Modomics - A Database of RNA Modifications

ID Card:

Full name: 7-cyano-7-deazaguanine tRNA-ribosyltransferase
Synonym: Tgt, HVO_2001
GI: 13516848
UniProt: Q9C4M3
Structures: | 1J2B |
Alpha Fold Predicted Structure: AF-Q9C4M3-F1
Enzyme type: transglycosylase
Position of modification - modification: t:15 - G+


PDB Structures:


1J2B

Structure Description:

Title: Crystal Structure Of Archaeosine tRNA-Guanine Transglycosylase Complexed With lambda-form tRNA(Val)
Classification: transferase/RNA
Technique: X-Ray Diffraction
Resolution: 3.3
R value free: 0.288
R value observed: 0.225
R value work: 0.225

Abstract of the PDB Structure's related Publication:

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.

Download RCSB-PDB Structures:

Pdb Files   1J2B.pdb  
Pdbx/mmCIF Files   1J2B.cif  


Protein sequence:

MRDHFELRDGDLAGRIGRLSVPRAGVTVETPALLPVVNPNIDTISPARLESEFGAEILITNSYIIKTNDHLREEALDVGLHEMLDFDGAIMTDSGSFQLAEYGEIDTTTEEILQFQRDIGTDIATPVDIPTPPDVAREQAEADLEITRQALADAEAADTGEMLVNAPVQGSTYPDLREEAGRHADATDLDVFPVGAVVPMMNAYRYDDMVDAVAAAKRGLGVDAPVHLFGAGHPMMLVLAVALGCDLFDSAAYALYARDGRYLTVRGTEHLEDLDYLPCTCPICTEYSPDDLREKGSKRQEQLLAEHNLHVTFAELRRIKQAIRDGDLMELVEERARSHPAMLDGYRALLAHVDQLEREDPASKGAFFYASNESAHRPEVARHHARMDRLTAEGHVLLTEGGVPSGDDFDATWRVVPPFGPFPRSLSETYPLTAEVPERLDRDAYEQAARGVSRLVEENPDAAFTLAHDDWPESALARVPESVELESLSAVSERLGDEASVGGDDGDDGGSASSAE

Comments:

tgtA belongs to the archaeosine tRNA-ribosyltransferase family. It exchanges the guanine residues with 7-cyano-7--deazoguanosine (preQ0) at position 15 in the dihydrouridine loop (D-loop) of archaeal tRNAs, a site not modified in any tRNA outside Archaea. Coupled with its molecular structure, which consists of an unusual 7-deazaguanosine core structure with a formaidine group on its 7th position, it is hypothesised that preQ0 stabilizes tRNA tertiary structure (Turner et al. 2020 ). In Haloferax volacanii tgtA modifies RNALysCUU (Watanabe et al. 1997 ). Its structure with tRNA was solved for TgtA from Pyrococcus horikoshii (1J2B).





Alpha Fold Predicted Structure:




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Protein sequence:

M R D H F E L R D G D L A G R I G R L S V P R A G V T V E T P A L L P V V N P N I D T I S P A R L E S E F G A E I L I T N S Y I I K T N D H L R E E A L D V G L H E M L D F D G A I M T D S G S F Q L A E Y G E I D T T T E E I L Q F Q R D I G T D I A T P V D I P T P P D V A R E Q A E A D L E I T R Q A L A D A E A A D T G E M L V N A P V Q G S T Y P D L R E E A G R H A D A T D L D V F P V G A V V P M M N A Y R Y D D M V D A V A A A K R G L G V D A P V H L F G A G H P M M L V L A V A L G C D L F D S A A Y A L Y A R D G R Y L T V R G T E H L E D L D Y L P C T C P I C T E Y S P D D L R E K G S K R Q E Q L L A E H N L H V T F A E L R R I K Q A I R D G D L M E L V E E R A R S H P A M L D G Y R A L L A H V D Q L E R E D P A S K G A F F Y A S N E S A H R P E V A R H H A R M D R L T A E G H V L L T E G G V P S G D D F D A T W R V V P P F G P F P R S L S E T Y P L T A E V P E R L D R D A Y E Q A A R G V S R L V E E N P D A A F T L A H D D W P E S A L A R V P E S V E L E S L S A V S E R L G D E A S V G G D D G D D G G S A S S A E
50100150200250300350400450500SequenceGHITBSN

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-Q9C4M3-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-Q9C4M3-F1.cif  
DSSP Secondary Structures   Q9C4M3.dssp  





Publications:

Links:

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