8IGI

Crystal structure of HP1526 (XthA)- a base excision DNA repair protein in Helicobacter pylori


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.168 

Starting Model: experimental
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Literature

Crystal structure of the apurinic/apyrimidinic endonuclease XthA (HP1526 protein) from Helicobacter pylori.

Dinh, T.Dao, O.Killivalavan, A.Ngo, D.Lee, K.H.

(2023) Biochem Biophys Res Commun 663: 8-15

  • DOI: https://doi.org/10.1016/j.bbrc.2023.04.047
  • Primary Citation of Related Structures:  
    8IGI

  • PubMed Abstract: 

    Helicobacter pylori is a bacterium that causes gastritis, peptic ulcer disease and adenocarcinoma while infecting human stomach. In the stomach H. pylori is under stresses caused by reactive oxygen and nitrogen species from host immune response, which causes oxidative DNA damage. The DNA damage in single base is repaired by base excision repair (BER) and/or nucleotide incision repair (NIR) pathways. H. pylori retains a minimal set of enzymes involved in the BER and NIR pathways. The HP1526 protein is a single apurinic/apyrimidinic (AP) endonuclease homologous to E. coli Xth protein but little is known for its structure up to now. In this study, the structure of the recombinant HP1526 protein from H. pylori (HpXthA) has been determined at a high resolution of 1.84 Å. From the structural analysis the HpXthA was found to belong to the Xth-like AP endonuclease family carrying the common fold of a central bilayer β-sheet flanked by α-helices with a divalent metal ion bound. A Mn 2+ ion and a 1,3-butanediol were unusually found and modeled around the active site. Structural and sequence comparisons among the AP endonucleases show well-conserved residues for metal and DNA binding and for catalysis. Interestingly, the presence of a small polar residue Ser201 of the HpXthA commonly found in NIR-proficient AP endonucleases instead of an aspartate residue in NIR-deficient enzymes suggests that the HpXthA retain a nucleotide incision repair activity.


  • Organizational Affiliation

    Department of Convergence Medical Science (BK21Plus), Gyeongsang National University, Jinju, 52727, Republic of Korea; Department of Microbiology, School of Medicine, Gyeongsang National University, Jinju, 52727, Republic of Korea.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Exodeoxyribonuclease (LexA)
A, B
251Helicobacter pylori 26695Mutation(s): 0 
Gene Names: HP_1526
UniProt
Find proteins for O26054 (Helicobacter pylori (strain ATCC 700392 / 26695))
Explore O26054 
Go to UniProtKB:  O26054
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO26054
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.168 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.096α = 90
b = 71.909β = 90
c = 108.033γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
HKL-2000data reduction
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Foundation (NRF, Korea)Korea, Republic Of--

Revision History  (Full details and data files)

  • Version 1.0: 2023-12-27
    Type: Initial release