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(-) Description

Title :  CRYSTAL STRUCTURE OF E. COLI PSEUDOURIDINE SYNTHASE RLUE
 
Authors :  H. Pan, J. D. Ho, R. M. Stroud, J. Finer-Moore
Date :  22 Jan 07  (Deposition) - 13 Mar 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.20
Chains :  Asym./Biol. Unit :  A
Keywords :  Bifurcated Beta Sheet, Thrombin-Cleaved, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Pan, J. D. Ho, R. M. Stroud, J. Finer-Moore
The Crystal Structure Of E. Coli Rrna Pseudouridine Synthase Rlue.
J. Mol. Biol. V. 367 1459 2007
PubMed-ID: 17320904  |  Reference-DOI: 10.1016/J.JMB.2007.01.084
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RIBOSOMAL LARGE SUBUNIT PSEUDOURIDINE SYNTHASE E
    Chains: A
    EC Number: 5.4.99.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET-28B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: CATALYTIC DOMAIN
    Gene: RLUE
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: RRNA-URIDINE ISOMERASE E, RRNA PSEUDOURIDYLATE SYNTHASE E

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 6)

Asymmetric/Biological Unit (1, 6)
No.NameCountTypeFull Name
1SO46Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:53 , PHE A:54 , THR A:55 , THR A:130 , HIS A:186 , HOH A:2011 , HOH A:2013 , HOH A:2014 , HOH A:2015BINDING SITE FOR RESIDUE SO4 A 1423
2AC2SOFTWAREARG A:77 , LEU A:78 , ASP A:79 , SER A:82 , TYR A:109 , HOH A:2030 , HOH A:2041 , HOH A:2044 , HOH A:2197BINDING SITE FOR RESIDUE SO4 A 1424
3AC3SOFTWARELEU A:131 , ASN A:132 , ARG A:182 , HOH A:2056 , HOH A:2064 , HOH A:2089 , HOH A:2209BINDING SITE FOR RESIDUE SO4 A 1425
4AC4SOFTWAREPRO A:101 , GLY A:102 , GLU A:174 , GLY A:175 , HOH A:2060 , HOH A:2077 , HOH A:2085 , HOH A:2107 , HOH A:2125BINDING SITE FOR RESIDUE SO4 A 1426
5AC5SOFTWAREGLN A:119 , ARG A:126 , HOH A:2063 , HOH A:2068BINDING SITE FOR RESIDUE SO4 A 1427
6AC6SOFTWARETYR A:48 , ARG A:153 , ARG A:158 , ARG A:181 , LEU A:192 , HOH A:2123 , HOH A:2149 , HOH A:2170BINDING SITE FOR RESIDUE SO4 A 1428

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2OML)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Asn A:154 -Pro A:155

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2OML)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PSI_RSUPS01149 Rsu family of pseudouridine synthase signature.RLUE_ECOLI76-90  1A:76-90

(-) Exons   (0, 0)

(no "Exon" information available for 2OML)

(-) 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:181
 aligned with RLUE_ECOLI | P75966 from UniProtKB/Swiss-Prot  Length:217

    Alignment length:182
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215  
           RLUE_ECOLI    36 NQPTRVILFNKPYDVLPQFTDEAGRKTLKEFIPVQGVYAAGRLDRDSEGLLVLTNNGALQARLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVDEPAWLWPRNPPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLANGEWREVTD 217
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeee...............hhhhh......ee........eeeeeee.hhhhhhhhhh......eeeeeeee...hhhhhhhhhhh.ee..ee....eeeee..............-.....eeeeeeee.....hhhhhhhhhh...eeeeeeeee..ee........eee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------PSI_RSU        ------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2oml A  36 NQPTRVILFNKPYDVLPQFTDEAGRKTLKEFIPVQGVYAAGRLDRDSEGLLVLTNNGALQARLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVDEPAWLWPRNPPIR-RKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLANGEWREVTD 217
                                    45        55        65        75        85        95       105       115       125       135       145       155  | |  165       175       185       195       205       215  
                                                                                                                                                    158 |                                                         
                                                                                                                                                      160
   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 2OML)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2OML)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2OML)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RLUE_ECOLI | P75966)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0016866    intramolecular transferase activity    Catalysis of the transfer of a functional group from one position to another within a single molecule.
    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: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.
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
        RLUE_ECOLI | P75966: 2olw

(-) Related Entries Specified in the PDB File

2olw FULL LENGTH E. COLI RLUE, 2 MOLECULES PER ASYMMETRIC UNIT, N-TERMINAL 37 AMINO ACIDS ARE DISORDERED