5XTU

Crystal Structure of GDSL Esterase of Photobacterium sp. J15

Summary for 5XTU

• Entry DOI: 10.2210/pdb5xtu/pdb
• Descriptor: GDSL-family esterase, DI(HYDROXYETHYL)ETHER, CHLORIDE ION, ... (8 entities in total)
• Functional Keywords: gdsl, sgnh, esterase, hydrolase, photobacterium
• Biological source: Photobacterium sp. J15(2011)
• Total number of polymer chains: 1
• Total formula weight: 39809.33

Authors

Mazlan, S.N.H.S.,Jonet, M.A.,Leow, T.C.,Ali, M.S.M.,Rahman, R.N.Z.R.A. (deposition date: 2017-06-21, release date: 2018-10-10, Last modification date: 2025-04-09)

Primary citation

Mazlan, S.N.H.S.,Ali, M.S.M.,Rahman, R.N.Z.R.A.,Sabri, S.,Jonet, M.A.,Leow, T.C.
Crystallization and structure elucidation of GDSL esterase of Photobacterium sp. J15.
Int. J. Biol. Macromol., 119:1188-1194, 2018

PubMed Abstract: GDSL esterase J15 (EstJ15) is a member of Family II of lipolytic enzyme. The enzyme was further classified in subgroup SGNH hydrolase due to the presence of highly conserve motif, Ser-Gly-Asn-His in four conserved blocks I, II, III, and V, respectively. X-ray quality crystal of EstJ15 was obtained from optimized formulation containing 0.10 M ammonium sulphate, 0.15 M sodium cacodylate trihydrate pH 6.5, and 20% PEG 8000. The crystal structure of EstJ15 was solved at 1.38 Å with one molecule per asymmetric unit. The structure exhibits α/β hydrolase fold and shared low amino acid sequence identity of 23% with the passenger domain of the autotransporter EstA of Pseudomonas aeruginosa. The active site is located at the centre of the structure, formed a narrow tunnel that hinder long substrates to be catalysed which was proven by the protein-ligand docking analysis. This study facilitates the understanding of high substrate specificity of EstJ15 and provide insights on its catalytic mechanism.

PubMed: 30102982
DOI: 10.1016/j.ijbiomac.2018.08.022

Experimental method

X-RAY DIFFRACTION (1.38 Å)