1SB7 | pdb_00001sb7

Crystal structure of the E.coli pseudouridine synthase TruD

• PDB DOI: https://doi.org/10.2210/pdb1SB7/pdb

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


• Deposited: 2004-02-10 Released: 2004-06-29 
• Deposition Author(s): Hoang, C., Ferre-D'Amare, A.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.254 (Depositor), 0.259 (DCC) 
• R-Value Work: 
  0.216 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.216 (Depositor) 

Literature

Crystal structure of the highly divergent pseudouridine synthase TruD reveals a circular permutation of a conserved fold.

Hoang, C., Ferre-D'Amare, A.R.

(2004) RNA 10: 1026-1033

• PubMed: 15208439 
• DOI: https://doi.org/10.1261/rna.7240504
• Primary Citation Related Structures: 
  1SB7


• PubMed Abstract: 
  

  The pseudouridine (Psi) synthases Pus7p and TruD define a family of RNA-modifying enzymes with no sequence similarity to previously characterized Psi synthases. The 2.2 A resolution structure of Escherichia coli TruD reveals a U-shaped molecule with a catalytic domain that superimposes closely on that of other Psi synthases. A domain that appears to be unique to TruD/Pus7p family enzymes hinges over the catalytic domain, possibly serving to clasp the substrate RNAs. The active site comprises residues that are conserved in other Psi synthases, although at least one comes from a structurally distinct part of the protein. Remarkably, the connectivity of the structural elements of the TruD catalytic domain is a circular permutation of that of its paralogs. Because the sequence of the permuted segment, a beta-strand that bisects the catalytic domain, is conserved among orthologs from bacteria, archaea and eukarya, the permutation likely happened early in evolution.

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Organizational Affiliation: 
• Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109-1024, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 83.38 kDa 
• Atom Count: 5,723 
• Modeled Residue Count: 686 
• Deposited Residue Count: 736 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
tRNA pseudouridine synthase D	A, B	368	Escherichia coli	Mutation(s): 4  Gene Names: TRUD, B2745 EC: 4.2.1.70 (PDB Primary Data), 5.4.99.27 (UniProt)
UniProt
Find proteins for Q57261 (Escherichia coli (strain K12)) Explore Q57261  Go to UniProtKB:  Q57261

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	E [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	C [auth A], D [auth A], F [auth B], G [auth B], H [auth B], I [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

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: 2.20 Å
• R-Value Free:  0.254 (Depositor), 0.259 (DCC) 
• R-Value Work:  0.216 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.216 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.665	α = 90
b = 108.78	β = 90
c = 111.855	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-06-29 
Deposition Author(s): Hoang, C., Ferre-D'Amare, A.R.

Revision History  

• Version 1.0: 2004-06-29
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary