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(-) Description

Title :  CRYSTAL STRUCTURE OF PSEUDOURIDINE SYNTHASE RLUD CATALYTIC MODULE
 
Authors :  J. Sivaraman, P. Iannuzzi, M. Cygler, A. Matte, Montreal-Kingston Bacterial Structural Genomics Initiative (Bsgi)
Date :  20 Jun 03  (Deposition) - 04 Nov 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Crystal Structure, Pseudouridine Synthase, Rlud, Montreal- Kingston Bacterial Structural Genomics Initiative, Bsgi, Structural Genomics, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Sivaraman, P. Iannuzzi, M. Cygler, A. Matte
Crystal Structure Of The Rlud Pseudouridine Synthase Catalytic Module, An Enzyme That Modifies 23S Rrna And Is Essential For Normal Cell Growth Of Escherichia Coli
J. Mol. Biol. V. 335 87 2003
PubMed-ID: 14659742  |  Reference-DOI: 10.1016/J.JMB.2003.10.003
(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
    Expression System Strain: DL41
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: CATALYTIC DOMAIN
    Gene: RLUD OR SFHB
    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, 10)

Asymmetric/Biological Unit (1, 10)
No.NameCountTypeFull Name
1MSE10Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 1PRZ)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PSI_RLUPS01129 Rlu family of pseudouridine synthase signature.RLUD_ECO57135-149  1A:135-149
RLUD_ECOLI135-149  1A:135-149

(-) Exons   (0, 0)

(no "Exon" information available for 1PRZ)

(-) 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:252
 aligned with RLUD_ECO57 | Q8X9F0 from UniProtKB/Swiss-Prot  Length:326

    Alignment length:252
                                    84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324  
           RLUD_ECO57    75 ARFEPQDIPLDIVYEDEDIIVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREYEAVAIGHMTAGGTVDEPISRHPTKRTHMAVHPMGKPAVTHYRIMEHFRVHTRLRLRLETGRTHQIRVHMAHITHPLVGDPVYGGRPRPPKGASEAFISTLRKFDRQALHATMLRLYHPISGIEMEWHAPIPQDMVELIEVMRADFEEHKDEVDWL 326
               SCOP domains d1prza_ A: Ribosomal large subunit pseudouridine synthase D, RluD                                                                                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains -----------------PseudoU_synth_2-1przA01 A:92-242                                                                                                                       ------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...........eeee...eeeeee...............hhhhhhhhhhhhhhhhhhhhh........eeeeeee.hhhhhhhhhhhhhh...eeeeeeeee......eeee..eee.......eee.......eeeeeeeee...eeeeeeee.....hhhhhhhhhh....................hhhhhhhhhhh....eeeeeeeee......eeeee...hhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------PSI_RLU        --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1prz A  75 ARFEPQDIPLDIVYEDEDIIVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLmVVAKTVPAQTRLVESLQRREITREYEAVAIGHmTAGGTVDEPISRHPTKRTHmAVHPmGKPAVTHYRImEHFRVHTRLRLRLETGRTHQIRVHmAHITHPLVGDPVYGGRPRPPKGASEAFISTLRKFDRQALHATmLRLYHPISGIEmEWHAPIPQDmVELIEVmRADFEEHKDEVDWL 326
                                    84        94       104       114       124       134       144 |     154       164       174    |  184       194    |  204       214|      224       234     | 244       254       264       274       284       294|      304|      314       324  
                                                                                                 146-MSE                          179-MSE             199-MSE|        215-MSE                  240-MSE                                    283-MSE     295-MSE   305-MSE  |              
                                                                                                                                                           204-MSE                                                                                                     312-MSE          


Chain A from PDB  Type:PROTEIN  Length:252
 aligned with RLUD_ECOLI | P33643 from UniProtKB/Swiss-Prot  Length:326

    Alignment length:252
                                    84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324  
           RLUD_ECOLI    75 ARFEPQDIPLDIVYEDEDIIIINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREYEAVAIGHMTAGGTVDEPISRHPTKRTHMAVHPMGKPAVTHYRIMEHFRVHTRLRLRLETGRTHQIRVHMAHITHPLVGDPVYGGRPRPPKGASEAFISTLRKFDRQALHATMLRLYHPISGIEMEWHAPIPQDMVELIEVMRADFEEHKDEVDWL 326
               SCOP domains d1prza_ A: Ribosomal large subunit pseudouridine synthase D, RluD                                                                                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains -----------------PseudoU_synth_2-1przA01 A:92-242                                                                                                                       ------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...........eeee...eeeeee...............hhhhhhhhhhhhhhhhhhhhh........eeeeeee.hhhhhhhhhhhhhh...eeeeeeeee......eeee..eee.......eee.......eeeeeeeee...eeeeeeee.....hhhhhhhhhh....................hhhhhhhhhhh....eeeeeeeee......eeeee...hhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (2) ------------------------------------------------------------PSI_RLU        --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1prz A  75 ARFEPQDIPLDIVYEDEDIIVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLmVVAKTVPAQTRLVESLQRREITREYEAVAIGHmTAGGTVDEPISRHPTKRTHmAVHPmGKPAVTHYRImEHFRVHTRLRLRLETGRTHQIRVHmAHITHPLVGDPVYGGRPRPPKGASEAFISTLRKFDRQALHATmLRLYHPISGIEmEWHAPIPQDmVELIEVmRADFEEHKDEVDWL 326
                                    84        94       104       114       124       134       144 |     154       164       174    |  184       194    |  204       214|      224       234     | 244       254       264       274       284       294|      304|      314       324  
                                                                                                 146-MSE                          179-MSE             199-MSE|        215-MSE                  240-MSE                                    283-MSE     295-MSE   305-MSE  |              
                                                                                                                                                           204-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 1PRZ)

(-) Pfam Domains  (1, 1)

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

(-) Gene Ontology  (11, 17)

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.

Chain A   (RLUD_ECO57 | Q8X9F0)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    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: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.

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  1prz
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  RLUD_ECOLI | P33643
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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

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