Modomics - A Database of RNA Modifications

ID Card:

Full name: tRNA pseudouridine synthase B
Synonym: TM_0856
GI: 15643619
COG: COG0130
UniProt: Q9WZW0
Structures: | 1ZE2 | 1ZE1 | 1R3E | 2AB4 |
Alpha Fold Predicted Structure: AF-Q9WZW0-F1
Enzyme type: pseudouridine synthase predicted
Position of modification - modification: t:55 - Y


PDB Structures:


1ZE2

Structure Description:

Title: Crystal Structure of tRNA Pseudouridine Synthase TruB and Its RNA Complex: RNA-protein Recognition Through a Combination of Rigid Docking and Induced Fit
Classification: LYASE
Technique: X-Ray Diffraction
Resolution: 1.85
R value free: 0.257
R value observed: 0.228
R value work: 0.228

Abstract of the PDB Structure's related Publication:

RNA pseudouridine synthase, TruB, catalyzes pseudouridine formation at U55 in tRNA. This posttranscriptional modification is almost universally conserved and occurs in the T arm of most tRNAs. We determined the crystal structure of Escherichia coli TruB apo enzyme, as well as the structure of Thermotoga maritima TruB in complex with RNA. Comparison of the RNA-free and -bound forms of TruB reveals that this enzyme undergoes significant conformational changes on binding to its substrate. These conformational changes include the ordering of the "thumb loop," which binds right into the RNA hairpin loop, and a 10 degree hinge movement of the C-terminal domain. Along with the result of docking experiments performed on apo TruB, we conclude that TruB recognizes its RNA substrate through a combination of rigid docking and induced fit, with TruB first rigidly binding to its target and then maximizing the interaction by induced fit.

Download RCSB-PDB Structures:

Pdb Files   1R3F.pdb   1ZE1.pdb   1ZE2.pdb  
Pdbx/mmCIF Files   1R3F.cif   1ZE1.cif   1ZE2.cif  


Protein sequence:

MKHGILVAYKPKGPTSHDVVDEVRKKLKTRKVGHGGTLDPFACGVLIIGVNQGTRILEFYKDLKKVYWVKMRLGLITETFDITGEVVEERECNVTEEEIREAIFSFVGEYDQVPPAYSAKKYKGERLYKLAREGKIINLPPKRVKIFKIWDVNIEGRDVSFRVEVSPGTYIRSLCMDIGYKLGCGATAVELVRESVGPHTIEESLNVFEAAPEEIENRIIPLEKCLEWLPRVVVHQESTKMILNGSQIHLEMLKEWDGFKKGEVVRVFNEEGRLLALAEAERNSSFLETLRKHERNERVLTLRKVFNTR

Comments:

Only enzyme-RNA complex formation was tested in vitro.





Alpha Fold Predicted Structure:






Clear Selection and Reset Camera

Protein sequence:

M K H G I L V A Y K P K G P T S H D V V D E V R K K L K T R K V G H G G T L D P F A C G V L I I G V N Q G T R I L E F Y K D L K K V Y W V K M R L G L I T E T F D I T G E V V E E R E C N V T E E E I R E A I F S F V G E Y D Q V P P A Y S A K K Y K G E R L Y K L A R E G K I I N L P P K R V K I F K I W D V N I E G R D V S F R V E V S P G T Y I R S L C M D I G Y K L G C G A T A V E L V R E S V G P H T I E E S L N V F E A A P E E I E N R I I P L E K C L E W L P R V V V H Q E S T K M I L N G S Q I H L E M L K E W D G F K K G E V V R V F N E E G R L L A L A E A E R N S S F L E T L R K H E R N E R V L T L R K V F N T R
50100150200250300SequenceGHTBSN

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-Q9WZW0-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-Q9WZW0-F1.cif  
DSSP Secondary Structures   Q9WZW0.dssp  





Publications: