1WDU | pdb_00001wdu

Endonuclease domain of TRAS1, a telomere-specific non-LTR retrotransposon

• PDB DOI: https://doi.org/10.2210/pdb1WDU/pdb

• Classification: RNA BINDING PROTEIN
• Organism(s): Bombyx mori
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2004-05-17 Released: 2004-08-10 
• Deposition Author(s): Maita, N., Anzai, T., Aoyagi, H., Mizuno, H., Fujiwara, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.253 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.225 (Depositor), 0.220 (DCC) 

Literature

Crystal structure of the endonuclease domain encoded by the telomere-specific long interspersed nuclear element, TRAS1

Maita, N., Anzai, T., Aoyagi, H., Mizuno, H., Fujiwara, H.

(2004) J Biological Chem 279: 41067-41076

• PubMed: 15247245 
• DOI: https://doi.org/10.1074/jbc.M406556200
• Primary Citation of Related Structures:  
  1WDU


• PubMed Abstract: 
  

  The telomere-specific long interspersed nuclear element, TRAS1, encodes an endonuclease domain, TRAS1-EN, which specifically cleaves the telomeric repeat targets (TTAGG)n of insects and (TTAGGG)n of vertebrates. To elucidate the sequence-specific recognition properties of TRAS1-EN, we determined the crystal structure at 2.4-A resolution. TRAS1-EN has a four-layered alpha/beta sandwich structure; its topology is similar to apurinic/apyrimidinic endonucleases, but the beta-hairpin (beta10-beta11) at the edge of the DNA-binding surface makes an extra loop that distinguishes TRAS1-EN from cellular apurinic/apyrimidinic endonucleases. A protein-DNA complex model suggests that the beta10-beta11 hairpin fits into the minor groove, enabling interaction with the telomeric repeats. Mutational studies of TRAS1-EN also indicated that the Asp-130 and beta10-beta11 hairpin structure are involved in specific recognition of telomeric repeats.

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Organizational Affiliation: 
• Department of Biochemistry, National Institute of Agrobiological Sciences, Tsukuba, 305-8602, Japan.

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: 55.18 kDa 
• Atom Count: 3,504 
• Modeled Residue Count: 436 
• Deposited Residue Count: 490 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TRAS1 ORF2p	A, B	245	Bombyx mori	Mutation(s): 1
UniProt
Find proteins for Q93139 (Bombyx mori) Explore Q93139  Go to UniProtKB:  Q93139

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	C [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
CL	D [auth A], E [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.253 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.225 (Depositor), 0.220 (DCC) 

Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.645	α = 90
b = 64.645	β = 90
c = 117.315	γ = 120

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
SOLVE	phasing
CNS	refinement
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-08-10 
Deposition Author(s): Maita, N., Anzai, T., Aoyagi, H., Mizuno, H., Fujiwara, H.

Revision History  

• Version 1.0: 2004-08-10
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-11-10
  Changes: Database references, Derived calculations
• Version 1.4: 2024-05-29
  Changes: Data collection