1OXW

The Crystal Structure of SeMet Patatin

Summary for 1OXW

• Entry DOI: 10.2210/pdb1oxw/pdb
• Descriptor: Patatin (2 entities in total)
• Functional Keywords: alpha/beta class fold with approximately three layers, alpha/beta/alpha in content. possesses a central six-stranded beta sheet with alpha-helices front & back, plant protein
• Biological source: Solanum cardiophyllum
• Cellular location: Vacuole : Q8LPW4
• Total number of polymer chains: 3
• Total formula weight: 125622.32

Authors

Rydel, T.J.,Williams, J.M.,Krieger, E.,Moshiri, F.,Stallings, W.C.,Brown, S.M.,Pershing, J.C.,Purcell, J.P.,Alibhai, M.F. (deposition date: 2003-04-03, release date: 2003-05-27, Last modification date: 2024-11-06)

Primary citation

Rydel, T.J.,Williams, J.M.,Krieger, E.,Moshiri, F.,Stallings, W.C.,Brown, S.M.,Pershing, J.C.,Purcell, J.P.,Alibhai, M.F.
The Crystal Structure, Mutagenesis, and Activity Studies Reveal that Patatin Is a Lipid Acyl Hydrolase with a Ser-Asp Catalytic Dyad
Biochemistry, 42:6696-6708, 2003

PubMed Abstract: Patatin is a nonspecific lipid acyl hydrolase that accounts for approximately 40% of the total soluble protein in mature potato tubers, and it has potent insecticidal activity against the corn rootworm. We determined the X-ray crystal structure of a His-tagged variant of an isozyme of patatin, Pat17, to 2.2 A resolution, employing SeMet multiwavelength anomalous dispersion (MAD) phasing methods. The patatin crystal structure has three molecules in the asymmetric unit, an R-factor of 22.0%, and an R(free) of 27.2% (for 10% of the data not included in the refinement) and includes 498 water molecules. The structure notably revealed that patatin has a Ser-Asp catalytic dyad and an active site like that of human cytosolic phospholipase A(2) (cPLA(2)) [Dessen, A., et al. (1999) Cell 97, 349-360]. In addition, patatin has a folding topology related to that of the catalytic domain of cPLA(2) and unlike the canonical alpha/beta-hydrolase fold. The structure confirms our site-directed mutagenesis and bioactivity data that initially suggested patatin possessed a Ser-Asp catalytic dyad. Alanine-scanning mutagenesis revealed that Ser77 and Asp215 were critical for both esterase and bioactivity, consistent with prior work implicating a Ser residue [Strickland, J. H., et al. (1995) Plant Physiol. 109, 667-674] and a Ser-Asp dyad [Hirschberg, H. J. H. B., et al. (2001) Eur. J. Biochem. 268, 5037-5044] in patatin's catalytic activity. The crystal structure aids the understanding of other structure-function relationships in patatin. Patatin does not display interfacial activation, a hallmark feature of lipases, and this is likely due to the fact that it lacks a flexible lid that can shield the active site.

PubMed: 12779324
DOI: 10.1021/bi027156r

Experimental method

X-RAY DIFFRACTION (2.2 Å)