1TUH

Structure of Bal32a from a Soil-Derived Mobile Gene Cassette


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Integron-associated Mobile Gene Cassettes Code for Folded Proteins: The Structure of Bal32a, a New Member of the Adaptable alpha+beta Barrel Family

Robinson, A.Wu, P.S.-C.Harrop, S.J.Schaeffer, P.M.Dosztanyi, Z.Gillings, M.R.Holmes, A.J.Nevalainen, K.M.H.Stokes, H.W.Otting, G.Dixon, N.E.Curmi, P.M.G.Mabbutt, B.C.

(2005) J Mol Biol 346: 1229-1241

  • DOI: 10.1016/j.jmb.2004.12.035
  • Primary Citation of Related Structures:  
    1TUH

  • PubMed Abstract: 
  • The wide-ranging physiology and large genetic variability observed for prokaryotes is largely attributed, not to the prokaryotic genome itself, but rather to mechanisms of lateral gene transfer. Cassette PCR has been used to sample the integron/gene ...

    The wide-ranging physiology and large genetic variability observed for prokaryotes is largely attributed, not to the prokaryotic genome itself, but rather to mechanisms of lateral gene transfer. Cassette PCR has been used to sample the integron/gene cassette metagenome from different natural environments without laboratory cultivation of the host organism, and without prior knowledge of any target protein sequence. Since over 90% of cassette genes are unrelated to any sequence in the current databases, it is not clear whether these genes code for folded functional proteins. We have selected a sample of eight cassette-encoded genes with no known homologs; five have been isolated as soluble protein products and shown by biophysical techniques to be folded. In solution, at least three of these proteins organise as stable oligomeric assemblies. The tertiary structure of one of these, Bal32a derived from a contaminated soil site, has been solved by X-ray crystallography to 1.8 A resolution. From the three-dimensional structure, Bal32a is found to be a member of the highly adaptable alpha+beta barrel family of transport proteins and enzymes. In Bal32a, the barrel cavity is unusually deep and inaccessible to solvent. Polar side-chains in its interior are reminiscent of catalytic sites of limonene-1,2-epoxide hydrolase and nogalonic acid methyl ester cyclase. These studies demonstrate the viability of direct sampling of mobile DNA as a route for the discovery of novel proteins.


    Organizational Affiliation

    Department of Chemistry, Macquarie University, NSW 2109, Australia.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
hypothetical protein EGC068A156uncultured bacteriumMutation(s): 0 
Gene Names: EGC068
Find proteins for Q99IU3 (uncultured bacterium)
Explore Q99IU3 
Go to UniProtKB:  Q99IU3
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.728α = 90
b = 60.728β = 90
c = 89.91γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
MLPHAREphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-07-06
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance