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(-) Description

Title :  CRYSTAL STRUCTURE OF ZYMOMONAS MOBILIS TRNA-GUANINE TRANSGLYCOSYLASE (TGT) COCRYSTALLISED WITH PREQ1 AT PH 5.5
 
Authors :  R. Brenk, M. T. Stubbs, A. Heine, K. Reuter, G. Klebe
Date :  10 Apr 03  (Deposition) - 30 Sep 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A
Keywords :  Protein-Substrate Complex, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Brenk, M. T. Stubbs, A. Heine, K. Reuter, G. Klebe
Flexible Adaptations In The Structure Of The Trna-Modifying Enzyme Trna-Guanine Transglycosylase And Their Implications For Substrate Selectivity, Reaction Mechanism And Structure-Based Drug Design
Chembiochem V. 4 1066 2003
PubMed-ID: 14523925  |  Reference-DOI: 10.1002/CBIC.200300644
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - QUEUINE TRNA-RIBOSYLTRANSFERASE
    Chains: A
    EC Number: 2.4.2.29
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET9D
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: TGT
    Organism Scientific: ZYMOMONAS MOBILIS
    Organism Taxid: 542
    Synonym: TRNA-GUANINE TRANSGLYCOSYLASE, GUANINE INSERTION ENZYME

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1PRF1Ligand/Ion7-DEAZA-7-AMINOMETHYL-GUANINE
2ZN1Ligand/IonZINC ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:318 , CYS A:320 , CYS A:323 , HIS A:349BINDING SITE FOR RESIDUE ZN A 400
2AC2SOFTWAREASP A:102 , TYR A:106 , ASP A:156 , CYS A:158 , ILE A:201 , GLN A:203 , GLY A:229 , GLY A:230 , LEU A:231 , VAL A:233 , MET A:260BINDING SITE FOR RESIDUE PRF A 900

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1P0E)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Thr A:39 -Pro A:40
2Arg A:77 -Pro A:78
3Tyr A:161 -Pro A:162

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1P0E)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1P0E)

(-) Exons   (0, 0)

(no "Exon" information available for 1P0E)

(-) 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:363
 aligned with TGT_ZYMMO | P28720 from UniProtKB/Swiss-Prot  Length:386

    Alignment length:373
                                    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       310       320       330       340       350       360       370       380   
            TGT_ZYMMO    11 RPRFSFSIAAREGKARTGTIEMKRGVIRTPAFMPVGTAATVKALKPETVRATGADIILGNTYHLMLRPGAERIAKLGGLHSFMGWDRPILTDSGGYQVMSLSSLTKQSEEGVTFKSHLDGSRHMLSPERSIEIQHLLGSDIVMAFDECTPYPATPSRAASSMERSMRWAKRSRDAFDSRKEQAENAALFGIQQGSVFENLRQQSADALAEIGFDGYAVGGLAVGEGQDEMFRVLDFSVPMLPDDKPHYLMGVGKPDDIVGAVERGIDMFDCVLPTRSGRNGQAFTWDGPINIRNARFSEDLTPLDSECHCAVCQKWSRAYIHHLIRAGEILGAMLMTEHNIAFYQQLMQKIRDSISEGRFSQFAQDFRARYFA 383
               SCOP domains d1p0ea_ A: Queosine tRNA-guanine transglycosylase                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 1p0eA00 A:11-383 tRNA-guanine (tRNA-G) transglycosylase                                                                                                                                                                                                                                                                                                                               CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------TGT-1p0eA01 A:138-379                                                                                                                                                                                                                             ---- Pfam domains
         Sec.struct. author ...eeeeeeeee..eeeeeeee..eeeee.eeeeee........hhhhhhhh....eeehhhhhhhh.hhhhhhhhhhhhhhhh....eee..hhhhhhhhh--.ee....ee.--------...hhhhhhhhhhhhh..eee..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheeeeee....hhhhhhhhhhhhhhhh..eeee......hhhhhhhhhhhhhhhhh.....eee....hhhhhhhhhhh...eeeehhhhhhhhhhee......ee..hhhhh...........hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1p0e A  11 RPRFSFSIAAREGKARTGTIEMKRGVIRTPAFMPVGTAATVKALKPETVRATGADIILGNTYHLMLRPGAERIAKLGGLHSFMGWDRPILTDSGGYQVMSLS--TKQSEEGVTF--------HMLSPERSIEIQHLLGSDIVMAFDECTPYPATPSRAASSMERSMRWAKRSRDAFDSRKEQAENAALFGIQQGSVFENLRQQSADALAEIGFDGYAVGGLAVGEGQDEMFRVLDFSVPMLPDDKPHYLMGVGKPDDIVGAVERGIDMFDCVLPTRSGRNGQAFTWDGPINIRNARFSEDLKPLDSECHCAVCQKWSRAYIHHLIRAGEILGAMLMTEHNIAFYQQLMQKIRDSISEGRFSQFAQDFRARYFA 383
                                    20        30        40        50        60        70        80        90       100       110 |  |  120   |     -  |    140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380   
                                                                                                                               112  |      124      133                                                                                                                                                                                                                                                          
                                                                                                                                  115
   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) (23833)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: TGT] (33)
(-)
Family: TGT (33)
(-)
Zymomonas mobilis (33)
1aTGT-1p0eA01A:138-379

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (TGT_ZYMMO | P28720)
molecular function
    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).
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
        TGT_ZYMMO | P28720: 1efz 1enu 1f3e 1k4g 1k4h 1n2v 1ozm 1ozq 1p0b 1p0d 1pud 1pxg 1q2r 1q2s 1q4w 1q63 1q65 1q66 1r5y 1s38 1s39 1wkd 1wke 1wkf 1y5v 1y5w 1y5x 2bbf 2nqz 2nso 2oko 2pot 2pwu 2pwv 2qii 2qzr 2z1v 2z1w 2z1x 2z7k 3bl3 3bld 3bll 3blo 3c2y 3eos 3eou 3gc4 3gc5 3ge7 3hfy 3rr4 3s1g 3sm0 3tll 3unt 3uvi 4dxx 4dy1 4e2v 4fps 4fr1 4fr6 4fsa 4gcx 4gd0 4gg9 4gh1 4gh3 4ghr 4gi4 4giy 4gkt 4h6e 4h7z 4hqv 4hsh 4htb 4hvx 4ipp 4jbr 4kwo 4l56 4lbu 4leq 4puj 4puk 4pul 4pum 4pun 4q4m 4q4o 4q4p 4q4q 4q4r 4q4s 4q8m 4q8n 4q8o 4q8p 4q8q 4q8t 4q8u 4q8v 4q8w 5egr 5i00 5i02 5i03 5i06 5i07 5i09 5j9m 5j9n 5j9o 5jgm 5jgo 5jsv 5jsw 5jt5 5jt6 5jt7 5jxq

(-) Related Entries Specified in the PDB File

1p0b CRYSTAL STRUCTURE OF TRNA-GUANINE TRANSGLYCOSYLASE (TGT) FROM ZYMOMONAS MOBILIS COMPLEXED WITH ARCHAEOSINE PRECURSOR, PREQ0
1p0d CRYSTAL STRUCTURE OF ZYMOMONAS MOBILIS TRNA-GUANINE TRANSGLYCOSYLASE (TGT) CRYSTALLISED AT PH 5.5
1pud TRNA-GUANINE TRANSGLYCOSYLASE