7at4

From Proteopedia

Structure of EstD11 in complex with Naproxen

PDB ID 7at4

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Structural highlights

7at4 is a 1 chain structure with sequence from Uncultured bacterium. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.7Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Publication Abstract from PubMed

A novel esterase, EstD11, has been discovered in a hot spring metagenomic library. It is a thermophilic and thermostable esterase with an optimum temperature of 60 degrees C. A detailed substrate preference analysis of EstD11 was done using a library of chromogenic ester substrate that revealed the broad substrate specificity of EstD11 with significant measurable activity against 16 substrates with varied chain length, steric hindrance, aromaticity and flexibility of the linker between the carboxyl and the alcohol moiety of the ester. The tridimensional structures of EstD11 and the inactive mutant have been determined at atomic resolutions. Structural and bioinformatic analysis, confirm that EstD11 belongs to the family IV, the hormone-sensitive lipase (HSL) family, from the alpha/beta-hydrolase superfamily. The canonical alpha/beta-hydrolase domain is completed by a cap domain, composed by two subdomains that can unmask of the active site to allow the substrate to enter. Eight crystallographic complexes were solved with different substrates and reaction products that allowed identification of the hot-spots in the active site underlying the specificity of the protein. Crystallization and/or incubation of EstD11 at high temperature provided unique information on cap dynamics and a first glimpse of enzymatic activity in vivo. Very interestingly, we have discovered a unique Met zipper lining the active site and the cap domains that could be essential in pivotal aspects as thermo-stability and substrate promiscuity in EstD11.

Biochemical and Structural Characterization of a novel thermophilic esterase EstD11 provide catalytic insights for the HSL family.,Miguel-Ruano V, Rivera I, Rajkovic J, Knapik K, Torrado A, Otero JM, Beneventi E, Becerra M, Sanchez-Costa M, Hidalgo A, Berenguer J, Gonzalez-Siso MI, Cruces J, Rua ML, Hermoso JA Comput Struct Biotechnol J. 2021 Feb 10;19:1214-1232. doi:, 10.1016/j.csbj.2021.01.047. eCollection 2021. PMID:33680362^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Miguel-Ruano V, Rivera I, Rajkovic J, Knapik K, Torrado A, Otero JM, Beneventi E, Becerra M, Sanchez-Costa M, Hidalgo A, Berenguer J, Gonzalez-Siso MI, Cruces J, Rua ML, Hermoso JA. Biochemical and Structural Characterization of a novel thermophilic esterase EstD11 provide catalytic insights for the HSL family. Comput Struct Biotechnol J. 2021 Feb 10;19:1214-1232. doi:, 10.1016/j.csbj.2021.01.047. eCollection 2021. PMID:33680362 doi:http://dx.doi.org/10.1016/j.csbj.2021.01.047