1R3E

Crystal Structure of tRNA Pseudouridine Synthase TruB and Its RNA Complex: RNA-protein Recognition Through a Combination of Rigid Docking and Induced Fit

• PDB DOI:  https://doi.org/10.2210/pdb1R3E/pdb
• NAKB: 1R3E

• Classification: LYASE/RNA
• Organism(s): Thermotoga maritima
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2003-10-01 Released: 2003-11-04 
• Deposition Author(s): Pan, H., Agarwalla, S., Moustakas, D.T., Finer-Moore, J., Stroud, R.M.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.273 
• R-Value Work: 0.223 
• R-Value Observed: 0.223 

Literature

Crystal Structure of tRNA Pseudouridine Synthase TruB and Its RNA Complex: RNA Recognition Through a Combination of Rigid Docking and Induced Fit

Pan, H., Agarwalla, S., Moustakas, D.T., Finer-Moore, J., Stroud, R.M.

(2003) Proc Natl Acad Sci U S A 100: 12648-12653

• PubMed: 14566049 
• DOI: https://doi.org/10.1073/pnas.2135585100
• Primary Citation of Related Structures:  
  1R3E, 1R3F


• PubMed Abstract: 
  

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.

---

Organizational Affiliation: 

Department of Biophysics and Biochemistry, University of California, San Francisco, CA 94143, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 51.69 kDa 
• Atom Count: 3,789 
• Modelled Residue Count: 356 
• Deposited Residue Count: 360 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
tRNA pseudouridine synthase B	D [auth A]	309	Thermotoga maritima	Mutation(s): 0  Gene Names: truB EC: 4.2.1.70 (PDB Primary Data), 5.4.99.25 (UniProt)
UniProt
Find proteins for Q9WZW0 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9WZW0  Go to UniProtKB:  Q9WZW0

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-R(*CP*UP*GP*UP*GP*UP*(FHU)P*CP*GP*AP*UP*CP*CP*AP*CP*AP*G)-3'	A [auth C]	17	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-R(*CP*UP*GP*UP*GP*UP*UP*CP*GP*AP*UP*CP*CP*AP*CP*AP*G)-3'	B [auth D], C [auth E]	17	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.273 
• R-Value Work: 0.223 
• R-Value Observed: 0.223 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.862	α = 90
b = 159.337	β = 97.77
c = 44.545	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-11-04 
Deposition Author(s): Pan, H., Agarwalla, S., Moustakas, D.T., Finer-Moore, J., Stroud, R.M.

Revision History  

• Version 1.0: 2003-11-04
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2011-11-16
  Changes: Atomic model
• Version 1.4: 2018-02-07
  Changes: Advisory, Experimental preparation