Modomics - A Database of RNA Modifications

ID Card:

Full name: 7-cyano-7-deazaguanine tRNA-ribosyltransferase
Synonym: PH1116
GI: 14590946
COG: COG0343
UniProt: O58843
Structures: | 1J2B | 1IT8 | 1IT7 | 1IQ8 |
Alpha Fold Predicted Structure: AF-O58843-F1
Enzyme type: transglycosylase
Position of modification - modification: t:15 - preQ1


PDB Structures:


1J2B

Structure Description:

Title:
Classification:
Technique:

Abstract of the PDB Structure's related Publication:

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.

Download RCSB-PDB Structures:

Pdb Files   1IQ8.pdb   1IT7.pdb   1IT8.pdb   1J2B.pdb  
Pdbx/mmCIF Files   1IQ8.cif   1IT7.cif   1IT8.cif   1J2B.cif  


Protein sequence:

MSRGDKMLKFEIKARDGAGRIGKLEVNGKKIETPAIMPVVNPKQMVVEPKELEKMGFEIIITNSYIIYKDEELRRKALELGIHRMLDYNGIIEVDSGSFQLMKYGSIEVSNREIIEFQHRIGVDIGTFLDIPTPPDAPREQAVKELEITLSRAREAEEIKEIPMNATIQGSTYTDLRRYAARRLSSMNFEIHPIGGVVPLLESYRFRDVVDIVISSKMALRPDRPVHLFGAGHPIVFALAVAMGVDLFDSASYALYAKDDRYMTPEGTKRLDELDYFPCSCPVCSKYTPQELREMPKEERTRLLALHNLWVIKEEIKRVKQAIKEGELWRLVDERARSHPKLYSAYKRLLEHYTFLEEFEPITKKSALFKISNESLRWPVVRRAKERAKSINERFGELVEHPIFGRVSRYLSLTYPFAQSEAEDDFKIEKPTKEDAIKYVMAIAEYQFGEGASRAFDDAKVELSKTGMPRQVKVNGKRLATVRADDGLLTLGIEGAKRLHRVLPYPRMRVVVNKEAEPFARKGKDVFAKFVIFADPGIRPYDEVLVVNENDELLATGQALLSGREMIVFQYGRAVKVRKGVE

Comments:

For more details on possible enzymatic activity see the entry for H. volcanii TgtA.





Alpha Fold Predicted Structure:






Clear Selection and Reset Camera

Protein sequence:

M S R G D K M L K F E I K A R D G A G R I G K L E V N G K K I E T P A I M P V V N P K Q M V V E P K E L E K M G F E I I I T N S Y I I Y K D E E L R R K A L E L G I H R M L D Y N G I I E V D S G S F Q L M K Y G S I E V S N R E I I E F Q H R I G V D I G T F L D I P T P P D A P R E Q A V K E L E I T L S R A R E A E E I K E I P M N A T I Q G S T Y T D L R R Y A A R R L S S M N F E I H P I G G V V P L L E S Y R F R D V V D I V I S S K M A L R P D R P V H L F G A G H P I V F A L A V A M G V D L F D S A S Y A L Y A K D D R Y M T P E G T K R L D E L D Y F P C S C P V C S K Y T P Q E L R E M P K E E R T R L L A L H N L W V I K E E I K R V K Q A I K E G E L W R L V D E R A R S H P K L Y S A Y K R L L E H Y T F L E E F E P I T K K S A L F K I S N E S L R W P V V R R A K E R A K S I N E R F G E L V E H P I F G R V S R Y L S L T Y P F A Q S E A E D D F K I E K P T K E D A I K Y V M A I A E Y Q F G E G A S R A F D D A K V E L S K T G M P R Q V K V N G K R L A T V R A D D G L L T L G I E G A K R L H R V L P Y P R M R V V V N K E A E P F A R K G K D V F A K F V I F A D P G I R P Y D E V L V V N E N D E L L A T G Q A L L S G R E M I V F Q Y G R A V K V R K G V E

Secondary Structure Alphabet

  • G: 3-turn helix (310helix)
  • H: α-helix
  • I: 𝝅-helix (5 - turn helix)
  • T: Hydrogen Bonded Turn
  • B: β-sheet
  • S: Bend
  • C: Coil (residues not present in any of the above conformations)
  • N: Not assigned

Download PDB Structures & DSSP Secondary Structures:

Alpha Fold Pdb Files   AF-O58843-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-O58843-F1.cif  
DSSP Secondary Structures   O58843.dssp  





Publications:

Title Authors Journal Details PubMed Id DOI
Crystal structure of archaeosine tRNA-guanine transglycosylase. Ishitani R, Nureki O, Fukai S, Kijimoto T, Nameki N, Watanabe M, Kondo H, Sekine M, Okada N, Nishimura S, Yokoyama S J Mol Biol [details] 12054814 -
Alternative tertiary structure of tRNA for recognition by a posttranscriptional modification enzyme. Ishitani R, Nureki O, Nameki N, Okada N, Nishimura S, Yokoyama S Cell [details] 12732145 -

Links:

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