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(-) Description

Title :  DISSECTING THE ROLES OF A STRICTLY CONSERVED TYROSINE IN SUBSTRATE RECOGNITION AND CATALYSIS BY PSEUDOURIDINE 55 SYNTHASE
 
Authors :  K. Phannachet, Y. Elias, R. H. Huang
Date :  14 Jul 05  (Deposition) - 13 Dec 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Rna Modifications, Isomerase/Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Phannachet, Y. Elias, R. H. Huang
Dissecting The Roles Of A Strictly Conserved Tyrosine In Substrate Recognition And Catalysis By Pseudouridine 55 Synthase.
Biochemistry V. 44 15488 2005
PubMed-ID: 16300397  |  Reference-DOI: 10.1021/BI050961W
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5'-R(*CP*CP*AP*CP*GP*GP*UP*(FHU) P*CP*GP*AP*AP*UP*CP*CP*GP*UP*GP*GP*C)-3'
    Chains: B
    Engineered: YES
    Synthetic: YES
 
Molecule 2 - TRNA PSEUDOURIDINE SYNTHASE B
    Chains: A
    EC Number: 5.4.99.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PLM1-Y55S-Y67F
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: TRUB
    Mutation: YES
    Organism Scientific: THERMOTOGA MARITIMA
    Organism Taxid: 2336
    Synonym: TRNA PSEUDOURIDINE 55 SYNTHASE, PSI55 SYNTHASE, TRNA-URIDINE ISOMERASE, TRNA PSEUDOURIDYLATE SYNTHASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1FHU1Mod. Nucleotide(5S,6R)-5-FLUORO-6-HYDROXY-PSEUDOURIDINE-5'-MONOPHOSPHATE
2ZN1Ligand/IonZINC ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:9 , CYS A:43BINDING SITE FOR RESIDUE ZN A 310

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:92 -A:184

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2AB4)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2AB4)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PUAPS50890 PUA domain profile.TRUB_THEMA229-306  1A:229-306

(-) Exons   (0, 0)

(no "Exon" information available for 2AB4)

(-) 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:300
 aligned with TRUB_THEMA | Q9WZW0 from UniProtKB/Swiss-Prot  Length:309

    Alignment length:308
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300        
           TRUB_THEMA     1 MKHGILVAYKPKGPTSHDVVDEVRKKLKTRKVGHGGTLDPFACGVLIIGVNQGTRILEFYKDLKKVYWVKMRLGLITETFDITGEVVEERECNVTEEEIREAIFSFVGEYDQVPPAYSAKKYKGERLYKLAREGKIINLPPKRVKIFKIWDVNIEGRDVSFRVEVSPGTYIRSLCMDIGYKLGCGATAVELVRESVGPHTIEESLNVFEAAPEEIENRIIPLEKCLEWLPRVVVHQESTKMILNGSQIHLEMLKEWDGFKKGEVVRVFNEEGRLLALAEAERNSSFLETLRKHERNERVLTLRKVFNT 308
               SCOP domains d2ab4a2 A:1-228 Pseudouridine synthase II TruB                                                                                                                                                                                      d2ab4a1 A:229-308 Pseudouridine synthase II TruB, C-termin        al domain      SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee....hhhhhhhhhhhhh....eee........eeeeeeee.hhhhhhhhhh...eeeeeeeee.eee........eeee.....hhhhhhhhhhh..eeeee.............hhhhhhhh........eeeeeeeeeeeeee..eeeeeeee....hhhhhhhhhhhhh...eeeeeeeeeee..ee..........hhhhhhhhhee.hhh.....eeee...hhhhhh....ee..............eeeeee......eeeee......--------...eeeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PUA  PDB: A:229-306 UniProt: 229-306                                          -- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ab4 A   1 MKHGILVAYKPKGPTSHDVVDEVRKKLKTRKVGHGGTLDPFACGVLIIGVNQGTRILEFYKDLKKVFWVKMRLGLITETFDITGEVVEERECNVTEEEIREAIFSFVGEYDQVPPAYSAKKYKGERLYKLAREGKIINLPPKRVKIFKIWDVNIEGRDVSFRVEVSPGTYIRSLCMDIGYKLGCGATAVELVRESVGPHTIEESLNVFEAAPEEIENRIIPLEKCLEWLPRVVVHQESTKMILNGSQIHLEMLKEWDGFKKGEVVRVFNEEGRLLALAEAERNSSF--------RQERVLTLRKVFQT 308
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280     |   -    |  300        
                                                                                                                                                                                                                                                                                                                       286      295             


Chain B from PDB  Type:RNA  Length:20
                                                    
                 2ab4 B   3 CCACGGUuCGAAUCCGUGGC  22
                                   |12        22
                                  10-FHU
   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: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2AB4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2AB4)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (TRUB_THEMA | Q9WZW0)
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:0006396    RNA processing    Any process involved in the conversion of one or more primary RNA transcripts into one or more mature RNA molecules.
    GO:1990481    mRNA pseudouridine synthesis    The intramolecular conversion of uridine to pseudouridine in an mRNA molecule.
    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:0006400    tRNA modification    The covalent alteration of one or more nucleotides within a tRNA molecule to produce a tRNA molecule with a sequence that differs from that coded genetically.
    GO:0008033    tRNA processing    The process in which a pre-tRNA molecule is converted to a mature tRNA, ready for addition of an aminoacyl group.
    GO:0031119    tRNA pseudouridine synthesis    The intramolecular conversion of uridine to pseudouridine in a tRNA molecule.

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 Related Entries

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

UniProtKB/Swiss-Prot
        TRUB_THEMA | Q9WZW0: 1r3e 1ze1 1ze2

(-) Related Entries Specified in the PDB File

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