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PDBsum entry 1pud

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protein metals links
Transferase PDB id
1pud
Jmol
Contents
Protein chain
372 a.a. *
Metals
_ZN
Waters ×262
* Residue conservation analysis
PDB id:
1pud
Name: Transferase
Title: tRNA-guanine transglycosylase
Structure: tRNA-guanine transglycosylase. Chain: a. Synonym: tgt. Engineered: yes
Source: Zymomonas mobilis. Organism_taxid: 542. Gene: tgt. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PQS)
Resolution:
1.85Å     R-factor:   0.190     R-free:   0.214
Authors: C.Romier,K.Reuter,D.Suck,R.Ficner
Key ref: C.Romier et al. (1996). Crystal structure of tRNA-guanine transglycosylase: RNA modification by base exchange. EMBO J, 15, 2850-2857. PubMed id: 8654383
Date:
28-Jun-96     Release date:   07-Jul-97    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P28720  (TGT_ZYMMO) -  Queuine tRNA-ribosyltransferase
Seq:
Struc:
386 a.a.
372 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.2.4.2.29  - tRNA-guanine(34) transglycosylase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction:
1. Guanine34 in tRNA + queuine = queuosine34 in tRNA + guanine
2. Guanine34 in tRNA + 7-aminomethyl-7-carbaguanine = 7-aminomethyl-7- carbaguanine34 in tRNA + guanine
Guanine(34) in tRNA
+ queuine
= queuosine(34) in tRNA
+ guanine
Guanine(34) in tRNA
+ 7-aminomethyl-7-carbaguanine
= 7-aminomethyl-7- carbaguanine(34) in tRNA
+ guanine
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     tRNA processing   3 terms 
  Biochemical function     transferase activity     4 terms  

 

 
    reference    
 
 
EMBO J 15:2850-2857 (1996)
PubMed id: 8654383  
 
 
Crystal structure of tRNA-guanine transglycosylase: RNA modification by base exchange.
C.Romier, K.Reuter, D.Suck, R.Ficner.
 
  ABSTRACT  
 
tRNA-guanine transglycosylases (TGT) are enzymes involved in the modification of the anticodon of tRNAs specific for Asn, Asp, His and Tyr, leading to the replacement of guanine-34 at the wobble position by the hypermodified base queuine. In prokaryotes TGT catalyzes the exchange of guanine-34 with the queuine (.)precursor 7-aminomethyl-7-deazaguanine (preQ1). The crystal structure of TGT from Zymomonas mobilis was solved by multiple isomorphous replacement and refined to a crystallographic R-factor of 19% at 1.85 angstrom resolution. The structure consists of an irregular (beta/alpha)8-barrel with a tightly attached C-terminal zinc-containing subdomain. The packing of the subdomain against the barrel is mediated by an alpha-helix, located close to the C-terminus, which displaces the eighth helix of the barrel. The structure of TGT in complex with preQ1 suggests a binding mode for tRNA where the phosphate backbone interacts with the zinc subdomain and the U33G34U35 sequence is recognized by the barrel. This model for tRNA binding is consistent with a base exchange mechanism involving a covalent tRNA-enzyme intermediate. This structure is the first example of a (beta/alpha)-barrel protein interacting specifically with a nucleic acid.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21131277 Y.C.Chen, A.F.Brooks, D.M.Goodenough-Lashua, J.D.Kittendorf, H.D.Showalter, and G.A.Garcia (2011).
Evolution of eukaryal tRNA-guanine transglycosylase: insight gained from the heterocyclic substrate recognition by the wild-type and mutant human and Escherichia coli tRNA-guanine transglycosylases.
  Nucleic Acids Res, 39, 2834-2844.  
20963777 X.Ming, and F.Seela (2010).
Efficient synthesis of the tRNA nucleoside preQ0, 7-cyano-7-deazaguanosine, via microwave-assisted iodo‚Üícarbonitrile exchange.
  Chem Biodivers, 7, 2616-2621.  
20354154 Y.C.Chen, V.P.Kelly, S.V.Stachura, and G.A.Garcia (2010).
Characterization of the human tRNA-guanine transglycosylase: confirmation of the heterodimeric subunit structure.
  RNA, 16, 958-968.  
19414587 C.Boland, P.Hayes, I.Santa-Maria, S.Nishimura, and V.P.Kelly (2009).
Queuosine Formation in Eukaryotic tRNA Occurs via a Mitochondria-localized Heteromeric Transglycosylase.
  J Biol Chem, 284, 18218-18227.  
19508719 O.V.Kalinina, M.S.Gelfand, and R.B.Russell (2009).
Combining specificity determining and conserved residues improves functional site prediction.
  BMC Bioinformatics, 10, 174.  
19894214 T.Ritschel, P.C.Kohler, G.Neudert, A.Heine, F.Diederich, and G.Klebe (2009).
How to Replace the Residual Solvation Shell of Polar Active Site Residues to Achieve Nanomolar Inhibition of tRNA-Guanine Transglycosylase.
  ChemMedChem, 4, 2012-2023.
PDB codes: 3eos 3eou 3gc4 3gc5 3ge7
19199329 T.Ritschel, S.Hoertner, A.Heine, F.Diederich, and G.Klebe (2009).
Crystal structure analysis and in silico pKa calculations suggest strong pKa shifts of ligands as driving force for high-affinity binding to TGT.
  Chembiochem, 10, 716-727.
PDB codes: 2z7k 3c2n 3c2y 3c2z
18491386 N.Cicmil, and R.H.Huang (2008).
Crystal structure of QueC from Bacillus subtilis: an enzyme involved in preQ1 biosynthesis.
  Proteins, 72, 1084-1088.
PDB code: 3bl5
17949745 N.Tidten, B.Stengl, A.Heine, G.A.Garcia, G.Klebe, and K.Reuter (2007).
Glutamate versus glutamine exchange swaps substrate selectivity in tRNA-guanine transglycosylase: insight into the regulation of substrate selectivity by kinetic and crystallographic studies.
  J Mol Biol, 374, 764-776.
PDB codes: 2oko 2pot 2pwu 2pwv 2qii 2z1v 2z1w 2z1x
17673081 S.M.Chervin, J.D.Kittendorf, and G.A.Garcia (2007).
Probing the intermediacy of covalent RNA enzyme complexes in RNA modification enzymes.
  Methods Enzymol, 425, 121-137.  
16401090 K.A.Todorov, and G.A.Garcia (2006).
Role of aspartate 143 in Escherichia coli tRNA-guanine transglycosylase: alteration of heterocyclic substrate specificity.
  Biochemistry, 45, 617-625.  
16206323 B.Stengl, K.Reuter, and G.Klebe (2005).
Mechanism and substrate specificity of tRNA-guanine transglycosylases (TGTs): tRNA-modifying enzymes from the three different kingdoms of life share a common catalytic mechanism.
  Chembiochem, 6, 1926-1939.  
15888313 G.A.Garcia, and J.D.Kittendorf (2005).
Transglycosylation: a mechanism for RNA modification (and editing?).
  Bioorg Chem, 33, 229-251.  
15951383 K.A.Todorov, X.J.Tan, S.T.Nonekowski, G.A.Garcia, and H.A.Carlson (2005).
The role of aspartic acid 143 in E. coli tRNA-guanine transglycosylase: insights from mutagenesis studies and computational modeling.
  Biophys J, 89, 1965-1977.  
14990747 K.Phannachet, and R.H.Huang (2004).
Conformational change of pseudouridine 55 synthase upon its association with RNA substrate.
  Nucleic Acids Res, 32, 1422-1429.
PDB codes: 1ze1 1ze2
15138304 M.Ibba, and C.Francklyn (2004).
Turning tRNA upside down: When aminoacylation is not a prerequisite to protein synthesis.
  Proc Natl Acad Sci U S A, 101, 7493-7494.  
12581659 A.R.Ferré-D'Amaré (2003).
RNA-modifying enzymes.
  Curr Opin Struct Biol, 13, 49-55.  
14513020 C.C.Correll (2003).
Caught in the act of modifying tRNA.
  Nat Struct Biol, 10, 772-773.  
12877882 D.M.Goodenough-Lashua, and G.A.Garcia (2003).
tRNA-guanine transglycosylase from E. coli: a ping-pong kinetic mechanism is consistent with nucleophilic catalysis.
  Bioorg Chem, 31, 331-344.  
12704200 H.Hori, S.Kubota, K.Watanabe, J.M.Kim, T.Ogasawara, T.Sawasaki, and Y.Endo (2003).
Aquifex aeolicus tRNA (Gm18) methyltransferase has unique substrate specificity. TRNA recognition mechanism of the enzyme.
  J Biol Chem, 278, 25081-25090.  
12909636 J.D.Kittendorf, T.Sgraja, K.Reuter, G.Klebe, and G.A.Garcia (2003).
An essential role for aspartate 264 in catalysis by tRNA-guanine transglycosylase from Escherichia coli.
  J Biol Chem, 278, 42369-42376.
PDB code: 1pxg
14523925 R.Brenk, M.T.Stubbs, A.Heine, K.Reuter, and G.Klebe (2003).
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, 4, 1066-1077.
PDB codes: 1ozm 1ozq 1p0b 1p0d 1p0e
12533518 S.G.Van Lanen, S.D.Kinzie, S.Matthieu, T.Link, J.Culp, and D.Iwata-Reuyl (2003).
tRNA modification by S-adenosylmethionine:tRNA ribosyltransferase-isomerase. Assay development and characterization of the recombinant enzyme.
  J Biol Chem, 278, 10491-10499.  
12949492 W.Xie, X.Liu, and R.H.Huang (2003).
Chemical trapping and crystal structure of a catalytic tRNA guanine transglycosylase covalent intermediate.
  Nat Struct Biol, 10, 781-788.
PDB codes: 1q2r 1q2s
11917006 V.Anantharaman, E.V.Koonin, and L.Aravind (2002).
Comparative genomics and evolution of proteins involved in RNA metabolism.
  Nucleic Acids Res, 30, 1427-1464.  
11679736 R.Ishitani, O.Nureki, T.Kijimoto, M.Watanabe, H.Kondo, N.Nameki, N.Okada, S.Nishimura, and S.Yokoyama (2001).
Crystallization and preliminary X-ray analysis of the archaeosine tRNA-guanine transglycosylase from Pyrococcus horikoshii.
  Acta Crystallogr D Biol Crystallogr, 57, 1659-1662.  
  11680848 S.T.Nonekowski, and G.A.Garcia (2001).
tRNA recognition by tRNA-guanine transglycosylase from Escherichia coli: the role of U33 in U-G-U sequence recognition.
  RNA, 7, 1432-1441.  
11327834 T.Soderberg, and C.D.Poulter (2001).
Escherichia coli dimethylallyl diphosphate:tRNA dimethylallyltransferase: site-directed mutagenesis of highly conserved residues.
  Biochemistry, 40, 1734-1740.  
10739928 C.Grimm, G.Klebe, R.Ficner, and K.Reuter (2000).
Screening orthologs as an important variable in crystallization: preliminary X-ray diffraction studies of the tRNA-modifying enzyme S-adenosyl-methionine:tRNA ribosyl transferase/isomerase.
  Acta Crystallogr D Biol Crystallogr, 56, 484-488.  
10688362 F.L.Kung, S.Nonekowski, and G.A.Garcia (2000).
tRNA-guanine transglycosylase from Escherichia coli: recognition of noncognate-cognate chimeric tRNA and discovery of a novel recognition site within the TpsiC arm of tRNA(Phe).
  RNA, 6, 233-244.  
10094308 J.N.Li, and G.R.Björk (1999).
Structural alterations of the tRNA(m1G37)methyltransferase from Salmonella typhimurium affect tRNA substrate specificity.
  RNA, 5, 395-408.  
  10082367 I.L.Alberts, K.Nadassy, and S.J.Wodak (1998).
Analysis of zinc binding sites in protein crystal structures.
  Protein Sci, 7, 1700-1716.  
9585540 V.Arluison, C.Hountondji, B.Robert, and H.Grosjean (1998).
Transfer RNA-pseudouridine synthetase Pus1 of Saccharomyces cerevisiae contains one atom of zinc essential for its native conformation and tRNA recognition.
  Biochemistry, 37, 7268-7276.  
9184155 E.Glasfeld, and P.Schimmel (1997).
Zinc-dependent tRNA binding by a peptide element within a tRNA synthetase.
  Biochemistry, 36, 6739-6744.  
9148919 H.C.Leung, Y.Chen, and M.E.Winkler (1997).
Regulation of substrate recognition by the MiaA tRNA prenyltransferase modification enzyme of Escherichia coli K-12.
  J Biol Chem, 272, 13073-13083.  
9242689 M.Watanabe, M.Matsuo, S.Tanaka, H.Akimoto, S.Asahi, S.Nishimura, J.R.Katze, T.Hashizume, P.F.Crain, J.A.McCloskey, and N.Okada (1997).
Biosynthesis of archaeosine, a novel derivative of 7-deazaguanosine specific to archaeal tRNA, proceeds via a pathway involving base replacement on the tRNA polynucleotide chain.
  J Biol Chem, 272, 20146-20151.  
9667869 V.L.Schramm (1997).
Enzymatic N-riboside scission in RNA and RNA precursors.
  Curr Opin Chem Biol, 1, 323-331.  
8961936 C.Romier, K.Reuter, D.Suck, and R.Ficner (1996).
Mutagenesis and crystallographic studies of Zymomonas mobilis tRNA-guanine transglycosylase reveal aspartate 102 as the active site nucleophile.
  Biochemistry, 35, 15734-15739.
PDB codes: 1wkd 1wke 1wkf
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.