1WKQ

Crystal Structure of Bacillus subtilis Guanine Deaminase. The first domain-swapped structure in the cytidine deaminase superfamily


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.17 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.161 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal Structure of Bacillus subtilis Guanine Deaminase: THE FIRST DOMAIN-SWAPPED STRUCTURE IN THE CYTIDINE DEAMINASE SUPERFAMILY

Liaw, S.H.Chang, Y.J.Lai, C.T.Chang, H.C.Chang, G.G.

(2004) J.Biol.Chem. 279: 35479-35485

  • DOI: 10.1074/jbc.M405304200

  • PubMed Abstract: 
  • Guanine deaminase, a key enzyme in the nucleotide metabolism, catalyzes the hydrolytic deamination of guanine into xanthine. The crystal structure of the 156-residue guanine deaminase from Bacillus subtilis has been solved at 1.17-A resolution. Unexp ...

    Guanine deaminase, a key enzyme in the nucleotide metabolism, catalyzes the hydrolytic deamination of guanine into xanthine. The crystal structure of the 156-residue guanine deaminase from Bacillus subtilis has been solved at 1.17-A resolution. Unexpectedly, the C-terminal segment is swapped to form an intersubunit active site and an intertwined dimer with an extensive interface of 3900 A(2) per monomer. The essential zinc ion is ligated by a water molecule together with His(53), Cys(83), and Cys(86). A transition state analog was modeled into the active site cavity based on the tightly bound imidazole and water molecules, allowing identification of the conserved deamination mechanism and specific substrate recognition by Asp(114) and Tyr(156'). The closed conformation also reveals that substrate binding seals the active site entrance, which is controlled by the C-terminal tail. Therefore, the domain swapping has not only facilitated the dimerization but has also ensured specific substrate recognition. Finally, a detailed structural comparison of the cytidine deaminase superfamily illustrates the functional versatility of the divergent active sites found in the guanine, cytosine, and cytidine deaminases and suggests putative specific substrate-interacting residues for other members such as dCMP deaminases.


    Related Citations: 
    • Crystallization and preliminary crystallographic analysis of Bacillus subtilis guanine deaminase
      Chang, Y.J.,Huang, C.H.,Hu, C.Y.,Liaw, S.H.
      (2004) ACTA CRYSTALLOGR.,SECT.D 60: 1152


    Organizational Affiliation

    Structural Biology Program, Faculty of Life Science, Institute of Biotechnology in Medicine, and Institute of Genetics, National Yang-Ming University, Taipei 11221, Taiwan. shliaw@ym.edu.tw




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Guanine deaminase
A, B
164Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: guaD (gde)
EC: 3.5.4.3
Find proteins for O34598 (Bacillus subtilis (strain 168))
Go to UniProtKB:  O34598
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
IMD
Query on IMD

Download SDF File 
Download CCD File 
A, B
IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.17 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.161 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 81.566α = 90.00
b = 91.267β = 90.00
c = 80.481γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
CNSrefinement
SCALEPACKdata scaling
HKL-2000data collection
SOLVEphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-07-13
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance