The crystal structure of WT Pedobacter heparinus SMUG2

  • Classification: LYASE
  • Organism(s): Pedobacter heparinus DSM 2366
  • Expression System: Escherichia coli
  • Mutation(s): Yes 

  • Deposited: 2016-10-04 Released: 2017-01-18 
  • Deposition Author(s): Xie, W., Cao, W., Pang, P.
  • Funding Organization(s): Fundamental Research Funds for the Central Universities, the Science and Technology Program of Guangzhou, Foundation of Key Laboratory of Gene Engineering of the Ministry of Education, Guangdong Innovative Research Team Program

Experimental Data Snapshot

  • Resolution: 2.25 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 

wwPDB Validation   3D Report Full Report

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SMUG2 DNA glycosylase from Pedobacter heparinus as a new subfamily of the UDG superfamily

Pang, P.Yang, Y.Li, J.Wang, Z.Cao, W.Xie, W.

(2017) Biochem J 474: 923-938

  • DOI: https://doi.org/10.1042/BCJ20160934
  • Primary Citation of Related Structures:  
    5H0J, 5H0K

  • PubMed Abstract: 

    Base deamination is a common type of DNA damage that occurs in all organisms. DNA repair mechanisms are essential to maintain genome integrity, in which the base excision repair (BER) pathway plays a major role in the removal of base damage. In the BER pathway, the uracil DNA glycosylase superfamily is responsible for excising the deaminated bases from DNA and generates apurinic/apyrimidinic (AP) sites. Using bioinformatics tools, we identified a family 3 SMUG1-like DNA glycoyslase from Pedobacter heparinus (named Phe SMUG2), which displays catalytic activities towards DNA containing uracil or hypoxanthine/xanthine. Phylogenetic analyses show that SMUG2 enzymes are closely related to family 3 SMUG1s but belong to a distinct branch of the family. The high-resolution crystal structure of the apoenzyme reveals that the general fold of Phe SMUG2 resembles SMUG1s, yet with several distinct local structural differences. Mutational studies, coupled with structural modeling, identified several important amino acid residues for glycosylase activity. Substitution of G65 with a tyrosine results in loss of all glycosylase activity. The crystal structure of the G65Y mutant suggests a potential misalignment at the active site due to the mutation. The relationship between the new subfamily and other families in the UDG superfamily is discussed. The present study provides new mechanistic insight into the molecular mechanism of the UDG superfamily.

  • Organizational Affiliation

    School of Pharmaceutical Sciences, The Sun Yat-Sen University, 132 E. Circle Rd. University City, Guangzhou, Guangdong 510006, People's Republic of China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized protein244Pedobacter heparinus DSM 2366Mutation(s): 1 
Gene Names: Phep_0752
Find proteins for C6Y1J8 (Pedobacter heparinus (strain ATCC 13125 / DSM 2366 / CIP 104194 / JCM 7457 / NBRC 12017 / NCIMB 9290 / NRRL B-14731 / HIM 762-3))
Explore C6Y1J8 
Go to UniProtKB:  C6Y1J8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC6Y1J8
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.25 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.714α = 90
b = 56.714β = 90
c = 144.539γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Fundamental Research Funds for the Central UniversitiesChina16lgjc76
the Science and Technology Program of GuangzhouChina201504010025
Foundation of Key Laboratory of Gene Engineering of the Ministry of EducationChina201502
Guangdong Innovative Research Team ProgramChinaNO. 2011Y038

Revision History  (Full details and data files)

  • Version 1.0: 2017-01-18
    Type: Initial release
  • Version 1.1: 2017-03-22
    Changes: Database references