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(-) Description

Title :  STRUCTURE OF RSUA
 
Authors :  J. Sivaraman, V. Sauve, R. Larocque, E. A. Stura, J. D. Schrag, M. Cygler, A. Matte
Date :  13 Jan 02  (Deposition) - 24 Apr 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Crystal Structure, Pseudouridine Synthase, Rsua, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Sivaraman, V. Sauve, R. Larocque, E. A. Stura, J. D. Schrag, M. Cygler, A. Matte
Structure Of The 16S Rrna Pseudouridine Synthase Rsua Bound To Uracil And Ump.
Nat. Struct. Biol. V. 9 353 2002
PubMed-ID: 11953756
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RIBOSOMAL SMALL SUBUNIT PSEUDOURIDINE SYNTHASE A
    Chains: A
    EC Number: 4.2.1.70
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: DL41
    Expression System Taxid: 562
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: 16S PSEUDOURIDYLATE 516 SYNTHASE, 16S PSEUDOURIDINE 516 SYNTHASE, URACIL HYDROLYASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric/Biological Unit (2, 5)
No.NameCountTypeFull Name
1MSE4Mod. Amino AcidSELENOMETHIONINE
2URA1Ligand/IonURACIL

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:102 , THR A:105 , TYR A:132 , HIS A:184 , GLN A:185 , VAL A:186BINDING SITE FOR RESIDUE URA A 232

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1S4PS50889 S4 RNA-binding domain profile.RSUA_ECOLI1-68  1A:1-68
2PSI_RSUPS01149 Rsu family of pseudouridine synthase signature.RSUA_ECOLI99-113  1A:99-113

(-) Exons   (0, 0)

(no "Exon" information available for 1KSK)

(-) 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:234
 aligned with RSUA_ECOLI | P0AA43 from UniProtKB/Swiss-Prot  Length:231

    Alignment length:234
                               1                                                                                                                                                                                                                                      
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227    
           RSUA_ECOLI     - ---MRLDKFIAQQLGVSRAIAGREIRGNRVTVDGEIVRNAAFKLLPEHDVAYDGNPLAQQHGPRYFMLNKPQGYVCSTDDPDHPTVLYFLDEPVAWKLHAAGRLDIDTTGLVLMTDDGQWSHRITSPRHHCEKTYLVTLESPVADDTAEQFAKGVQLHNEKDLTKPAVLEVITPTQVRLTISEGRYHQVKRMFAAVGNHVVELHRERIGGITLDADLAPGEYRPLTEEEIASVV 231
               SCOP domains ---d1kska3 A:1-59                                             d1kska4 A:60-231 Ribosomal small subunit pseudouridine 516 synthase RsuA                                                                                                     SCOP domains
               CATH domains 1kskA01 A:1A-63                                                   ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ---S4-1kskA01 A:1-47                              -------------PseudoU_synth_2-1kskA02 A:61-192                                                                                                    --------------------------------------- Pfam domains
         Sec.struct. author ...eehhhhhhhhhh.hhhhhhhhhhh.......ee......ee.....eee..eee.......eeeeee..............hhhhhh...hhhhhee........eeeeeee.hhhhhhhhhh......eeeeeee......hhhhhhhhh.............eeeeee..eeeeee.....hhhhhhhhhh...eeeeeeeee..ee.........eee.hhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---S4  PDB: A:1-68 UniProt: 1-68                                       ------------------------------PSI_RSU        ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1ksk A  1A GSHmRLDKFIAQQLGVSRAIAGREIRGNRVTVDGEIVRNAAFKLLPEHDVAYDGNPLAQQHGPRYFmLNKPQGYVCSTDDPDHPTVLYFLDEPVAWKLHAAGRLDIDTTGLVLmTDDGQWSHRITSPRHHCEKTYLVTLESPVADDTAEQFAKGVQLHNEKDLTKPAVLEVITPTQVRLTISEGRYHQVKRmFAAVGNHVVELHRERIGGITLDADLAPGEYRPLTEEEIASVV 231
                            ||||     7        17        27        37        47        57      | 67        77        87        97       107   |   117       127       137       147       157       167       177       187 |     197       207       217       227    
                            ||||                                                             64-MSE                                        111-MSE                                                                       189-MSE                                      
                           1A|||                                                                                                                                                                                                                                      
                            1B||                                                                                                                                                                                                                                      
                             1C|                                                                                                                                                                                                                                      
                               1-MSE
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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  (2, 2)

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

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: S4 (23)
(-)
Clan: no clan defined [family: PseudoU_synth_2] (8)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RSUA_ECOLI | P0AA43)
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: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.
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
        RSUA_ECOLI | P0AA43: 1ksl 1ksv

(-) Related Entries Specified in the PDB File

1ksl STRUCTURE OF RSUA
1ksv STRUCTURE OF RSUA