1SZW

Crystal structure of E. coli tRNA pseudouridine synthase TruD

• PDB DOI: https://doi.org/10.2210/pdb1SZW/pdb

• Classification: LYASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2004-04-06 Released: 2004-04-20 
• Deposition Author(s): Ericsson, U.B., Nordlund, P., Hallberg, B.M., Structural Proteomics in Europe (SPINE)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.239 
• R-Value Work: 0.192 
• R-Value Observed: 0.194 

Literature

X-ray structure of tRNA pseudouridine synthase TruD reveals an inserted domain with a novel fold

Ericsson, U.B., Nordlund, P., Hallberg, B.M.

(2004) FEBS Lett 565: 59-64

• PubMed: 15135053 
• DOI: https://doi.org/10.1016/j.febslet.2004.03.085
• Primary Citation of Related Structures:  
  1SZW


• PubMed Abstract: 
  

  Pseudouridine synthases catalyse the isomerisation of uridine to pseudouridine in structural RNA. The pseudouridine synthase TruD, that modifies U13 in tRNA, belongs to a recently identified and large family of pseudouridine synthases present in all kingdoms of life. We report here the crystal structure of Escherichia coli TruD at 2.0 A resolution. The structure reveals an overall V-shaped molecule with an RNA-binding cleft formed between two domains: a catalytic domain and an insertion domain. The catalytic domain has a fold similar to that of the catalytic domains of previously characterised pseudouridine synthases, whereas the insertion domain displays a novel fold.

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Organizational Affiliation: 

Department of Biochemistry and Biophysics, Stockholm University, Roslagstullsbacken 15, SE-114 21 Stockholm, Sweden.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 85.93 kDa 
• Atom Count: 5,727 
• Modelled Residue Count: 664 
• Deposited Residue Count: 758 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
tRNA pseudouridine synthase D	A, B	379	Escherichia coli	Mutation(s): 4  Gene Names: TRUD EC: 4.2.1.70
UniProt
Find proteins for Q57261 (Escherichia coli (strain K12)) Explore Q57261  Go to UniProtKB:  Q57261

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.239 
• R-Value Work: 0.192 
• R-Value Observed: 0.194 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.18	α = 90
b = 108.11	β = 90
c = 112.52	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MAR345	data collection
XDS	data scaling
SHELXD	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-04-20 
Deposition Author(s): Ericsson, U.B., Nordlund, P., Hallberg, B.M., Structural Proteomics in Europe (SPINE)

Revision History  

• Version 1.0: 2004-04-20
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description