8H0B image
Entry Detail
PDB ID:
8H0B
Keywords:
Title:
Structure of the thermolabile hemolysin from Vibrio alginolyticus (in complex with oleic acid)
Biological Source:
Source Organism:
PDB Version:
Deposition Date:
2022-09-28
Release Date:
2023-08-16
Method Details:
Experimental Method:
Resolution:
1.93 Å
R-Value Free:
0.22
R-Value Work:
0.19
R-Value Observed:
0.19
Space Group:
P 1 21 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:SGNH/GDSL hydrolase family protein
Chain IDs:A, B
Chain Length:426
Number of Molecules:2
Biological Source:Vibrio alginolyticus
Primary Citation
Catalytic site flexibility facilitates the substrate and catalytic promiscuity of Vibrio dual lipase/transferase.
Nat Commun 14 4795 4795 (2023)
PMID: 37558668 DOI: 10.1038/s41467-023-40455-y

Abstact

Although enzyme catalysis is typified by high specificity, enzymes can catalyze various substrates (substrate promiscuity) and/or different reaction types (catalytic promiscuity) using a single active site. This interesting phenomenon is widely distributed in enzyme catalysis, with both fundamental and applied importance. To date, the mechanistic understanding of enzyme promiscuity is very limited. Herein, we report the structural mechanism underlying the substrate and catalytic promiscuity of Vibrio dual lipase/transferase (VDLT). Crystal structures of the VDLT from Vibrio alginolyticus (ValDLT) and its fatty acid complexes were solved, revealing prominent structural flexibility. In particular, the "Ser-His-Asp" catalytic triad machinery of ValDLT contains an intrinsically flexible oxyanion hole. Analysis of ligand-bound structures and mutagenesis showed that the flexible oxyanion hole and other binding residues can undergo distinct conformational changes to facilitate substrate and catalytic promiscuity. Our study reveals a previously unknown flexible form of the famous catalytic triad machinery and proposes a "catalytic site tuning" mechanism to expand the mechanistic paradigm of enzyme promiscuity.

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