3W9Z | pdb_00003w9z

Crystal structure of DusC

• PDB DOI: https://doi.org/10.2210/pdb3W9Z/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-04-19 Released: 2013-07-31 
• Deposition Author(s): Chen, M., Yu, J., Tanaka, Y., Tanaka, I., Yao, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.235 (Depositor), 0.238 (DCC) 
• R-Value Work: 
  0.221 (Depositor), 0.223 (DCC) 
• R-Value Observed: 
  0.221 (Depositor) 

Literature

Structure of dihydrouridine synthase C (DusC) from Escherichia coli

Chen, M., Yu, J., Tanaka, Y., Tanaka, M., Tanaka, I., Yao, M.

(2013) Acta Crystallogr Sect F Struct Biol Cryst Commun 69: 834-838

• PubMed: 23908023 
• DOI: https://doi.org/10.1107/S1744309113019489
• Primary Citation Related Structures: 
  3W9Z


• PubMed Abstract: 
  

  Dihydrouridine (D) is one of the most widely conserved tRNA modifications. Dihydrouridine synthase (Dus) is responsible for introducing D modifications into RNA by the reduction of uridine. Recently, a unique substrate-recognition mechanism using a small adapter molecule has been proposed for Thermus thermophilus Dus (TthDusC). To acquire insight regarding its substrate-recognition mechanism, the crystal structure of DusC from Escherichia coli (EcoDusC) was determined at 2.1 Å resolution. EcoDusC was shown to be composed of two domains: an N-terminal catalytic domain and a C-terminal tRNA-binding domain. An L-shaped electron density surrounded by highly conserved residues was found in the active site, as observed for TthDus. Structure comparison with TthDus indicated that the N-terminal region has a similar structure, whereas the C-terminal domain has marked differences in its relative orientation to the N-terminal domain as well as in its own structure. These observations suggested that Dus proteins adopt a common substrate-recognition mechanism using an adapter molecule, whereas the manner of tRNA binding is diverse.

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Organizational Affiliation: 
• Graduate School of Life Sciences, Hokkaido University, Sapporo 060-0810, Japan.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 36.65 kDa 
• Atom Count: 2,444 
• Modeled Residue Count: 290 
• Deposited Residue Count: 322 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
tRNA-dihydrouridine synthase C	A	322	Escherichia coli K-12	Mutation(s): 0  Gene Names: b2140, dusC, JW2128, yohI EC: 1.3.1
UniProt
Find proteins for P33371 (Escherichia coli (strain K12)) Explore P33371  Go to UniProtKB:  P33371

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMN	B [auth A]	FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.235 (Depositor), 0.238 (DCC) 
• R-Value Work:  0.221 (Depositor), 0.223 (DCC) 
• R-Value Observed: 0.221 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.252	α = 90
b = 93.252	β = 90
c = 115.499	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHELX	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
SHELXD	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-07-31 
Deposition Author(s): Chen, M., Yu, J., Tanaka, Y., Tanaka, I., Yao, M.

Revision History  

• Version 1.0: 2013-07-31
  Type: Initial release
  
• Version 1.1: 2013-08-21
  Changes: Database references
• Version 1.2: 2017-11-22
  Changes: Refinement description
• Version 1.3: 2024-03-20
  Changes: Data collection, Database references, Derived calculations