2PAJ

Crystal structure of an amidohydrolase from an environmental sample of Sargasso sea

Summary for 2PAJ

• Entry DOI: 10.2210/pdb2paj/pdb
• Descriptor: putative cytosine/guanine deaminase, ZINC ION (3 entities in total)
• Functional Keywords: nysgxrc, 9339a, psi-ii, amidohydrolase, sargasso sea, environmental sample, structural genomics, protein structure initiative, new york sgx research center for structural genomics, hydrolase
• Biological source: unidentified
• Total number of polymer chains: 1
• Total formula weight: 53092.46

Authors

Agarwal, R.,Burley, S.K.,Swaminathan, S.,New York SGX Research Center for Structural Genomics (NYSGXRC) (deposition date: 2007-03-27, release date: 2007-04-03, Last modification date: 2024-02-21)

Primary citation

Hall, R.S.,Agarwal, R.,Hitchcock, D.,Sauder, J.M.,Burley, S.K.,Swaminathan, S.,Raushel, F.M.
Discovery and structure determination of the orphan enzyme isoxanthopterin deaminase.
Biochemistry, 49:4374-4382, 2010

PubMed Abstract: Two previously uncharacterized proteins have been identified that efficiently catalyze the deamination of isoxanthopterin and pterin 6-carboxylate. The genes encoding these two enzymes, NYSGXRC-9339a ( gi|44585104 ) and NYSGXRC-9236b ( gi|44611670 ), were first identified from DNA isolated from the Sargasso Sea as part of the Global Ocean Sampling Project. The genes were synthesized, and the proteins were subsequently expressed and purified. The X-ray structure of Sgx9339a was determined at 2.7 A resolution (Protein Data Bank entry 2PAJ ). This protein folds as a distorted (beta/alpha)(8) barrel and contains a single zinc ion in the active site. These enzymes are members of the amidohydrolase superfamily and belong to cog0402 within the clusters of orthologous groups (COG). Enzymes in cog0402 have previously been shown to catalyze the deamination of guanine, cytosine, S-adenosylhomocysteine, and 8-oxoguanine. A small compound library of pteridines, purines, and pyrimidines was used to probe catalytic activity. The only substrates identified in this search were isoxanthopterin and pterin 6-carboxylate. The kinetic constants for the deamination of isoxanthopterin with Sgx9339a were determined to be 1.0 s(-1), 8.0 muM, and 1.3 x 10(5) M(-1) s(-1) (k(cat), K(m), and k(cat)/K(m), respectively). The active site of Sgx9339a most closely resembles the active site for 8-oxoguanine deaminase (Protein Data Bank entry 2UZ9 ). A model for substrate recognition of isoxanthopterin by Sgx9339a was proposed on the basis of the binding of guanine and xanthine in the active site of guanine deaminase. Residues critical for substrate binding appear to be conserved glutamine and tyrosine residues that form hydrogen bonds with the carbonyl oxygen at C4, a conserved threonine residue that forms hydrogen bonds with N5, and another conserved threonine residue that forms hydrogen bonds with the carbonyl group at C7. These conserved active site residues were used to identify 24 other genes which are predicted to deaminate isoxanthopterin.

PubMed: 20415463
DOI: 10.1021/bi100252s

Experimental method

X-RAY DIFFRACTION (2.7 Å)