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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 :  3.90
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,B,E,F  (1x)
Biol. Unit 2:  C,D,G,H  (1x)
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: E, F, G, H
    Engineered: YES
    Other Details: OCCURS NATURALLY IN E. COLI. TRNA IS OBTAINED BY IN VITRO TRANSCRIPTION.
    Synthetic: YES
 
Molecule 2 - TRNA PSEUDOURIDINE SYNTHASE A
    Chains: A, B, C, D
    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

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (1x): AB  EF  
Biological Unit 2 (1x):   CD  GH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2NR0)

(-) Sites  (0, 0)

(no "Site" information available for 2NR0)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2NR0)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Gly A:264 -Pro A:265
2Gly B:264 -Pro B:265
3Gly C:264 -Pro C:265
4Gly D:264 -Pro D:265

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2NR0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2NR0)

(-) Exons   (0, 0)

(no "Exon" information available for 2NR0)

(-) 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:264
 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 d2nr0a1 A:7-270 Pseudouridine synthase I TruA                                                                                                                                                                                                                            SCOP domains
               CATH domains 2nr0A01 A:7-113  [code=3.30.70.580, no name defined]                                                       2nr0A02 A:114-251  [code=3.30.70.660, no name defined]                                                                                    ------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeeeee.hhhh..........hhhhhhhhhhhhhhh................eeeeeeeeee.........hhhhhh.....eeeeeeee............eeeeeeeee........hhhhhee.....hhhhhhhhh....eeee.hhhh.........eeeeeeeeeeee..eeeeeeee.....hhhhhhhhhhhhhhh.....hhhhhhhhhh.............eeeeeee................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2nr0 A   7 PPVYKIALGIEYDGSKYYGWQRQNEVRSVQEKLEKALSQVANEPITVFCAGRTDAGVHGTGQVVHFETTALRKDAAWTLGVNANLPGDIAVRWVKTVPDDFHARFSATARRYRYIIYNHRLRPAVLSKGVTHFYEPLDAERMHRAAQCLLGENDFTSFRAVQCQSRTPWRNVMHINVTRHGPYVVVDIKANAFVHHMVRNIVGSLMEVGAHNQPESWIAELLAAKDRTLAAATAKAEGLYLVAVDYPDRYDLPKPPMGPLFLAD 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    


Chain B from PDB  Type:PROTEIN  Length:264
 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 d2nr0b1 B:7-270 Pseudouridine synthase I TruA                                                                                                                                                                                                                            SCOP domains
               CATH domains 2nr0B01 B:7-113  [code=3.30.70.580, no name defined]                                                       2nr0B02 B:114-251  [code=3.30.70.660, no name defined]                                                                                    ------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeeeee.hhhh..........hhhhhhhhhhhhhhh................eeeeeeeeee..........hhhhhh....eeeeeeee............eeeeeeeeee.......hhhhheee....hhhhhhhhh....eeee.hhhh.........eeeeeeeeeeee..eeeeeeee.....hhhhhhhhhhhhhhh.....hhhhhhhhhh.............eeeeeee................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2nr0 B   7 PPVYKIALGIEYDGSKYYGWQRQNEVRSVQEKLEKALSQVANEPITVFCAGRTDAGVHGTGQVVHFETTALRKDAAWTLGVNANLPGDIAVRWVKTVPDDFHARFSATARRYRYIIYNHRLRPAVLSKGVTHFYEPLDAERMHRAAQCLLGENDFTSFRAVQCQSRTPWRNVMHINVTRHGPYVVVDIKANAFVHHMVRNIVGSLMEVGAHNQPESWIAELLAAKDRTLAAATAKAEGLYLVAVDYPDRYDLPKPPMGPLFLAD 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    


Chain C from PDB  Type:PROTEIN  Length:264
 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 d2nr0c1 C:7-270 Pseudouridine synthase I TruA                                                                                                                                                                                                                            SCOP domains
               CATH domains 2nr0C01 C:7-113  [code=3.30.70.580, no name defined]                                                       2nr0C02 C:114-251  [code=3.30.70.660, no name defined]                                                                                    ------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeeeee.hhhh..........hhhhhhhhhhhhhhh................eeeeeeeeee...........hhhhh....eeeeeeee............eeeeeeeeee.......hhhhheee....hhhhhhhhh....eeee.hhhh.........eeeeeeeeeeee..eeeeeeee.....hhhhhhhhhhhhhh......hhhhhhhhhh.............eeeeeee................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2nr0 C   7 PPVYKIALGIEYDGSKYYGWQRQNEVRSVQEKLEKALSQVANEPITVFCAGRTDAGVHGTGQVVHFETTALRKDAAWTLGVNANLPGDIAVRWVKTVPDDFHARFSATARRYRYIIYNHRLRPAVLSKGVTHFYEPLDAERMHRAAQCLLGENDFTSFRAVQCQSRTPWRNVMHINVTRHGPYVVVDIKANAFVHHMVRNIVGSLMEVGAHNQPESWIAELLAAKDRTLAAATAKAEGLYLVAVDYPDRYDLPKPPMGPLFLAD 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    


Chain D from PDB  Type:PROTEIN  Length:264
 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 d2nr0d1 D:7-270 Pseudouridine synthase I TruA                                                                                                                                                                                                                            SCOP domains
               CATH domains 2nr0D01 D:7-113  [code=3.30.70.580, no name defined]                                                       2nr0D02 D:114-251  [code=3.30.70.660, no name defined]                                                                                    ------------------- CATH domains
           Pfam domains (1) ------------------------------------------------------------------------------------------------------------------------------------------------PseudoU_synth_1-2nr0D01 D:151-253                                                                      ----------------- Pfam domains (1)
           Pfam domains (2) ------------------------------------------------------------------------------------------------------------------------------------------------PseudoU_synth_1-2nr0D02 D:151-253                                                                      ----------------- Pfam domains (2)
           Pfam domains (3) ------------------------------------------------------------------------------------------------------------------------------------------------PseudoU_synth_1-2nr0D03 D:151-253                                                                      ----------------- Pfam domains (3)
           Pfam domains (4) ------------------------------------------------------------------------------------------------------------------------------------------------PseudoU_synth_1-2nr0D04 D:151-253                                                                      ----------------- Pfam domains (4)
           Pfam domains (5) ------------------------------------------------------------------------------------------------------------------------------------------------PseudoU_synth_1-2nr0D05 D:151-253                                                                      ----------------- Pfam domains (5)
           Pfam domains (6) ------------------------------------------------------------------------------------------------------------------------------------------------PseudoU_synth_1-2nr0D06 D:151-253                                                                      ----------------- Pfam domains (6)
           Pfam domains (7) ------------------------------------------------------------------------------------------------------------------------------------------------PseudoU_synth_1-2nr0D07 D:151-253                                                                      ----------------- Pfam domains (7)
           Pfam domains (8) ------------------------------------------------------------------------------------------------------------------------------------------------PseudoU_synth_1-2nr0D08 D:151-253                                                                      ----------------- Pfam domains (8)
         Sec.struct. author ...eeeeeeeee.hhhh..........hhhhhhhhhhhhhhh................eeeeeeeeee.........hhhhhh.....eeeeeeee............eeeeeeeeee.......hhhhheee....hhhhhhhhh....eeee.hhhh.........eeeeeeeeeeee..eeeeeeee......hhhhhhhhhhhhhh.....hhhhhhhhhh.............eeeeeee................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2nr0 D   7 PPVYKIALGIEYDGSKYYGWQRQNEVRSVQEKLEKALSQVANEPITVFCAGRTDAGVHGTGQVVHFETTALRKDAAWTLGVNANLPGDIAVRWVKTVPDDFHARFSATARRYRYIIYNHRLRPAVLSKGVTHFYEPLDAERMHRAAQCLLGENDFTSFRAVQCQSRTPWRNVMHINVTRHGPYVVVDIKANAFVHHMVRNIVGSLMEVGAHNQPESWIAELLAAKDRTLAAATAKAEGLYLVAVDYPDRYDLPKPPMGPLFLAD 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    


Chain E from PDB  Type:DNA/RNA  Length:81
                                                                                                                 
                 2nr0 E   2 CCGAGGUGGUGGAAUUGGUAGACACGCUACCUUGAGGUGGUAGUGCCCAAUAGGGCUUACGGGUUCAAGUCCCGUCCUCGG  71
                                    11       20A        30        40    |||45F||||||  50        60        70 
                                             20A                      45A||||||46J||                         
                                                                       45B||||||46K|                         
                                                                        45C||||||46L                         
                                                                         45D|||||                            
                                                                          45E||||                            
                                                                           45F|||                            
                                                                            45G||                            
                                                                             45H|                            
                                                                              46I                            


Chain F from PDB  Type:RNA  Length:72
                                                                                                        
                 2nr0 F   3 CGAGGUGGUGGAAUUGGUAGACACGCUACCUUGAGGUGGUAGUGCCCCUUACGGGUUCAAGUCCCGUCCUCG  70
                                    12        21        31        41   |||||48        58        68  
                                            20A                      45A||||                        
                                                                      45B|||                        
                                                                       45C||                        
                                                                        45D|                        
                                                                         46L                        


Chain G from PDB  Type:RNA  Length:67
                                                                                                   
                 2nr0 G   5 AGGUGGUGGAAUUGGUAGACACGCUACCUUGAGGUGGUAGUGCGCUUACGGGUUCAAGUCCCGUCCU  68
                                    14      | 23        33        43 ||||   51        61       
                                          20A                      45A|||                      
                                                                    45B||                      
                                                                     46K|                      
                                                                      46L                      


Chain H from PDB  Type:DNA/RNA  Length:65
                                                                                                 
                 2nr0 H   4 GAGGUGGUGGAAUUGGUAGACACGCUACCUGGUAGUGCCGGCUUACGGGUUCAAGUCCCGUCCUC  69
                                    13       |22        38      |46J||      54        64     
                                           20A         31|    45A|||||                       
                                                        38     45B||||                       
                                                                45C|||                       
                                                                 46J||                       
                                                                  46K|                       
                                                                   46L
   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, 4)

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

(-) CATH Domains  (2, 8)

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

(-) Pfam Domains  (1, 8)

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

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (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 2nre

(-) Related Entries Specified in the PDB File

1dj0 APO TRUA ENZYME
2nqp
2nre