3FCX

Crystal structure of human esterase D

Summary for 3FCX

• Entry DOI: 10.2210/pdb3fcx/pdb
• Descriptor: S-formylglutathione hydrolase, MAGNESIUM ION, CALCIUM ION, ... (4 entities in total)
• Functional Keywords: retinoblastoma, genetic marker, esterase, hydrolase, cytoplasm, cytoplasmic vesicle, polymorphism, serine esterase
• Biological source: Homo sapiens (Human)
• Cellular location: Cytoplasm: P10768
• Total number of polymer chains: 2
• Total formula weight: 63260.13

Authors

Wu, D.,Li, Y.,Song, G.,Zhang, D.,Shaw, N.,Liu, Z.J. (deposition date: 2008-11-24, release date: 2008-12-09, Last modification date: 2023-11-01)

Primary citation

Wu, D.,Li, Y.,Song, G.,Zhang, D.,Shaw, N.,Liu, Z.J.
Crystal structure of human esterase D: a potential genetic marker of retinoblastoma
Faseb J., 23:1441-1446, 2009

PubMed Abstract: Retinoblastoma (RB), a carcinoma of the retina, is caused by mutations in the long arm of chromosome 13, band 13q14. The esterase D (ESD) gene maps at a similar location as the RB gene locus and therefore serves as a potential marker for the prognosis of retinoblastoma. Because very little is known about the structure and function of ESD, we determined the 3-dimensional structure of the enzyme at 1.5 A resolution using X-ray crystallography. ESD shows a single domain with an alpha/beta-hydrolase fold. A number of insertions are observed in the canonical alpha/beta-hydrolase fold. The active site is located in a positively charged, shallow cleft on the surface lined by a number of aromatic residues. Superimposition studies helped identify the typical catalytic triad residues--Ser-153, His264, and Asp230--involved in catalysis. Mutagenesis of any of the catalytic triad residues to alanine abolished the enzyme activity. Backbone amides of Leu54 and Met150 are involved in the formation of the oxyanion hole. Interestingly, a M150A mutation increased the enzyme activity by 62%. The structure of human ESD determined in this study will aid the elucidation of the physiological role of the enzyme in the human body and will assist in the early diagnosis of retinoblastoma.

PubMed: 19126594
DOI: 10.1096/fj.08-125286

Experimental method

X-RAY DIFFRACTION (1.5 Å)