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Crystal structure of a bacterial L-arabinonate dehydratase contains [2Fe-2S] cluster
DOI:
10.1021/acschembio.7b00304
Authors:
Mohammad Mubinur
Rahman
(University of Eastern Finland)
,
Martina Blomster
Andberg
(VTT Technical Research Centre of Finland Ltd)
,
Senthil Kumar
Thangaraj
(University of Eastern Finland)
,
Tarja
Parkkinen
(University of Eastern Finland)
,
Merja
Penttilä
(VTT Technical Research Centre of Finland Ltd)
,
Janne
Jänis
(University of Eastern Finland)
,
Anu
Koivula
(VTT Technical Research Centre of Finland Ltd)
,
Juha
Rouvinen
(University of Eastern Finland)
,
Nina
Hakulinen
(University of Eastern Finland)
Co-authored by industrial partner:
No
Type:
Journal Paper
Journal:
Acs Chemical Biology
State:
Published (Approved)
Published:
June 2017
Diamond Proposal Number(s):
10291
Abstract: We present a novel crystal structure of the IlvD/EDD family enzyme, L-arabinonate dehydratase from Rhizobium leguminosarum bv. trifolii (RlArDHT, EC 4.2.1.25), which catalyzes the conversion of L-arabinonate to 2-dehydro-3-deoxy-L-arabinonate. The enzyme is a tetramer consisting of a dimer of dimers, where each monomer is composed of two domains. The active site contains a catalytically important [2Fe-2S] cluster and Mg2+ ion, and is buried between two domains, and also at the dimer interface. The active site Lys129 was found to be carbamylated. Ser480 and Thr482 were shown to be essential residues for catalysis, and the S480A mutant structure showed an unexpected open conformation in which the active site was more accessible for the substrate. This structure showed the partial binding of L-arabinonate, which allowed us to suggest that the alkoxide ion form of the Ser480 side chain functions as a base and the [2Fe-2S] cluster functions as a Lewis acid in the elimination reaction.
Journal Keywords: L-arabinonate dehydratase; hydrolyase; iron-sulfur cluster; [2Fe-2S]; pentose sugar acid; IlvD/EDD family
Diamond Keywords: Enzymes; Bacteria
Subject Areas:
Chemistry,
Biology and Bio-materials
Instruments:
I04-Macromolecular Crystallography
Other Facilities: European Synchrotron Radiation Facility
Added On:
05/06/2017 08:55
Discipline Tags:
Biochemistry
Chemistry
Structural biology
Life Sciences & Biotech
Technical Tags:
Diffraction
Macromolecular Crystallography (MX)