4E0Y | pdb_00004e0y

Protelomerase tela covalently complexed with mutated substrate DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 
    0.270 (Depositor), 0.262 (DCC) 
  • R-Value Work: 
    0.216 (Depositor), 0.208 (DCC) 
  • R-Value Observed: 
    0.219 (Depositor) 

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted TMPClick on this verticalbar to view details

This is version 2.0 of the entry. See complete history


Literature

An enzyme-catalyzed multistep DNA refolding mechanism in hairpin telomere formation.

Shi, K.Huang, W.M.Aihara, H.

(2013) PLoS Biol 11: e1001472-e1001472

  • DOI: https://doi.org/10.1371/journal.pbio.1001472
  • Primary Citation of Related Structures:  
    4DWP, 4E0G, 4E0J, 4E0P, 4E0Y, 4E0Z, 4E10

  • PubMed Abstract: 

    Hairpin telomeres of bacterial linear chromosomes are generated by a DNA cutting-rejoining enzyme protelomerase. Protelomerase resolves a concatenated dimer of chromosomes as the last step of chromosome replication, converting a palindromic DNA sequence at the junctions between chromosomes into covalently closed hairpins. The mechanism by which protelomerase transforms a duplex DNA substrate into the hairpin telomeres remains largely unknown. We report here a series of crystal structures of the protelomerase TelA bound to DNA that represent distinct stages along the reaction pathway. The structures suggest that TelA converts a linear duplex substrate into hairpin turns via a transient strand-refolding intermediate that involves DNA-base flipping and wobble base-pairs. The extremely compact di-nucleotide hairpin structure of the product is fully stabilized by TelA prior to strand ligation, which drives the reaction to completion. The enzyme-catalyzed, multistep strand refolding is a novel mechanism in DNA rearrangement reactions.


  • Organizational Affiliation

    Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, United States of America.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protelomerase462Agrobacterium fabrum str. C58Mutation(s): 0 
Gene Names: telAAtu2523
UniProt
Find proteins for Q7CWV1 (Agrobacterium fabrum (strain C58 / ATCC 33970))
Explore Q7CWV1 
Go to UniProtKB:  Q7CWV1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7CWV1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
PTR
Query on PTR
A
L-PEPTIDE LINKINGC9 H12 N O6 PTYR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free:  0.270 (Depositor), 0.262 (DCC) 
  • R-Value Work:  0.216 (Depositor), 0.208 (DCC) 
  • R-Value Observed: 0.219 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 116.984α = 90
b = 119.442β = 112.42
c = 56.922γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted TMPClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-02-13
    Type: Initial release
  • Version 1.1: 2024-10-09
    Changes: Data collection, Database references, Derived calculations, Structure summary
  • Version 2.0: 2025-02-12
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary