4RG8

Structural and biochemical studies of a moderately thermophilic Exonuclease I from Methylocaldum szegediense


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.224 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural and Biochemical Studies of a Moderately Thermophilic Exonuclease I from Methylocaldum szegediense.

Fei, L.Tian, S.Moysey, R.Misca, M.Barker, J.J.Smith, M.A.McEwan, P.A.Pilka, E.S.Crawley, L.Evans, T.Sun, D.

(2015) PLoS One 10: e0117470-e0117470

  • DOI: 10.1371/journal.pone.0117470
  • Primary Citation of Related Structures:  
    4RG8

  • PubMed Abstract: 
  • A novel exonuclease, designated as MszExo I, was cloned from Methylocaldum szegediense, a moderately thermophilic methanotroph. It specifically digests single-stranded DNA in the 3' to 5' direction. The protein is composed of 479 amino acids, and it ...

    A novel exonuclease, designated as MszExo I, was cloned from Methylocaldum szegediense, a moderately thermophilic methanotroph. It specifically digests single-stranded DNA in the 3' to 5' direction. The protein is composed of 479 amino acids, and it shares 47% sequence identity with E. coli Exo I. The crystal structure of MszExo I was determined to a resolution of 2.2 Å and it aligns well with that of E. coli Exo I. Comparative studies revealed that MszExo I and E. coli Exo I have similar metal ion binding affinity and similar activity at mesophilic temperatures (25-47°C). However, the optimum working temperature of MszExo I is 10°C higher, and the melting temperature is more than 4°C higher as evaluated by both thermal inactivation assays and DSC measurements. More importantly, two thermal transitions during unfolding of MszExo I were monitored by DSC while only one transition was found in E. coli Exo I. Further analyses showed that magnesium ions not only confer structural stability, but also affect the unfolding of MszExo I. MszExo I is the first reported enzyme in the DNA repair systems of moderately thermophilic bacteria, which are predicted to have more efficient DNA repair systems than mesophilic ones.


    Organizational Affiliation

    New England Biolabs Shanghai R&D Center, Building 5, 917 Halei Road, Pudong District, Shanghai, China.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Exonuclease IA523Methylocaldum szegedienseMutation(s): 0 
Gene Names: Exonuclease I
EC: 3.1.11.1
Find proteins for A0A0A0R5X6 (Methylocaldum szegediense)
Explore A0A0A0R5X6 
Go to UniProtKB:  A0A0A0R5X6
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.224 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.967α = 90
b = 97.02β = 90
c = 111.411γ = 90
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
xia2data reduction
xia2data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-02-25
    Type: Initial release
  • Version 1.1: 2017-11-22
    Changes: Refinement description