A computational analysis of the three isoforms of glutamate dehydrogenase reveals structural features of the isoform EC 1.4.1.4 supporting a key role in ammonium assimilation by plants

Emmanuel Jaspard

doi:10.1186/1745-6150-1-38

Abstract

BackgroundThere are three isoforms of glutamate dehydrogenase. The isoform EC 1.4.1.4 (GDH4) catalyses glutamate synthesis from 2-oxoglutarate and ammonium, using NAD(P)H. Ammonium assimilation is critical for plant growth. Although GDH4 from animals and prokaryotes are well characterized, there are few data concerning plant GDH4, even from those whose genomes are well annotated.ResultsA large set of the three GDH isoforms was built resulting in 116 non-redundant full polypeptide sequences. A computational analysis was made to gain more information concerning the structure – function relationship of GDH4 from plants (Eukaryota, Viridiplantae). The tested plant GDH4 sequences were the two ones known to date, those of Chlorella sorokiniana. This analysis revealed several structural features specific of plant GDH4: (i) the lack of a structure called "antenna"; (ii) the NAD(P)-binding motif GAGNVA; and (iii) a second putative coenzyme-binding motif GVLTGKG together with four residues involved in the binding of the reduced form of NADP.ConclusionA number of structural features specific of plant GDH4 have been found. The results reinforce the probable key role of GDH4 in ammonium assimilation by plants.ReviewersThis article was reviewed by Tina Bakolitsa (nominated by Eugene Koonin), Martin Jambon (nominated by Laura Landweber), Sandor Pangor and Franck Eisenhaber.

Highlights

There are three isoforms of glutamate dehydrogenase
The tested plant GDH4 sequences were the two ones known to date, those of Chlorella sorokiniana [19]
The functional specificity of GDH4 is the formation of glutamate using NADPH

Summary

Introduction

There are three isoforms of glutamate dehydrogenase. The isoform EC 1.4.1.4 (GDH4) catalyses glutamate synthesis from 2-oxoglutarate and ammonium, using NAD(P)H. Ammonium assimilation is critical for plant growth. GDH4 from animals and prokaryotes are well characterized, there are few data concerning plant GDH4, even from those whose genomes are well annotated. GDH4 is known to play an anabolic role in ammonium assimilation in the yeast Candida utilis [5]. Biology Direct 2006, 1:38 http://www.biology-direct.com/content/1/1/38 the major route of ammonium assimilation in plants involves the glutamine synthetase – glutamate synthase couple [6]. High ammonium concentration deactivates glutamine synthetase and induces GDH [7,8]. Data on the actual role of GDH4 from plants either in ammonium assimilation or in the formation of 2oxoglutarate are controversial

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