1K8W

Crystal structure of the E. coli pseudouridine synthase TruB bound to a T stem-loop RNA

• PDB DOI: https://doi.org/10.2210/pdb1K8W/pdb
• NAKB: 1K8W

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


• Deposited: 2001-10-25 Released: 2001-12-31 
• Deposition Author(s): Hoang, C., Ferre-D'Amare, A.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.211 
• R-Value Work: 0.184 
• R-Value Observed: 0.184 

Literature

Cocrystal structure of a tRNA Psi55 pseudouridine synthase: nucleotide flipping by an RNA-modifying enzyme.

Hoang, C., Ferre-D'Amare, A.R.

(2001) Cell 107: 929-939

• PubMed: 11779468 
• DOI: https://doi.org/10.1016/s0092-8674(01)00618-3
• Primary Citation of Related Structures:  
  1K8W


• PubMed Abstract: 
  

  Pseudouridine (Psi) synthases catalyze the isomerization of specific uridines in cellular RNAs to pseudouridines and may function as RNA chaperones. TruB is responsible for the Psi residue present in the T loops of virtually all tRNAs. The close homolog Cbf5/dyskerin is the catalytic subunit of box H/ACA snoRNPs. These carry out the pseudouridylation of eukaryotic rRNA and snRNAs. The 1.85 A resolution structure of TruB bound to RNA reveals that this enzyme recognizes the preformed three-dimensional structure of the T loop, primarily through shape complementarity. It accesses its substrate uridyl residue by flipping out the nucleotide and disrupts the tertiary structure of tRNA. Structural comparisons with TruB demonstrate that all Psi synthases are descended from a common molecular ancestor.

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Organizational Affiliation: 

Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 44.66 kDa 
• Atom Count: 3,166 
• Modelled Residue Count: 326 
• Deposited Residue Count: 349 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
tRNA Pseudouridine Synthase B	B [auth A]	327	Escherichia coli	Mutation(s): 0  EC: 4.2.1.70 (PDB Primary Data), 5.4.99.25 (UniProt)
UniProt
Find proteins for P60340 (Escherichia coli (strain K12)) Explore P60340  Go to UniProtKB:  P60340

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-R(*GP*GP*CP*AP*AP*CP*GP*GP*UP*(FHU)P*CP*GP*AP*UP*CP*CP*CP*GP*UP*UP*GP*C)-3'	A [auth B]	22	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth B], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.211 
• R-Value Work: 0.184 
• R-Value Observed: 0.184 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 145.054	α = 90
b = 40.361	β = 110.6
c = 77.987	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2001-12-31 
Deposition Author(s): Hoang, C., Ferre-D'Amare, A.R.

Revision History  

• Version 1.0: 2001-12-31
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-07
  Changes: Data collection, Database references, Derived calculations