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(-) Description

Title :  CRYSTAL STRUCTURE OF ARCHAEOSINE TRNA-GUANINE TRANSGLYCOSYLASE COMPLEXED WITH LAMBDA-FORM TRNA(VAL)
 
Authors :  R. Ishitani, O. Nureki, N. Nameki, N. Okada, S. Nishimura, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  29 Dec 02  (Deposition) - 27 May 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.30
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Transferase, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Genomics, Transferase/Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Ishitani, O. Nureki, N. Nameki, N. Okada, S. Nishimura, S. Yokoyama
Alternative Tertiary Structure Of Trna For Recognition By A Posttranscriptional Modification Enzyme
Cell(Cambridge, Mass. ) V. 113 383 2003
PubMed-ID: 12732145  |  Reference-DOI: 10.1016/S0092-8674(03)00280-0
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TRNA(VAL)
    Chains: C, D
    Engineered: YES
    Other Details: SYNTHETIC TRNA TRANSCRIPT;
SEQUENCE FROM PYROCOCCUS HORIKOSHII
    Synthetic: YES
 
Molecule 2 - ARCHAEOSINE TRNA-GUANINE TRANSGLYCOSYLASE
    Chains: A, B
    EC Number: 2.4.2.29
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET3A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: PYROCOCCUS HORIKOSHII
    Organism Taxid: 53953

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric/Biological Unit (2, 6)
No.NameCountTypeFull Name
1MG4Ligand/IonMAGNESIUM ION
2ZN2Ligand/IonZINC ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:262 , CYS A:279 , CYS A:281 , CYS A:284 , HIS A:307BINDING SITE FOR RESIDUE ZN A 600
2AC2SOFTWAREALA A:528 , VAL A:531 , MET A:566 , ILE A:567 , PHE A:569BINDING SITE FOR RESIDUE MG A 601
3AC3SOFTWAREARG B:573BINDING SITE FOR RESIDUE MG B 602
4AC4SOFTWARECYS B:279 , CYS B:281 , CYS B:284 , HIS B:307BINDING SITE FOR RESIDUE ZN B 600
5AC5SOFTWAREALA B:528 , LYS B:529 , VAL B:531 , MET B:566 , ILE B:567 , PHE B:569 , GLN B:570BINDING SITE FOR RESIDUE MG B 1601
6AC6SOFTWAREARG A:573BINDING SITE FOR RESIDUE MG C 1602

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1J2B)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Thr A:33 -Pro A:34
2Tyr A:415 -Pro A:416
3Tyr A:505 -Pro A:506
4Thr B:33 -Pro B:34
5Tyr B:415 -Pro B:416
6Tyr B:505 -Pro B:506

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1J2B)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PUAPS50890 PUA domain profile.ATGT_PYRHO507-582
 		  2A:507-582
B:507-582

(-) Exons   (0, 0)

(no "Exon" information available for 1J2B)

(-) 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:576
 aligned with ATGT_PYRHO | O58843 from UniProtKB/Swiss-Prot  Length:582

    Alignment length:576
                                    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       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576      
           ATGT_PYRHO     7 MLKFEIKARDGAGRIGKLEVNGKKIETPAIMPVVNPKQMVVEPKELEKMGFEIIITNSYIIYKDEELRRKALELGIHRMLDYNGIIEVDSGSFQLMKYGSIEVSNREIIEFQHRIGVDIGTFLDIPTPPDAPREQAVKELEITLSRAREAEEIKEIPMNATIQGSTYTDLRRYAARRLSSMNFEIHPIGGVVPLLESYRFRDVVDIVISSKMALRPDRPVHLFGAGHPIVFALAVAMGVDLFDSASYALYAKDDRYMTPEGTKRLDELDYFPCSCPVCSKYTPQELREMPKEERTRLLALHNLWVIKEEIKRVKQAIKEGELWRLVDERARSHPKLYSAYKRLLEHYTFLEEFEPITKKSALFKISNESLRWPVVRRAKERAKSINERFGELVEHPIFGRVSRYLSLTYPFAQSEAEDDFKIEKPTKEDAIKYVMAIAEYQFGEGASRAFDDAKVELSKTGMPRQVKVNGKRLATVRADDGLLTLGIEGAKRLHRVLPYPRMRVVVNKEAEPFARKGKDVFAKFVIFADPGIRPYDEVLVVNENDELLATGQALLSGREMIVFQYGRAVKVRKGVE 582
               SCOP domains d1j2ba2 A:7-360 Archaeosine tRNA-guanine transglycosylase, N-terminal domain                                                                                                                                                                                                                                                                                      d1j2ba3 A:361-505 Archaeosine tRNA-guanine transglycosylase, C2 domain                                                                           d1j2ba1 A:506-582 Archaeosine tRNA-guanine transglycosylase, C3 domain        SCOP domains
               CATH domains 1j2bA01 A:7-360 tRNA-guanine (tRNA-G) transglycosylase                                                                                                                                                                                                                                                                                                            1j2bA02 A:361-430  [code=3.90.1020.10, no name defined]               1j2bA03 A:431-504  [code=3.10.450.90, no name defined]                    1j2bA04 A:505-582  [code=2.30.130.10, no name defined]                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeeee..eeeeeeee..eeeee.eeeeeehhhhh..hhhhhhhhh..eeeeehhhhhhhhhhhhhhhhhh.........eeeee.hhhhhhhh.....hhhhhhhhhhhh....ee..........hhhhhhhhhhhhhhhhhhh.......ee.......hhhhhhhhhhhhhhh....eee..hhhhhhh.hhhhhhhhhhhhhhhh.....eeee...hhhhhhhhhh....eeeehhhhhhhhh.eeee..eeee..........hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh.hhhhhhhhh.......ee...hhhhhhhhhhhhhhhhhhhhhhhh.eeee...eeee...........ee.............hhhhhhhhhhhhhh..hhhhhhh..eeee.....eeeeee..eeeeee......eee.hhhhhhhhhhh.....eeee...hhhhhhhh..ee...eeee........eeeeee....eeeeeee..hhhhhh.....eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PUA  PDB: A:507-582 UniProt: 507-582                                         PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1j2b A   7 MLKFEIKARDGAGRIGKLEVNGKKIETPAIMPVVNPKQMVVEPKELEKMGFEIIITNSYIIYKDEELRRKALELGIHRMLDYNGIIEVDSGSFQLMKYGSIEVSNREIIEFQHRIGVDIGTFLDIPTPPDAPREQAVKELEITLSRAREAEEIKEIPMNATIQGSTYTDLRRYAARRLSSMNFEIHPIGGVVPLLESYRFRDVVDIVISSKMALRPDRPVHLFGAGHPIVFALAVAMGVDLFDSASYALYAKDDRYMTPEGTKRLDELDYFPCSCPVCSKYTPQELREMPKEERTRLLALHNLWVIKEEIKRVKQAIKEGELWRLVDERARSHPKLYSAYKRLLEHYTFLEEFEPITKKSALFKISNESLRWPVVRRAKERAKSINERFGELVEHPIFGRVSRYLSLTYPFAQSEAEDDFKIEKPTKEDAIKYVMAIAEYQFGEGASRAFDDAKVELSKTGMPRQVKVNGKRLATVRADDGLLTLGIEGAKRLHRVLPYPRMRVVVNKEAEPFARKGKDVFAKFVIFADPGIRPYDEVLVVNENDELLATGQALLSGREMIVFQYGRAVKVRKGVE 582
                                    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       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576      


Chain B from PDB  Type:PROTEIN  Length:576
 aligned with ATGT_PYRHO | O58843 from UniProtKB/Swiss-Prot  Length:582

    Alignment length:576
                                    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       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576      
           ATGT_PYRHO     7 MLKFEIKARDGAGRIGKLEVNGKKIETPAIMPVVNPKQMVVEPKELEKMGFEIIITNSYIIYKDEELRRKALELGIHRMLDYNGIIEVDSGSFQLMKYGSIEVSNREIIEFQHRIGVDIGTFLDIPTPPDAPREQAVKELEITLSRAREAEEIKEIPMNATIQGSTYTDLRRYAARRLSSMNFEIHPIGGVVPLLESYRFRDVVDIVISSKMALRPDRPVHLFGAGHPIVFALAVAMGVDLFDSASYALYAKDDRYMTPEGTKRLDELDYFPCSCPVCSKYTPQELREMPKEERTRLLALHNLWVIKEEIKRVKQAIKEGELWRLVDERARSHPKLYSAYKRLLEHYTFLEEFEPITKKSALFKISNESLRWPVVRRAKERAKSINERFGELVEHPIFGRVSRYLSLTYPFAQSEAEDDFKIEKPTKEDAIKYVMAIAEYQFGEGASRAFDDAKVELSKTGMPRQVKVNGKRLATVRADDGLLTLGIEGAKRLHRVLPYPRMRVVVNKEAEPFARKGKDVFAKFVIFADPGIRPYDEVLVVNENDELLATGQALLSGREMIVFQYGRAVKVRKGVE 582
               SCOP domains d1j2bb2 B:7-360 Archaeosine tRNA-guanine transglycosylase, N-terminal domain                                                                                                                                                                                                                                                                                      d1j2bb3 B:361-505 Archaeosine tRNA-guanine transglycosylase, C2 domain                                                                           d1j2bb1 B:506-582 Archaeosine tRNA-guanine transglycosylase, C3 domain        SCOP domains
               CATH domains 1j2bB01 B:7-360 tRNA-guanine (tRNA-G) transglycosylase                                                                                                                                                                                                                                                                                                            1j2bB02 B:361-430  [code=3.90.1020.10, no name defined]               1j2bB03 B:431-504  [code=3.10.450.90, no name defined]                    1j2bB04 B:505-582  [code=2.30.130.10, no name defined]                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeeee..eeeeeeee..eeeee.eeeeeehhhhh..hhhhhhhhh..eeeehhhhhhhhhhhhhhhhhhhhhhhh....eeee..hhhhhhhh.....hhhhhhhhhhhh....ee...........hhhhhhhhhhhhhhhhhh.......ee.......hhhhhhhhhhhhhhh....eee..hhhhhhh.hhhhhhhhhhhhhhhh.....eeee...hhhhhhhhhh....eeeehhhhhhhhh.eeee..eeee..........hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh.hhhhhhhhh.......ee...hhhhhhhhhhhhhhhhhhhhhhhh.eeee...eeee.hhh.......ee.............hhhhhhhhhhhhhh..hhhhhhh..eeee.....eeeeee..eeeeee......eee.hhhhhhhhhhh.....eeee...hhhhhhhh..ee...eeee........eeeeee....eeeeeee..hhhhhh.....eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PUA  PDB: B:507-582 UniProt: 507-582                                         PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1j2b B   7 MLKFEIKARDGAGRIGKLEVNGKKIETPAIMPVVNPKQMVVEPKELEKMGFEIIITNSYIIYKDEELRRKALELGIHRMLDYNGIIEVDSGSFQLMKYGSIEVSNREIIEFQHRIGVDIGTFLDIPTPPDAPREQAVKELEITLSRAREAEEIKEIPMNATIQGSTYTDLRRYAARRLSSMNFEIHPIGGVVPLLESYRFRDVVDIVISSKMALRPDRPVHLFGAGHPIVFALAVAMGVDLFDSASYALYAKDDRYMTPEGTKRLDELDYFPCSCPVCSKYTPQELREMPKEERTRLLALHNLWVIKEEIKRVKQAIKEGELWRLVDERARSHPKLYSAYKRLLEHYTFLEEFEPITKKSALFKISNESLRWPVVRRAKERAKSINERFGELVEHPIFGRVSRYLSLTYPFAQSEAEDDFKIEKPTKEDAIKYVMAIAEYQFGEGASRAFDDAKVELSKTGMPRQVKVNGKRLATVRADDGLLTLGIEGAKRLHRVLPYPRMRVVVNKEAEPFARKGKDVFAKFVIFADPGIRPYDEVLVVNENDELLATGQALLSGREMIVFQYGRAVKVRKGVE 582
                                    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       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576      


Chain C from PDB  Type:RNA  Length:77
                                                                                                             
                 1j2b C 901 GGGCCCGUGGUCUAGUUGGUCAUGACGCCGCCCUUACGAGGCGGAGGUCCGGGGUUCAAGUCCCCGCGGGCCCACCA 977
                                   910       920       930       940       950       960       970       


Chain D from PDB  Type:RNA  Length:71
                                                                                                       
                 1j2b D 901 GGGCCCGUGGUCUAGUUGACGCCGCCCUUACGAGGCGGAGGUCCGGGGUUCAAGUCCCCGCGGGCCCACCA 977
                                   910      |926       936       946       956       966       976 
                                          917|                                                     
                                           924
   Legend:   → Mismatch (orange background)
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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  (3, 6)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (4, 8)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1J2B)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (ATGT_PYRHO | O58843)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008479    queuine tRNA-ribosyltransferase activity    Catalysis of the reaction: tRNA guanine + queuine = tRNA queuine + guanine.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0016757    transferase activity, transferring glycosyl groups    Catalysis of the transfer of a glycosyl group from one compound (donor) to another (acceptor).
    GO:0016763    transferase activity, transferring pentosyl groups    Catalysis of the transfer of a pentosyl group from one compound (donor) to another (acceptor).
biological process
    GO:0008616    queuosine biosynthetic process    The chemical reactions and pathways resulting in the formation of queuosines, any of a series of nucleosides found in tRNA and having an additional pentenyl ring added via an NH group to the methyl group of 7-methylguanosine. The pentenyl ring may carry other substituents.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        ATGT_PYRHO | O58843: 1iq8 1it7 1it8

(-) Related Entries Specified in the PDB File

1iq8 LIGAND-FREE FORM RELATED ID: TRT001000258.1 RELATED DB: TARGETDB