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PDBsum entry 1j2b

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protein dna_rna metals Protein-protein interface(s) links
Transferase/RNA PDB id
1j2b
Jmol
Contents
Protein chains
576 a.a. *
DNA/RNA
Metals
_MG ×4
_ZN ×2
Waters ×41
* Residue conservation analysis
PDB id:
1j2b
Name: Transferase/RNA
Title: Crystal structure of archaeosine tRNA-guanine transglycosylase complexed with lambda-form tRNA(val)
Structure: tRNA(val). Chain: c, d. Engineered: yes. Archaeosine tRNA-guanine transglycosylase. Chain: a, b. Engineered: yes
Source: Synthetic: yes. Other_details: synthetic tRNA transcript. Sequence from pyrococcus horikoshii. Organism_taxid: 53953. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Biol. unit: Tetramer (from PQS)
Resolution:
3.30Å     R-factor:   0.225     R-free:   0.288
Authors: R.Ishitani,O.Nureki,N.Nameki,N.Okada,S.Nishimura,S.Yokoyama, Riken Structural Genomics/proteomics Initiative (Rsgi)
Key ref:
R.Ishitani et al. (2003). Alternative tertiary structure of tRNA for recognition by a posttranscriptional modification enzyme. Cell, 113, 383-394. PubMed id: 12732145 DOI: 10.1016/S0092-8674(03)00280-0
Date:
29-Dec-02     Release date:   27-May-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
O58843  (ATGT_PYRHO) -  tRNA-guanine(15) transglycosylase
Seq:
Struc:
 
Seq:
Struc:
582 a.a.
576 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: Guanine15 in tRNA + 7-cyano-7-carbaguanine = 7-cyano-7-carbaguanine15 in tRNA + guanine
Guanine(15) in tRNA
+ 7-cyano-7-carbaguanine
= 7-cyano-7-carbaguanine(15) 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     7 terms  

 

 
    Added reference    
 
 
DOI no: 10.1016/S0092-8674(03)00280-0 Cell 113:383-394 (2003)
PubMed id: 12732145  
 
 
Alternative tertiary structure of tRNA for recognition by a posttranscriptional modification enzyme.
R.Ishitani, O.Nureki, N.Nameki, N.Okada, S.Nishimura, S.Yokoyama.
 
  ABSTRACT  
 
Transfer RNA (tRNA) canonically has the clover-leaf secondary structure with the acceptor, D, anticodon, and T arms, which are folded into the L-shaped tertiary structure. To strengthen the L form, posttranscriptional modifications occur on nucleotides buried within the core, but the modification enzymes are paradoxically inaccessible to them in the L form. In this study, we determined the crystal structure of tRNA bound with archaeosine tRNA-guanine transglycosylase, which modifies G15 of the D arm in the core. The bound tRNA assumes an alternative conformation ("lambda form") drastically different from the L form. All of the D-arm secondary base pairs and the canonical tertiary interactions are disrupted. Furthermore, a helical structure is reorganized, while the rest of the D arm is single stranded and protruded. Consequently, the enzyme precisely locates the exposed G15 in the active site, by counting the nucleotide number from G1 to G15 in the lambda form.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. A tRNA Modification Enzyme, ArcTGT, Replaces the Base at Position 15 in the D Loop, which Is Deeply Buried in the Canonical L Form of tRNA(A) The secondary and tertiary structures of tRNA in the canonical L form. The acceptor, D, anticodon, and T arms, and the variable loop are colored red, yellow, green, purple, and sky blue, respectively. The secondary structure is shown in the clover-leaf (left) and L-shape (center) diagrams. The RNA backbones are shown with thick lines, while the Watson-Crick base pairs are indicated with short thin lines. In the tertiary structure (right), the RNA backbone is shown as a tube model and the Watson-Crick base pairs are shown with sticks. The ArcTGT target site, G15, which is buried deeply in the tRNA tertiary structure, is circled.(B) Biosynthetic pathway of archaeosine. The guanine moiety of G15 is replaced with preQ[0] by the transglycosylation catalyzed by ArcTGT. Afterwards, the preQ[0] at position 15 is further modified to archaeosine on the polynucleotide chain, by an unknown pathway (Watanabe et al., 1997). The biosynthetic pathway of preQ[0] is also unknown.
Figure 2.
Figure 2. Overall Structure of the P. horikoshii ArcTGT·tRNA^Val Complex(A) Stereo view of the ArcTGT·tRNA^Val complex. ArcTGT and tRNA are shown as ribbon models. The catalytic domain and the C-terminal domains of the ArcTGT subunit A are colored green and brown, while those of subunit B are colored deep blue and purple, respectively. tRNA-I and -II are colored sky blue and pink, respectively.(B and C) Close-ups of the ArcTGT-tRNA interaction interfaces. (B) The anticodon arm and the DV helix are accommodated into the cleft formed between the catalytic and C-terminal domains. (C) U8 to U17 of the protruded D arm are recognized by the C-terminal domains of subunit A and the catalytic domain of subunit B, and G15 is accommodated into the catalytic pocket. The coloring schemes of (B) and (C) are the same as in (A).(D) Schematic diagram of the ArcTGT-tRNA interactions.
 
  The above figures are reprinted by permission from Cell Press: Cell (2003, 113, 383-394) copyright 2003.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21397180 A.Guelorget, and B.Golinelli-Pimpaneau (2011).
Mechanism-based strategies for trapping and crystallizing complexes of RNA-modifying enzymes.
  Structure, 19, 282-291.  
20541511 B.W.Shen, D.F.Heiter, S.H.Chan, H.Wang, S.Y.Xu, R.D.Morgan, G.G.Wilson, and B.L.Stoddard (2010).
Unusual target site disruption by the rare-cutting HNH restriction endonuclease PacI.
  Structure, 18, 734-743.
PDB codes: 3ldy 3m7k
  20871851 B.de Koning, F.Blombach, S.J.Brouns, and J.van der Oost (2010).
Fidelity in archaeal information processing.
  Archaea, 2010, 0.  
20558546 J.Widmann, J.K.Harris, C.Lozupone, A.Wolfson, and R.Knight (2010).
Stable tRNA-based phylogenies using only 76 nucleotides.
  RNA, 16, 1469-1477.  
20106954 M.Hengesbach, F.Voigts-Hoffmann, B.Hofmann, and M.Helm (2010).
Formation of a stalled early intermediate of pseudouridine synthesis monitored by real-time FRET.
  RNA, 16, 610-620.  
20348443 O.Kolesnikova, H.Kazakova, C.Comte, S.Steinberg, P.Kamenski, R.P.Martin, I.Tarassov, and N.Entelis (2010).
Selection of RNA aptamers imported into yeast and human mitochondria.
  RNA, 16, 926-941.  
19298824 A.Alian, A.DeGiovanni, S.L.Griner, J.S.Finer-Moore, and R.M.Stroud (2009).
Crystal structure of an RluF-RNA complex: a base-pair rearrangement is the key to selectivity of RluF for U2604 of the ribosome.
  J Mol Biol, 388, 785-800.
PDB code: 3dh3
19114708 A.Urban, I.Behm-Ansmant, C.Branlant, and Y.Motorin (2009).
RNA Sequence and Two-dimensional Structure Features Required for Efficient Substrate Modification by the Saccharomyces cerevisiae RNA:{Psi}-Synthase Pus7p.
  J Biol Chem, 284, 5845-5858.  
19191354 C.Bertonati, M.Punta, M.Fischer, G.Yachdav, F.Forouhar, W.Zhou, A.P.Kuzin, J.Seetharaman, M.Abashidze, T.A.Ramelot, M.A.Kennedy, J.R.Cort, A.Belachew, J.F.Hunt, L.Tong, G.T.Montelione, and B.Rost (2009).
Structural genomics reveals EVE as a new ASCH/PUA-related domain.
  Proteins, 75, 760-773.
PDB codes: 1zce 2eve 2g2x 2gbs
19742176 I.Agmon (2009).
The dimeric proto-ribosome: structural details and possible implications on the origin of life.
  Int J Mol Sci, 10, 2921-2934.  
19144910 J.A.Hammond, R.P.Rambo, M.E.Filbin, and J.S.Kieft (2009).
Comparison and functional implications of the 3D architectures of viral tRNA-like structures.
  RNA, 15, 294-307.  
19767615 M.Messmer, J.Pütz, T.Suzuki, T.Suzuki, C.Sauter, M.Sissler, and F.Catherine (2009).
Tertiary network in mammalian mitochondrial tRNAAsp revealed by solution probing and phylogeny.
  Nucleic Acids Res, 37, 6881-6895.  
19749755 S.Goto-Ito, T.Ito, M.Kuratani, Y.Bessho, and S.Yokoyama (2009).
Tertiary structure checkpoint at anticodon loop modification in tRNA functional maturation.
  Nat Struct Mol Biol, 16, 1109-1115.
PDB codes: 2zzm 2zzn
19287006 Y.Suzuki, A.Noma, T.Suzuki, R.Ishitani, and O.Nureki (2009).
Structural basis of tRNA modification with CO2 fixation and methylation by wybutosine synthesizing enzyme TYW4.
  Nucleic Acids Res, 37, 2910-2925.
PDB codes: 2zw9 2zwa 2zzk
  18997348 A.P.Silva, R.T.Byrne, M.Chechik, C.Smits, D.G.Waterman, and A.A.Antson (2008).
Expression, purification, crystallization and preliminary X-ray studies of the TAN1 orthologue from Methanothermobacter thermautotrophicus.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 1083-1086.  
18653523 H.Walbott, N.Leulliot, H.Grosjean, and B.Golinelli-Pimpaneau (2008).
The crystal structure of Pyrococcus abyssi tRNA (uracil-54, C5)-methyltransferase provides insights into its tRNA specificity.
  Nucleic Acids Res, 36, 4929-4940.
PDB codes: 2jjq 2vs1
18984158 J.Holzmann, P.Frank, E.Löffler, K.L.Bennett, C.Gerner, and W.Rossmanith (2008).
RNase P without RNA: identification and functional reconstitution of the human mitochondrial tRNA processing enzyme.
  Cell, 135, 462-474.  
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
18836497 R.Giegé (2008).
Toward a more complete view of tRNA biology.
  Nat Struct Mol Biol, 15, 1007-1014.  
18539024 R.Ishitani, S.Yokoyama, and O.Nureki (2008).
Structure, dynamics, and function of RNA modification enzymes.
  Curr Opin Struct Biol, 18, 330-339.  
18332121 W.A.Decatur, and M.N.Schnare (2008).
Different mechanisms for pseudouridine formation in yeast 5S and 5.8S rRNAs.
  Mol Cell Biol, 28, 3089-3100.  
17580114 H.Li (2007).
Complexes of tRNA and maturation enzymes: shaping up for translation.
  Curr Opin Struct Biol, 17, 293-301.  
17567576 H.Walbott, S.Auxilien, H.Grosjean, and B.Golinelli-Pimpaneau (2007).
The carboxyl-terminal extension of yeast tRNA m5C methyltransferase enhances the catalytic efficiency of the amino-terminal domain.
  J Biol Chem, 282, 23663-23671.  
17803682 I.Pérez-Arellano, J.Gallego, and J.Cervera (2007).
The PUA domain - a structural and functional overview.
  FEBS J, 274, 4972-4984.  
17574834 K.Ye (2007).
H/ACA guide RNAs, proteins and complexes.
  Curr Opin Struct Biol, 17, 287-292.  
18073113 M.Kuratani, Y.Yoshikawa, Y.Bessho, K.Higashijima, T.Ishii, R.Shibata, S.Takahashi, K.Yutani, and S.Yokoyama (2007).
Structural basis of the initial binding of tRNA(Ile) lysidine synthetase TilS with ATP and L-lysine.
  Structure, 15, 1642-1653.
PDB codes: 2e21 2e89
17652139 R.Oliva, A.Tramontano, and L.Cavallo (2007).
Mg2+ binding and archaeosine modification stabilize the G15 C48 Levitt base pair in tRNAs.
  RNA, 13, 1427-1436.  
17507661 R.Tyagi, and D.H.Mathews (2007).
Predicting helical coaxial stacking in RNA multibranch loops.
  RNA, 13, 939-951.  
17284456 S.L.Reichow, T.Hamma, A.R.Ferré-D'Amaré, and G.Varani (2007).
The structure and function of small nucleolar ribonucleoproteins.
  Nucleic Acids Res, 35, 1452-1464.  
17868690 T.Christian, and Y.M.Hou (2007).
Distinct determinants of tRNA recognition by the TrmD and Trm5 methyl transferases.
  J Mol Biol, 373, 623-632.  
17188032 C.Hoang, J.Chen, C.A.Vizthum, J.M.Kandel, C.S.Hamilton, E.G.Mueller, and A.R.Ferré-D'Amaré (2006).
Crystal structure of pseudouridine synthase RluA: indirect sequence readout through protein-induced RNA structure.
  Mol Cell, 24, 535-545.
PDB code: 2i82
16809540 H.Oshikane, K.Sheppard, S.Fukai, Y.Nakamura, R.Ishitani, T.Numata, R.L.Sherrer, L.Feng, E.Schmitt, M.Panvert, S.Blanquet, Y.Mechulam, D.Söll, and O.Nureki (2006).
Structural basis of RNA-dependent recruitment of glutamine to the genetic code.
  Science, 312, 1950-1954.
PDB code: 2d6f
16600901 I.Zegers, D.Gigot, F.van Vliet, C.Tricot, S.Aymerich, J.M.Bujnicki, J.Kosinski, and L.Droogmans (2006).
Crystal structure of Bacillus subtilis TrmB, the tRNA (m7G46) methyltransferase.
  Nucleic Acids Res, 34, 1925-1934.
PDB code: 2fca
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.  
16943774 L.Li, and K.Ye (2006).
Crystal structure of an H/ACA box ribonucleoprotein particle.
  Nature, 443, 302-307.
PDB code: 2hvy
16452298 M.Helm (2006).
Post-transcriptional nucleotide modification and alternative folding of RNA.
  Nucleic Acids Res, 34, 721-733.  
16427014 R.Rashid, B.Liang, D.L.Baker, O.A.Youssef, Y.He, K.Phipps, R.M.Terns, M.P.Terns, and H.Li (2006).
Crystal structure of a Cbf5-Nop10-Gar1 complex and implications in RNA-guided pseudouridylation and dyskeratosis congenita.
  Mol Cell, 21, 249-260.
PDB code: 2ey4
17085441 S.Hur, R.M.Stroud, and J.Finer-Moore (2006).
Substrate recognition by RNA 5-methyluridine methyltransferases and pseudouridine synthases: a structural perspective.
  J Biol Chem, 281, 38969-38973.  
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.  
  16511140 E.Pleshe, J.Truesdell, and R.T.Batey (2005).
Structure of a class II TrmH tRNA-modifying enzyme from Aquifex aeolicus.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 722-728.
PDB code: 1zjr
15987815 M.H.Renalier, N.Joseph, C.Gaspin, P.Thebault, and A.Mougin (2005).
The Cm56 tRNA modification in archaea is catalyzed either by a specific 2'-O-methylase, or a C/D sRNP.
  RNA, 11, 1051-1063.  
15972857 R.Hao, M.W.Zhao, Z.X.Hao, Y.N.Yao, and E.D.Wang (2005).
A T-stem slip in human mitochondrial tRNALeu(CUN) governs its charging capacity.
  Nucleic Acids Res, 33, 3606-3613.  
16163389 S.Chimnaronk, M.Gravers Jeppesen, T.Suzuki, J.Nyborg, and K.Watanabe (2005).
Dual-mode recognition of noncanonical tRNAs(Ser) by seryl-tRNA synthetase in mammalian mitochondria.
  EMBO J, 24, 3369-3379.
PDB code: 1wle
15899842 S.K.Purushothaman, J.M.Bujnicki, H.Grosjean, and B.Lapeyre (2005).
Trm11p and Trm112p are both required for the formation of 2-methylguanosine at position 10 in yeast tRNA.
  Mol Cell Biol, 25, 4359-4370.  
15963891 S.R.Holbrook (2005).
RNA structure: the long and the short of it.
  Curr Opin Struct Biol, 15, 302-308.  
16286935 T.Hamma, S.L.Reichow, G.Varani, and A.R.Ferré-D'Amaré (2005).
The Cbf5-Nop10 complex is a molecular bracket that organizes box H/ACA RNPs.
  Nat Struct Mol Biol, 12, 1101-1107.
PDB codes: 2apo 2aqa 2aqc
15766524 T.T.Lee, S.Agarwalla, and R.M.Stroud (2005).
A unique RNA Fold in the RumA-RNA-cofactor ternary complex contributes to substrate selectivity and enzymatic function.
  Cell, 120, 599-611.
PDB code: 2bh2
15028724 B.N.Chaudhuri, S.Chan, L.J.Perry, and T.O.Yeates (2004).
Crystal structure of the apo forms of psi 55 tRNA pseudouridine synthase from Mycobacterium tuberculosis: a hinge at the base of the catalytic cleft.
  J Biol Chem, 279, 24585-24591.
PDB code: 1sgv
15037613 C.T.Lauhon, W.M.Erwin, and G.N.Ton (2004).
Substrate specificity for 4-thiouridine modification in Escherichia coli.
  J Biol Chem, 279, 23022-23029.  
15358762 H.Okamoto, K.Watanabe, Y.Ikeuchi, T.Suzuki, Y.Endo, and H.Hori (2004).
Substrate tRNA recognition mechanism of tRNA (m7G46) methyltransferase from Aquifex aeolicus.
  J Biol Chem, 279, 49151-49159.  
15210688 J.Armengaud, J.Urbonavicius, B.Fernandez, G.Chaussinand, J.M.Bujnicki, and H.Grosjean (2004).
N2-methylation of guanosine at position 10 in tRNA is catalyzed by a THUMP domain-containing, S-adenosylmethionine-dependent methyltransferase, conserved in Archaea and Eukaryota.
  J Biol Chem, 279, 37142-37152.  
14730022 M.Del Campo, J.Ofengand, and A.Malhotra (2004).
Crystal structure of the catalytic domain of RluD, the only rRNA pseudouridine synthase required for normal growth of Escherichia coli.
  RNA, 10, 231-239.
PDB code: 1qyu
15102450 P.W.Haebel, S.Gutmann, and N.Ban (2004).
Dial tm for rescue: tmRNA engages ribosomes stalled on defective mRNAs.
  Curr Opin Struct Biol, 14, 58-65.  
14999002 Y.Kaya, M.Del Campo, J.Ofengand, and A.Malhotra (2004).
Crystal structure of TruD, a novel pseudouridine synthase with a new protein fold.
  J Biol Chem, 279, 18107-18110.
PDB code: 1si7
14513020 C.C.Correll (2003).
Caught in the act of modifying tRNA.
  Nat Struct Biol, 10, 772-773.  
14602911 M.L.Bortolin, J.P.Bachellerie, and B.Clouet-d'Orval (2003).
In vitro RNP assembly and methylation guide activity of an unusual box C/D RNA, cis-acting archaeal pre-tRNA(Trp).
  Nucleic Acids Res, 31, 6524-6535.  
12732135 P.Schimmel, and K.Tamura (2003).
tRNA structure goes from L to lambda.
  Cell, 113, 276-278.  
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
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 codes are shown on the right.