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PDBsum entry 1it7
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protein ligands metals Protein-protein interface(s) links
Transferase PDB id
1it7

 

 

 

 

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Contents
Protein chains
577 a.a. *
Ligands
GUN
Metals
_MG ×2
_ZN ×2
Waters ×184
* Residue conservation analysis
PDB id:
1it7
Name: Transferase
Title: Crystal structure of archaeosine tRNA-guanine transglycosylase complexed with guanine
Structure: Archaeosine tRNA-guanine transglycosylase. Chain: a, b. Engineered: yes
Source: Pyrococcus horikoshii. Organism_taxid: 53953. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Biol. unit: Dimer (from PQS)
Resolution:
2.30Å     R-factor:   0.229     R-free:   0.271
Authors: R.Ishitani,O.Nureki,S.Fukai,T.Kijimoto,N.Nameki,M.Watanabe,H.Kondo, M.Sekine,N.Okada,S.Nishimura,S.Yokoyama,Riken Structural Genomics/proteomics Initiative (Rsgi)
Key ref:
R.Ishitani et al. (2002). Crystal structure of archaeosine tRNA-guanine transglycosylase. J Mol Biol, 318, 665-677. PubMed id: 12054814 DOI: 10.1016/S0022-2836(02)00090-6
Date:
11-Jan-02     Release date:   22-May-02    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
O58843  (ATGT_PYRHO) -  tRNA-guanine(15) transglycosylase from Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)
Seq:
Struc: 		 
Seq:
Struc: 		582 a.a.
577 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.2.4.2.48  - tRNA-guanine(15) transglycosylase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: guanosine15 in tRNA + 7-cyano-7-deazaguanine = 7-cyano-7- carbaguanosine15 in tRNA + guanine
guanosine(15) in tRNA
 + 7-cyano-7-deazaguanine
 = 7-cyano-7- carbaguanosine(15) in tRNA
 +
guanine
Bound ligand (Het Group name = GUN)
corresponds exactly
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    Added reference    
 
 
DOI no: 10.1016/S0022-2836(02)00090-6 J Mol Biol 318:665-677 (2002)
PubMed id: 12054814  
 
 
Crystal structure of archaeosine tRNA-guanine transglycosylase.
R.Ishitani, O.Nureki, S.Fukai, T.Kijimoto, N.Nameki, M.Watanabe, H.Kondo, M.Sekine, N.Okada, S.Nishimura, S.Yokoyama.
 
  ABSTRACT  
 
Archaeosine tRNA-guanine transglycosylase (ArcTGT) catalyzes the exchange of guanine at position 15 in the D-loop of archaeal tRNAs with a free 7-cyano-7-deazaguanine (preQ(0)) base, as the first step in the biosynthesis of an archaea-specific modified base, archaeosine (7-formamidino-7-deazaguanosine). We determined the crystal structures of ArcTGT from Pyrococcus horikoshii at 2.2 A resolution and its complexes with guanine and preQ(0), at 2.3 and 2.5 A resolutions, respectively. The N-terminal catalytic domain folds into an (alpha/beta)(8) barrel with a characteristic zinc-binding site, showing structural similarity with that of the bacterial queuosine TGT (QueTGT), which is involved in queuosine (7-[[(4,5-cis-dihydroxy-2-cyclopenten-1-yl)-amino]methyl]-7-deazaguanosine) biosynthesis and targets the tRNA anticodon. ArcTGT forms a dimer, involving the zinc-binding site and the ArcTGT-specific C-terminal domain. The C-terminal domains have novel folds, including an OB fold-like "PUA domain", whose sequence is widely conserved in eukaryotic and archaeal RNA modification enzymes. Therefore, the C-terminal domains may be involved in tRNA recognition. In the free-form structure of ArcTGT, an alpha-helix located at the rim of the (alpha/beta)(8) barrel structure is completely disordered, while it is ordered in the guanine-bound and preQ(0)-bound forms. Structural comparison of the ArcTGT.preQ(0), ArcTGT.guanine, and QueTGT.preQ(1) complexes provides novel insights into the substrate recognition mechanisms of ArcTGT.
 
  Selected figure(s)  
 
Figure 3.
Figure 3. Domain architecture of the ArcTGT subunit. (a) Ribbon diagram of the ArcTGT subunit. The catalytic domain, domains C1, C2, and C3 are colored yellow, emerald green, sky blue, and dark blue, respectively. Zinc and magnesium ions are shown as metallic balls. (b) Topology diagram of the ArcTGT structure. a-Helices are represented with circles or tubes, and b-strands are shown with rectangles or arrows. 		Figure 7.
Figure 7. The catalytic domain of the preQ[0]-bound form of (a) ArcTGT and (b) the base-free form of QueTGT. The viewpoints of (a) and (b) are adjusted to that of Figure 6. The color of helix a5 corresponds to the atomic B-factors, as indicated below. The arrows indicate the major structural differences between the ArcTGT and QueTGT, which are discussed in the text.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2002, 318, 665-677) copyright 2002.  
  Figures were selected by an automated process.  

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.  
20507607 J.S.Luz, C.R.Ramos, M.C.Santos, P.P.Coltri, F.L.Palhano, D.Foguel, N.I.Zanchin, and C.C.Oliveira (2010).
Identification of archaeal proteins that affect the exosome function in vitro.
  BMC Biochem, 11, 22.  
19925456 M.Vinayak, and C.Pathak (2010).
Queuosine modification of tRNA: its divergent role in cellular machinery.
  Biosci Rep, 30, 135-148.  
20963777 X.Ming, and F.Seela (2010).
Efficient synthesis of the tRNA nucleoside preQ0, 7-cyano-7-deazaguanosine, via microwave-assisted iodo→carbonitrile exchange.
  Chem Biodivers, 7, 2616-2621.  
  19478918 B.E.Yacoubi, G.Phillips, I.K.Blaby, C.E.Haas, Y.Cruz, J.Greenberg, and V.de Crécy-Lagard (2009).
A Gateway platform for functional genomics in Haloferax volcanii: deletion of three tRNA modification genes.
  Archaea, 2, 211-219.  
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.  
19139072 S.Muller, A.Urban, A.Hecker, F.Leclerc, C.Branlant, and Y.Motorin (2009).
Deficiency of the tRNATyr:Psi 35-synthase aPus7 in Archaea of the Sulfolobales order might be rescued by the H/ACA sRNA-guided machinery.
  Nucleic Acids Res, 37, 1308-1322.  
18802692 H.Takagi (2008).
Proline as a stress protectant in yeast: physiological functions, metabolic regulations, and biotechnological applications.
  Appl Microbiol Biotechnol, 81, 211-223.  
18831030 K.Miyazono, Y.Nishimura, Y.Sawano, T.Makino, and M.Tanokura (2008).
Crystal structure of hypothetical protein PH0734.1 from hyperthermophilic archaea Pyrococcus horikoshii OT3.
  Proteins, 73, 1068-1071.
PDB code: 3d79
17394648 B.Gao, and R.S.Gupta (2007).
Phylogenomic analysis of proteins that are distinctive of Archaea and its main subgroups and the origin of methanogenesis.
  BMC Genomics, 8, 86.  
17803682 I.Pérez-Arellano, J.Gallego, and J.Cervera (2007).
The PUA domain - a structural and functional overview.
  FEBS J, 274, 4972-4984.  
17253090 J.Payandeh, and E.F.Pai (2007).
Enzyme-driven speciation: crystallizing Archaea via lipid capture.
  J Mol Evol, 64, 364-374.  
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
17673083 V.de Crécy-Lagard (2007).
Identification of genes encoding tRNA modification enzymes by comparative genomics.
  Methods Enzymol, 425, 153-183.  
16407303 J.Sabina, and D.Söll (2006).
The RNA-binding PUA domain of archaeal tRNA-guanine transglycosylase is not required for archaeosine formation.
  J Biol Chem, 281, 6993-7001.  
16322048 L.M.Iyer, A.M.Burroughs, and L.Aravind (2006).
The ASCH superfamily: novel domains with a fold related to the PUA domain and a potential role in RNA metabolism.
  Bioinformatics, 22, 257-263.  
16456033 X.Manival, C.Charron, J.B.Fourmann, F.Godard, B.Charpentier, and C.Branlant (2006).
Crystal structure determination and site-directed mutagenesis of the Pyrococcus abyssi aCBF5-aNOP10 complex reveal crucial roles of the C-terminal domains of both proteins in H/ACA sRNP activity.
  Nucleic Acids Res, 34, 826-839.
PDB code: 2aus
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.  
15630082 S.Yang, R.F.Doolittle, and P.E.Bourne (2005).
Phylogeny determined by protein domain content.
  Proc Natl Acad Sci U S A, 102, 373-378.  
16260766 W.Sun, X.Xu, M.Pavlova, A.M.Edwards, A.Joachimiak, A.Savchenko, and D.Christendat (2005).
The crystal structure of a novel SAM-dependent methyltransferase PH1915 from Pyrococcus horikoshii.
  Protein Sci, 14, 3121-3128.
PDB code: 2as0
15502337 I.Pérez-Arellano, F.Gil-Ortiz, J.Cervera, and V.Rubio (2004).
Glutamate-5-kinase from Escherichia coli: gene cloning, overexpression, purification and crystallization of the recombinant enzyme and preliminary X-ray studies.
  Acta Crystallogr D Biol Crystallogr, 60, 2091-2094.  
12581659 A.R.Ferré-D'Amaré (2003).
RNA-modifying enzymes.
  Curr Opin Struct Biol, 13, 49-55.  
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.  
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
12732145 R.Ishitani, O.Nureki, N.Nameki, N.Okada, S.Nishimura, and S.Yokoyama (2003).
Alternative tertiary structure of tRNA for recognition by a posttranscriptional modification enzyme.
  Cell, 113, 383-394.
PDB code: 1j2b
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
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 code is shown on the right.

 

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