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(-) Description

Title :  STRUCTURE OF THE CATALYTIC DOMAIN OF 23S RRNA PSEUDOURIDINE SYNTHASE RLUD
 
Authors :  M. Del Campo, J. Ofengand, A. Malhotra
Date :  12 Sep 03  (Deposition) - 09 Dec 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Catalytic Domain, Rlud, Pseudouridine Synthase, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Del Campo, J. Ofengand, A. Malhotra
Crystal Structure Of The Catalytic Domain Of Rlud, The Only Rrna Pseudouridine Synthase Required For Normal Growth Of Escherichia Coli
Rna V. 10 231 2004
PubMed-ID: 14730022  |  Reference-DOI: 10.1261/RNA.5187404
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RIBOSOMAL LARGE SUBUNIT PSEUDOURIDINE SYNTHASE D
    Chains: A
    EC Number: 4.2.1.70
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET28A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: CATALYTIC DOMAIN
    Gene: RLUD
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: E. COLI 23S RNA PSEUDOURIDINE SYNTHASE RLUD

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 9)

Asymmetric/Biological Unit (1, 9)
No.NameCountTypeFull Name
1MSE9Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 1QYU)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PSI_RLUPS01129 Rlu family of pseudouridine synthase signature.RLUD_ECOLI135-149  1A:135-149

(-) Exons   (0, 0)

(no "Exon" information available for 1QYU)

(-) 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:250
 aligned with RLUD_ECOLI | P33643 from UniProtKB/Swiss-Prot  Length:326

    Alignment length:250
                                    86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326
           RLUD_ECOLI    77 FEPQDIPLDIVYEDEDIIIINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREYEAVAIGHMTAGGTVDEPISRHPTKRTHMAVHPMGKPAVTHYRIMEHFRVHTRLRLRLETGRTHQIRVHMAHITHPLVGDPVYGGRPRPPKGASEAFISTLRKFDRQALHATMLRLYHPISGIEMEWHAPIPQDMVELIEVMRADFEEHKDEVDWL 326
               SCOP domains d1qyua_ A: Ribosomal large subunit pseudouridine synthase D, RluD                                                                                                                                                                                          SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------PseudoU_synth_2-1qyuA01 A:92-242                                                                                                                       ------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........eeee...eeeeee...............hhhhhhhhhhhhhhhhhhhhh........eeeeeee.hhhhhhhhhhhhhh...eeeeeeeee......eeee..eee.......eee.......eeeeeeeee...eeeeeeee.....hhhhhhhhhh....................hhhhhhhhhhh....eeeeeeeee......eeeee...hhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------PSI_RLU        --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qyu A  77 FEPQDIPLDIVYEDEDIIIINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLmVVAKTVPAQTRLVESLQRREITREYEAVAIGHmTAGGTVDEPISRHPTKRTHmAVHPMGKPAVTHYRImEHFRVHTRLRLRLETGRTHQIRVHmAHITHPLVGDPVYGGRPRPPKGASEAFISTLRKFDRQALHATmLRLYHPISGIEmEWHAPIPQDmVELIEVmRADFEEHKDEVDWL 326
                                    86        96       106       116       126       136       146       156       166       176  |    186       196  |    206       216       226       236   |   246       256       266       276      |286       296       306     | 316       326
                                                                                               146-MSE                          179-MSE             199-MSE         215-MSE                  240-MSE                                    283-MSE     295-MSE   305-MSE  |              
                                                                                                                                                                                                                                                                     312-MSE
   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  (1, 1)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: PseudoU_synth_2] (8)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RLUD_ECOLI | P33643)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0019239    deaminase activity    Catalysis of the removal of an amino group from a substrate, producing ammonia (NH3).
    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:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    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:0000455    enzyme-directed rRNA pseudouridine synthesis    The intramolecular conversion of uridine to pseudouridine during ribosome biogenesis where the enzyme specifies the site that becomes pseudouridylated without using a guide RNA.
    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:0000027    ribosomal large subunit assembly    The aggregation, arrangement and bonding together of constituent RNAs and proteins to form the large ribosomal subunit.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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 Related Entries

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

UniProtKB/Swiss-Prot
        RLUD_ECOLI | P33643: 1prz 1v9f 2ist

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