5H9I

Crystal structure of Geobacter metallireducens SMUG1 with xanthine

  • Classification: HYDROLASE
  • Organism(s): Geobacter metallireducens GS-15
  • Expression System: Escherichia coli BL21(DE3)
  • Mutation(s): No 

  • Deposited: 2015-12-28 Released: 2016-04-27 
  • Deposition Author(s): Xie, W., Cao, W., Zhang, Z., Shen, J.
  • Funding Organization(s): Science and Technology Program of Guangzhou, Foundation of Key Laboratory of Gene Engineering of the Ministry of Education, Guangdong Innovative Research Team, the Fundamental Research Funds for the Central Universities

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.173 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structural Basis of Substrate Specificity in Geobacter metallireducens SMUG1

Zhang, Z.Shen, J.Yang, Y.Li, J.Cao, W.Xie, W.

(2016) ACS Chem Biol 11: 1729-1736

  • DOI: https://doi.org/10.1021/acschembio.6b00164
  • Primary Citation of Related Structures:  
    5H93, 5H98, 5H99, 5H9I

  • PubMed Abstract: 

    Base deamination is a common type of DNA damage that occurs in all organisms. DNA repair mechanisms are critical to maintain genome integrity, in which the base excision repair pathway plays an essential role. In the BER pathway, the uracil DNA glycosylase superfamily is responsible for removing the deaminated bases from DNA and generates apurinic/apyrimidinic (AP) sites. Geobacter metallireducens SMUG1 (GmeSMUG1) is an interesting family 3 enzyme in the UDG superfamily, with dual substrate specificities for DNA with uracil or xanthine. In contrast, the mutant G63P of GmeSMUG1 has exclusive activity for uracil, while N58D is inactive for both substrates, as we have reported previously. However, the structural bases for these substrate specificities are not well understood. In this study, we solved a series of crystal structures of WT and mutants of GmeSMUG1 at relatively high resolutions. These structures provide insight on the molecular mechanism of xanthine recognition for GmeSMUG1 and indicate that H210 plays a key role in xanthine recognition, which is in good agreement with the results of our EMSA and activity assays. More importantly, our mutant structures allow us to build models to rationalize our previous experimental observations of altered substrate activities of these mutants.


  • Organizational Affiliation

    State Key Laboratory for Biocontrol, School of Life Sciences, The Sun Yat-Sen University , 135 W. Xingang Rd., Guangzhou, Guangdong 510275, People's Republic of China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Geobacter metallireducens SMUG1240Geobacter metallireducens GS-15Mutation(s): 0 
Gene Names: Gmet_0095
UniProt
Find proteins for Q39ZI0 (Geobacter metallireducens (strain ATCC 53774 / DSM 7210 / GS-15))
Explore Q39ZI0 
Go to UniProtKB:  Q39ZI0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ39ZI0
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
XAN
Query on XAN

Download Ideal Coordinates CCD File 
B [auth A]XANTHINE
C5 H4 N4 O2
LRFVTYWOQMYALW-UHFFFAOYSA-N
LEA
Query on LEA

Download Ideal Coordinates CCD File 
H [auth A]PENTANOIC ACID
C5 H10 O2
NQPDZGIKBAWPEJ-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
BME
Query on BME

Download Ideal Coordinates CCD File 
F [auth A]BETA-MERCAPTOETHANOL
C2 H6 O S
DGVVWUTYPXICAM-UHFFFAOYSA-N
IPA
Query on IPA

Download Ideal Coordinates CCD File 
G [auth A]ISOPROPYL ALCOHOL
C3 H8 O
KFZMGEQAYNKOFK-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.173 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.972α = 90
b = 64.339β = 111.4
c = 45.654γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Science and Technology Program of GuangzhouChina201504010025
Foundation of Key Laboratory of Gene Engineering of the Ministry of EducationChina201502
Guangdong Innovative Research TeamChina2011Y038
the Fundamental Research Funds for the Central UniversitiesChina15lgjc02

Revision History  (Full details and data files)

  • Version 1.0: 2016-04-27
    Type: Initial release
  • Version 1.1: 2016-06-29
    Changes: Database references
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description