3HPA

Crystal structure of an amidohydrolase gi:44264246 from an evironmental sample of sargasso sea

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.232 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

The hunt for 8-oxoguanine deaminase.

Hall, R.S., Fedorov, A.A., Marti-Arbona, R., Fedorov, E.V., Kolb, P., Sauder, J.M., Burley, S.K., Shoichet, B.K., Almo, S.C., Raushel, F.M.

(2010) J.Am.Chem.Soc. 132: 1762-1763

  • DOI: 10.1021/ja909817d

  • PubMed Abstract: 

    • An enzyme from Pseudomonas aeruginosa, Pa0142 (gi|9945972), that is able to catalyze the deamination of 8-oxoguanine (8-oxoG) to uric acid has been identified for the first time. 8-Oxoguanine is formed by the oxidation of guanine residues within DNA ...

    An enzyme from Pseudomonas aeruginosa, Pa0142 (gi|9945972), that is able to catalyze the deamination of 8-oxoguanine (8-oxoG) to uric acid has been identified for the first time. 8-Oxoguanine is formed by the oxidation of guanine residues within DNA by reactive oxygen species, and this lesion results in G:C to T:A transversions. The value of k(cat)/K(m) for the deamination of 8-oxoG by Pa0142 at pH 8.0 and 30 degrees C is 2.0 x 10(4) M(-1) s(-1). This enzyme can also catalyze the deamination of isocystosine and guanine at rates that are approximately an order of magnitude lower. The three-dimensional structure of a homologous enzyme (gi|44264246) from the Sargasso Sea has been determined by X-ray diffraction methods to a resolution of 2.2 A (PDB entry). The enzyme folds as a (beta/alpha)(8) barrel and is a member of the amidohydrolase superfamily with a single zinc in the active site. This enzyme catalyzes the deamination of 8-oxoG with a k(cat)/K(m) value of 2.7 x 10(5) M(-1) s(-1). Computational docking of potential high-energy intermediates for the deamination reaction to the X-ray crystal structure suggests that active-site binding of 8-oxoG is facilitated by hydrogen-bond interactions from a conserved glutamine that follows beta-strand 1 with the carbonyl group at C6, a conserved tyrosine that follows beta-strand 2 with N7, and a conserved cysteine residue that follows beta-strand 4 with the carbonyl group at C8. A bioinformatic analysis of available protein sequences suggests that approximately 200 other bacteria possess an enzyme capable of catalyzing the deamination of 8-oxoG.

    Organizational Affiliation: 

    Department of Chemistry, Texas A&M University, P.O. Box 30012, College Station, Texas 77842-3012, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
AMIDOHYDROLASE
A, B
479N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.232 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 83.304α = 90.00
b = 83.304β = 90.00
c = 229.125γ = 120.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
BALBESphasing
ADSCdata collection
CNSrefinement
DENZOdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-06-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2018-01-24
    Type: Structure summary