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(-) Description

Title :  CRYSTAL STRUCTURE OF PSEUDOURIDYLATE SYNTHASE
 
Authors :  Structural Genomix
Date :  01 Dec 03  (Deposition) - 30 Dec 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.59
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Matte, G. V. Louie, J. Sivaraman, M. Cygler, S. K. Burley
Structure Of The Pseudouridine Synthase Rsua From Haemophilus Influenzae.
Acta Crystallogr. , Sect. F V. 61 350 2005
PubMed-ID: 16511038  |  Reference-DOI: 10.1107/S1744309105005920
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RIBOSOMAL SMALL SUBUNIT PSEUDOURIDINE SYNTHASE A
    Chains: A, B
    EC Number: 4.2.1.70
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: RSUA, HI1243
    Organism Scientific: HAEMOPHILUS INFLUENZAE
    Organism Taxid: 727
    Synonym: 16S PSEUDOURIDYLATE 516 SYNTHASE, 16S PSEUDOURIDINE 516 SYNTHASE, URACIL HYDROLYASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1BU14Ligand/Ion1,4-BUTANEDIOL

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:59 , GLN A:61 , LEU A:91 , HOH A:340 , HOH A:455 , HOH A:472 , ARG B:220 , HOH B:287 , HOH B:331BINDING SITE FOR RESIDUE BU1 A 242
2AC2SOFTWAREASP A:102 , THR A:105 , TYR A:132 , GLN A:185 , VAL A:186 , HOH A:255 , HOH A:359BINDING SITE FOR RESIDUE BU1 A 243
3AC3SOFTWAREASP A:104 , THR A:105 , LYS A:187 , LEU A:200 , HOH A:394BINDING SITE FOR RESIDUE BU1 A 244
4AC4SOFTWAREASN A:175 , HIS A:201 , HOH A:262 , HOH A:521BINDING SITE FOR RESIDUE BU1 A 245

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Tyr A:89 -Pro A:90
2Tyr B:89 -Pro B:90

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1S4PS50889 S4 RNA-binding domain profile.RSUA_HAEIN1-68
 		  2A:2-68
B:2-68
2PSI_RSUPS01149 Rsu family of pseudouridine synthase signature.RSUA_HAEIN99-113
 		  2A:99-113
B:99-113

(-) Exons   (0, 0)

(no "Exon" information available for 1VIO)

(-) 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:230
 aligned with RSUA_HAEIN | P45124 from UniProtKB/Swiss-Prot  Length:232

    Alignment length:232
                             1                                                                                                                                                                                                                                      
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229  
           RSUA_HAEIN     - -MRLDKFIAENVGLTRSQATKAIRQSAVKINGEIVKSGSVQISQEDEIYFEDELLTWIEEGQYFMLNKPQGCVCSNDDGDYPTIYQFFDYPLAGKLHSAGRLDVDTTGLVLLTDDGQWSHRITSPKHHCEKTYLVTLADPVEENYSAACAEGILLRGEKEPTKPAKLEILDDYNVNLTISEGRYHQVKRMFAALGNKVVGLHRWKIGDVVLDESLEEGEYRPLTQSEIEKLV 231
               SCOP domains d1vioa2 A:0-57                                            d1vioa1 A:58-231 Ri  bosomal small subunit pseudouridine 516 synthase RsuA                                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eehhhhhhhhhh.hhhhhhhhhhh..eee..ee......ee.....eee..ee........eeeeee.........--...hhhhhh..hhhhhhee........eeeeeee.hhhhhhhhhh......eeeeeee......hhhhhhhhh.............eeee....eeeeee.....hhhhhhhhhh...eeeeeeeee..ee.........eee.hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -S4  PDB: A:2-68 UniProt: 1-68                                       ------------------------------PSI_RSU        ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vio A   0 SLRLDKFIAENVGLTRSQATKAIRQSAVKINGEIVKSGSVQISQEDEIYFEDELLTWIEEGQYFMLNKPQGCVCSND--DYPTIYQFFDYPLAGKLHSAGRLDVDTTGLVLLTDDGQWSHRITSPKHHCEKTYLVTLADPVEENYSAACAEGILLRGEKEPTKPAKLEILDDYNVNLTISEGRYHQVKRMFAALGNKVVGLHRWKIGDVVLDESLEEGEYRPLTQSEIEKLV 231
                                     9        19        29        39        49        59        69      | 79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229  
                                                                                                       76 79                                                                                                                                                        


Chain B from PDB  Type:PROTEIN  Length:230
 aligned with RSUA_HAEIN | P45124 from UniProtKB/Swiss-Prot  Length:232

    Alignment length:232
                             1                                                                                                                                                                                                                                      
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229  
           RSUA_HAEIN     - -MRLDKFIAENVGLTRSQATKAIRQSAVKINGEIVKSGSVQISQEDEIYFEDELLTWIEEGQYFMLNKPQGCVCSNDDGDYPTIYQFFDYPLAGKLHSAGRLDVDTTGLVLLTDDGQWSHRITSPKHHCEKTYLVTLADPVEENYSAACAEGILLRGEKEPTKPAKLEILDDYNVNLTISEGRYHQVKRMFAALGNKVVGLHRWKIGDVVLDESLEEGEYRPLTQSEIEKLV 231
               SCOP domains d1viob2 B:0-57                                            d1viob1 B:58-231 Ri  bosomal small subunit pseudouridine 516 synthase RsuA                                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --S4-1vioB01 B:2-47                             -------------PseudoU_synth_2-  1vioB03 B:61-192                                                                                                  --------------------------------------- Pfam domains (1)
           Pfam domains (2) --S4-1vioB02 B:2-47                             -------------PseudoU_synth_2-  1vioB04 B:61-192                                                                                                  --------------------------------------- Pfam domains (2)
         Sec.struct. author .eehhhhhhhhhh.hhhhhhhhhhh..eee..ee......ee.....eee..eee.......eeeeee.........--...hhhhhh...hhhhhee........eeeeeee.hhhhhhhhhhhhhh..eeeeeee......hhhhhhhhh.............eeee....eeeeee.....hhhhhhhhhh...eeeeeeeee..ee.........eee.hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -S4  PDB: B:2-68 UniProt: 1-68                                       ------------------------------PSI_RSU        ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vio B   0 SLRLDKFIAENVGLTRSQATKAIRQSAVKINGEIVKSGSVQISQEDEIYFEDELLTWIEEGQYFMLNKPQGCVCSND--DYPTIYQFFDYPLAGKLHSAGRLDVDTTGLVLLTDDGQWSHRITSPKHHCEKTYLVTLADPVEENYSAACAEGILLRGEKEPTKPAKLEILDDYNVNLTISEGRYHQVKRMFAALGNKVVGLHRWKIGDVVLDESLEEGEYRPLTQSEIEKLV 231
                                     9        19        29        39        49        59        69      | 79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229  
                                                                                                       76 79
   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  (2, 4)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (2, 4)

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

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (RSUA_HAEIN | P45124)
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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