Revealing Escherichia coli type II l-asparaginase active site flexible loop in its open, ligand-free conformation

Abstract Since 1993, when the structure of Escherichia coli type II l-asparaginase (EcAII) in complex with l-aspartate was firstly reported, many structures of the wild type and mutated enzyme have been deposited in the Protein Data Bank. None of them report the full structure of the monomer in its...

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Autores principales:	Maristella Maggi, Massimiliano Meli, Giorgio Colombo, Claudia Scotti
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/49aed1935a314d82b04c6c1f5c29f49a
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spelling	oai:doaj.org-article:49aed1935a314d82b04c6c1f5c29f49a2021-12-02T18:14:40ZRevealing Escherichia coli type II l-asparaginase active site flexible loop in its open, ligand-free conformation10.1038/s41598-021-98455-12045-2322https://doaj.org/article/49aed1935a314d82b04c6c1f5c29f49a2021-09-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-98455-1https://doaj.org/toc/2045-2322Abstract Since 1993, when the structure of Escherichia coli type II l-asparaginase (EcAII) in complex with l-aspartate was firstly reported, many structures of the wild type and mutated enzyme have been deposited in the Protein Data Bank. None of them report the full structure of the monomer in its ligand-free, open conformation, mainly because of the high dynamic and flexibility of the active site flexible loop. Here we report for the first time the structure of EcAII wild type in its open conformation comprising, for at least one protomer, clear electron density for the active site flexible loop (PDB ID: 6YZI). The structural element is highly mobile and it is transposed onto the rigid part of the active site upon substrate binding to allow completion of the enzyme catalytic center, thanks to key residues that serve as hinges and anchoring points. In the substrate binding pocket, several highly conserved water molecules are coordinated by residues involved in substrate binding, comprising two water molecules very likely involved in the enzyme catalytic process. We also describe, by molecular dynamics simulations, how the transposition of the loop, besides providing the proximity of residues needed for catalysis, causes a general stabilization of the protein.Maristella MaggiMassimiliano MeliGiorgio ColomboClaudia ScottiNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-12 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Maristella Maggi Massimiliano Meli Giorgio Colombo Claudia Scotti Revealing Escherichia coli type II l-asparaginase active site flexible loop in its open, ligand-free conformation
description	Abstract Since 1993, when the structure of Escherichia coli type II l-asparaginase (EcAII) in complex with l-aspartate was firstly reported, many structures of the wild type and mutated enzyme have been deposited in the Protein Data Bank. None of them report the full structure of the monomer in its ligand-free, open conformation, mainly because of the high dynamic and flexibility of the active site flexible loop. Here we report for the first time the structure of EcAII wild type in its open conformation comprising, for at least one protomer, clear electron density for the active site flexible loop (PDB ID: 6YZI). The structural element is highly mobile and it is transposed onto the rigid part of the active site upon substrate binding to allow completion of the enzyme catalytic center, thanks to key residues that serve as hinges and anchoring points. In the substrate binding pocket, several highly conserved water molecules are coordinated by residues involved in substrate binding, comprising two water molecules very likely involved in the enzyme catalytic process. We also describe, by molecular dynamics simulations, how the transposition of the loop, besides providing the proximity of residues needed for catalysis, causes a general stabilization of the protein.
format	article
author	Maristella Maggi Massimiliano Meli Giorgio Colombo Claudia Scotti
author_facet	Maristella Maggi Massimiliano Meli Giorgio Colombo Claudia Scotti
author_sort	Maristella Maggi
title	Revealing Escherichia coli type II l-asparaginase active site flexible loop in its open, ligand-free conformation
title_short	Revealing Escherichia coli type II l-asparaginase active site flexible loop in its open, ligand-free conformation
title_full	Revealing Escherichia coli type II l-asparaginase active site flexible loop in its open, ligand-free conformation
title_fullStr	Revealing Escherichia coli type II l-asparaginase active site flexible loop in its open, ligand-free conformation
title_full_unstemmed	Revealing Escherichia coli type II l-asparaginase active site flexible loop in its open, ligand-free conformation
title_sort	revealing escherichia coli type ii l-asparaginase active site flexible loop in its open, ligand-free conformation
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/49aed1935a314d82b04c6c1f5c29f49a
work_keys_str_mv	AT maristellamaggi revealingescherichiacolitypeiilasparaginaseactivesiteflexibleloopinitsopenligandfreeconformation AT massimilianomeli revealingescherichiacolitypeiilasparaginaseactivesiteflexibleloopinitsopenligandfreeconformation AT giorgiocolombo revealingescherichiacolitypeiilasparaginaseactivesiteflexibleloopinitsopenligandfreeconformation AT claudiascotti revealingescherichiacolitypeiilasparaginaseactivesiteflexibleloopinitsopenligandfreeconformation
_version_	1718378390718775296

Revealing Escherichia coli type II l-asparaginase active site flexible loop in its open, ligand-free conformation

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