ID: 19478803  |  Reference-DOI: 10.1038/NSMB.1624

(-) Compounds

Molecule 1 - PSEUDOURIDINE SYNTHASE CBF5
    Chains: A
    EC Number: 5.4.99.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21 CODON PLUS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: CBF5
    Gene: PF1785
    Organism Scientific: PYROCOCCUS FURIOSUS
    Organism Taxid: 2261
    Strain: DSM 3638
    Synonym: TRNA PSEUDOURIDINE 55 SYNTHASE, PSI55 SYNTHASE, TRNA-URIDINE ISOMERASE, TRNA PSEUDOURIDYLATE SYNTHASE
 
Molecule 2 - RIBOSOME BIOGENESIS PROTEIN NOP10
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21 CODON PLUS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: NOP10
    Gene: PF1141
    Organism Scientific: PYROCOCCUS FURIOSUS
    Organism Taxid: 2261
    Strain: DSM 3638
 
Molecule 3 - 5'-R(*GP*GP*GP*CP*UP*CP*CP*GP*GP*AP*AP*AP*CP*CP*GP*CP*GP*GP *CP*GP*C)-3'
    Chains: C
    Engineered: YES
    Fragment: GUIDE RNA_A
    Synthetic: YES
 
Molecule 4 - RNA (25-MER)
    Chains: D
    Engineered: YES
    Fragment: GUIDE RNA_B
    Synthetic: YES
 
Molecule 5 - 5'-R(*GP*GP*AP*GP*CP*GP*UP*GP*CP*GP*GP*UP*UP*U)-3'
    Chains: E
    Engineered: YES
    Fragment: SUBSTRATE RNA
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345
Asymmetric/Biological Unit : ABCDE

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3HJY)

(-) Sites  (0, 0)

(no "Site" information available for 3HJY)

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1B:8 -B:20
2B:11 -B:23

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3HJY)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3HJY)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PUAPS50890 PUA domain profile.TRUB_PYRFU250-325  1A:253-328

(-) Exons   (0, 0)

(no "Exon" information available for 3HJY)

(-) 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:320
 aligned with TRUB_PYRFU | Q7LWY0 from UniProtKB/Swiss-Prot  Length:340

    Alignment length:327
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       
           TRUB_PYRFU     8 RILPADIKREVLIKDENAETNPDWGFPPEKRPIEMHIQFGVINLDKPPGPTSHEVVAWIKKILNLEKAGHGGTLDPKVSGVLPVALEKATRVVQALLPAGKEYVALMHLHGDVPEDKIIQVMKEFEGEIIQRPPLRSAVKRRLRTRKVYYIEVLEIEGRDVLFRVGVEAGTYIRSLIHHIGLALGVGAHMSELRRTRSGPFKEDETLITLHDLVDYYYFWKEDGIEEYFRKAIQPMEKAVEHLPKVWIKDSAVAAVTHGADLAVPGIAKLHAGIKRGDLVAIMTLKDELVALGKAMMTSQEMLEKTKGIAVDVEKVFMPRDWYPKLW 334
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eee..................hhhhhhhheeeeeee....hhhhhhhhhhhhh....eee........eeeeeeee.hhhhhhhhhh...eeeeeeeee....hhhhhhhhhh...eeee.....-------..eeeeeeeeeeeee..eeeeeeee....hhhhhhhhhhhhh...eeeeeeeeeee.........eehhhhhhhhhhhhh...hhhhhhheee.hhhh....eeeehhhhhhhhhh...ee...eeeee.......eeeee.....eeeeeee..hhhhhhhh...eeeeeeee........... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PUA  PDB: A:253-328 UniProt: 250-325                                        --------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hjy A  11 RILPADIKREVLIKDENAETNPDWGFPPEKRPIEMHIQFGVINLDKPPGPTSHEVVAWIKKILNLEKAGHGGTLDPKVSGVLPVALEKATRVVQALLPAGKEYVALMHLHGDVPEDKIIQVMKEFEGEIIQRPPL-------LRTRKVYYIEVLEIEGRDVLFRVGVEAGTYIRSLIHHIGLALGVGAHMSELRRTRSGPFKEDETLITLHDLVDYYYFWKEDGIEEYFRKAIQPMEKAVEHLPKVWIKDSAVAAVTHGADLAVPGIAKLHAGIKRGDLVAIMTLKDELVALGKAMMTSQEMLEKTKGIAVDVEKVFMPRDWYPKLW 337
                                    20        30        40        50        60        70        80        90       100       110       120       130       140    |    -  |    160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       
                                                                                                                                                                145     153                                                                                                                                                                                        


Chain B from PDB  Type:PROTEIN  Length:53
 aligned with NOP10_PYRFU | Q8U1R4 from UniProtKB/Swiss-Prot  Length:60

    Alignment length:53
                                    12        22        32        42        52   
          NOP10_PYRFU     3 FRIRKCPKCGRYTLKEVCPVCGEKTKVAHPPRFSPEDPYGEYRRRWKREVLGI  55
               SCOP domains ----------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------- Pfam domains
         Sec.struct. author ...ee....................ee...........hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------- Transcript
                 3hjy B   3 FRIRKCPKCGRYTLKEVCPVCGEKTKVAHPPRFSPEDPYGEYRRRWKREVLGI  55
                                    12        22        32        42        52   


Chain C from PDB  Type:RNA  Length:21
                                                     
                 3hjy C   1 GGGCUCCGGAAACCGCGGCGC  21
                                    10        20 


Chain D from PDB  Type:RNA  Length:25
                                                         
                 3hjy D   1 GCGCUUCGCUCCCGGAGCCCACACU  25
                                    10        20     


Chain E from PDB  Type:RNA  Length:14
                                              
                 3hjy E   4 GGAGCGUGCGGUUU  17
                                    13
   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  (0, 0)

(no "SCOP Domain" information available for 3HJY)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3HJY)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3HJY)

(-) Gene Ontology  (12, 13)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (TRUB_PYRFU | Q7LWY0)
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: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.

Chain B   (NOP10_PYRFU | Q8U1R4)
molecular function
    GO:0030515    snoRNA binding    Interacting selectively and non-covalently with small nucleolar RNA.
biological process
    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:0006364    rRNA processing    Any process involved in the conversion of a primary ribosomal RNA (rRNA) transcript into one or more mature rRNA molecules.
    GO:0042254    ribosome biogenesis    A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of ribosome subunits; includes transport to the sites of protein synthesis.
cellular component
    GO:0030529    intracellular ribonucleoprotein complex    An intracellular macromolecular complex containing both protein and RNA molecules.

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  TRUB_PYRFU | Q7LWY0
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 Related Entries

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

UniProtKB/Swiss-Prot
        NOP10_PYRFU | Q8U1R4: 2ey4 2hvy 2rfk 3hax 3hay 3hjw 3lwo 3lwp 3lwq 3lwr 3lwv 3mqk
        TRUB_PYRFU | Q7LWY0: 2ey4 2hvy 2rfk 3hax 3hay 3hjw 3lwo 3lwp 3lwq 3lwr 3lwv 3mqk

(-) Related Entries Specified in the PDB File

3hjw CBF5, NOP10, L7AE AND FULL-LENGTH PF9_PF6 COMPOSITE GUIDE RNA COMPLEXED WITH THE SUBSTRATE RNA, CONTAINING 5- FLUORURIDINE AT THE MODIFICATION POSITION