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(-) Description

Title :  CRYSTAL STRUCTURE OF CATALYTIC DOMAIN OF PSEUDOURIDINE SYNTHASE RLUD FROM ESCHERICHIA COLI
 
Authors :  K. Mizutani, Y. Machida, S. Unzai, S. -Y. Park, J. R. H. Tame
Date :  26 Jan 04  (Deposition) - 18 May 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A
Keywords :  Pseudouridine Synthase, Rna Binding, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Mizutani, Y. Machida, S. Unzai, S. -Y. Park, J. R. H. Tame
Crystal Structures Of The Catalytic Domains Of Pseudouridine Synthases Rluc And Rlud From Escherichia Coli
Biochemistry V. 43 4454 2004
PubMed-ID: 15078091  |  Reference-DOI: 10.1021/BI036079C
(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: PET28B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: RLUD
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: PSEUDOURIDYLATE SYNTHASE, URACIL HYDROLYASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1PO41Ligand/IonPHOSPHATE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:139 , LYS A:140 , HIS A:234 , ARG A:237 , HOH A:409 , HOH A:412 , HOH A:425 , HOH A:437 , HOH A:444 , HOH A:462 , HOH A:483 , HOH A:513BINDING SITE FOR RESIDUE PO4 A 400

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1V9F)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1V9F)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1V9F)

(-) 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 1V9F)

(-) 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 d1v9fa_ A: Ribosomal large subunit pseudouridine synthase D, RluD                                                                                                                                                                                          SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------PseudoU_synth_2-1v9fA01 A:92-242                                                                                                                       ------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........eeee...eeeeee...............hhhhhhhhhhhhhhhhhhhhh........eeeeeee.hhhhhhhhhhhhhh...eeeeeeeee......eeee..eee.......eee.......eeeeeeeee...eeeeeeee.....hhhhhhhhhh....................hhhhhhhhhhh....eeeeeeeee......eeeee...hhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------PSI_RLU        --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1v9f 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
   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 1V9F)

(-) 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 1qyu 2ist

(-) Related Entries Specified in the PDB File

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