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(-) Description

Title :  CRYSTAL STRUCTURE OF PSEUDOUDIRINDE SYNTHASE TRUA IN COMPLEX WITH LEUCYL TRNA
 
Authors :  S. Hur, R. M. Stroud
Date :  01 Nov 06  (Deposition) - 15 May 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  4.00
Chains :  Asym. Unit :  A,F
Biol. Unit 1:  A,F  (2x)
Keywords :  Pseudouridine Synthase, Anticodon Stem Loop, Trna, Multisite Specificity, Isomerase/Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Hur, R. M. Stroud
How U38, 39, And 40 Of Many Trnas Become The Targets For Pseudouridylation By Trua.
Mol. Cell V. 26 189 2007
PubMed-ID: 17466622  |  Reference-DOI: 10.1016/J.MOLCEL.2007.02.027
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - LEUCYL TRNA
    Chains: F
    Engineered: YES
    Other Details: OCCURS NATURALLY IN E. COLI. SYNTHESIZED BY T7 IN VITRO TRANSCRIPTION
    Synthetic: YES
 
Molecule 2 - TRNA PSEUDOURIDINE SYNTHASE A
    Chains: A
    EC Number: 5.4.99.12
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET28B
    Expression System Strain: BL21/DE3
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: TRUA
    Organism Scientific: ESCHERICHIA COLI K12
    Organism Taxid: 83333
    Strain: K-12
    Synonym: TRNA-URIDINE ISOMERASE I, TRNA PSEUDOURIDYLATE SYNTHASE I, PSU-I

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AF
Biological Unit 1 (2x): AF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1K2Ligand/IonPOTASSIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1K-1Ligand/IonPOTASSIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREC F:30BINDING SITE FOR RESIDUE K F 77
2AC2SOFTWAREU F:17 , G F:18BINDING SITE FOR RESIDUE K F 78

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Gly A:264 -Pro A:265

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2NRE)

(-) Exons   (0, 0)

(no "Exon" information available for 2NRE)

(-) Sequences/Alignments

Asymmetric 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:259
 aligned with TRUA_ECOLI | P07649 from UniProtKB/Swiss-Prot  Length:270

    Alignment length:264
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266    
           TRUA_ECOLI     7 PPVYKIALGIEYDGSKYYGWQRQNEVRSVQEKLEKALSQVANEPITVFCAGRTDAGVHGTGQVVHFETTALRKDAAWTLGVNANLPGDIAVRWVKTVPDDFHARFSATARRYRYIIYNHRLRPAVLSKGVTHFYEPLDAERMHRAAQCLLGENDFTSFRAVQCQSRTPWRNVMHINVTRHGPYVVVDIKANAFVHHMVRNIVGSLMEVGAHNQPESWIAELLAAKDRTLAAATAKAEGLYLVAVDYPDRYDLPKPPMGPLFLAD 270
               SCOP domains d2nrea1 A:7-270 Pseudouridine synthase I TruA                                                                                                                                                                                                                            SCOP domains
               CATH domains 2nreA01 A:7-113  [code=3.30.70.580, no name defined]                                                       2nreA02 A:114-251  [code=3.30.70.660, no name defined]                                                                                    ------------------- CATH domains
           Pfam domains (1) ------------------------------------------------------------------------------------------------------------------------------------------------PseudoU_synth_1-2     nreA01 A:151-253                                                                 ----------------- Pfam domains (1)
           Pfam domains (2) ------------------------------------------------------------------------------------------------------------------------------------------------PseudoU_synth_1-2     nreA02 A:151-253                                                                 ----------------- Pfam domains (2)
         Sec.struct. author ...eeeeeeeee...............hhhhhhhhhhhhh.......ee........ee...eeeeee...........hhhhh....eeeeeeee.....hhhhhh.eeeeeeee.....................hhhhhhhhhh......hhhhh...-----..........ee.....eeeee........hhhhhhhhhhhhhhh....hhhhhhhhhh..............ee.eee................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2nre A   7 PPVYKIALGIEYDGSKYYGWQRQNEVRSVQEKLEKALSQVANEPITVFCAGRTDAGVHGTGQVVHFETTALRKDAAWTLGVNANLPGDIAVRWVKTVPDDFHARFSATARRYRYIIYNHRLRPAVLSKGVTHFYEPLDAERMHRAAQCLLGENDFTSFRAV-----TPWRNVMHINVTRHGPYVVVDIKANAFVHHMVRNIVGSLMEVGAHNQPESWIAELLAAKDRTLAAATAKAEGLYLVAVDYPDRYDLPKPPMGPLFLAD 270
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166|     |176       186       196       206       216       226       236       246       256       266    
                                                                                                                                                                                          167   173                                                                                                 


Chain F from PDB  Type:RNA  Length:56
                                                                                        
                 2nre F   5 AGGUGGUGGAAUUGGUAGACACGCUACCGGUAGUUACGGGUUCAAGUCCCGUCCUC  69
                                    14      | 23       |40   ||   53        63      
                                          20A         31|   44|                     
                                                       39    48
   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 Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: no clan defined [family: PseudoU_synth_1] (4)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A   (TRUA_ECOLI | P07649)
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.
    GO:0000049    tRNA binding    Interacting selectively and non-covalently with transfer RNA.
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: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
        TRUA_ECOLI | P07649: 1dj0 2nqp 2nr0

(-) Related Entries Specified in the PDB File

1dj0 APO TRUA
2nqp
2nr0