Open Access Highly Accessed Open Badges Research article

Crystal structures of a halophilic archaeal malate synthase from Haloferax volcanii and comparisons with isoforms A and G

Colten D Bracken1, Amber M Neighbor1, Kenneth K Lamlenn13, Geoffrey C Thomas14, Heidi L Schubert2, Frank G Whitby2 and Bruce R Howard1*

  • * Corresponding author: Bruce R Howard

  • † Equal contributors

Author Affiliations

1 Department of Physical Science, Southern Utah University, Cedar City, UT 84720-2470, USA

2 Department of Biochemistry, University of Utah, Salt Lake City, UT 84112-5650, USA

3 Department of Pharmacology, Georgetown University Medical Center, Washington, DC. 20057-1411, USA

4 Department of Chemistry, University of Utah, Salt Lake City, UT 84112-0850, USA

For all author emails, please log on.

BMC Structural Biology 2011, 11:23  doi:10.1186/1472-6807-11-23

Published: 10 May 2011



Malate synthase, one of the two enzymes unique to the glyoxylate cycle, is found in all three domains of life, and is crucial to the utilization of two-carbon compounds for net biosynthetic pathways such as gluconeogenesis. In addition to the main isoforms A and G, so named because of their differential expression in E. coli grown on either acetate or glycolate respectively, a third distinct isoform has been identified. These three isoforms differ considerably in size and sequence conservation. The A isoform (MSA) comprises ~530 residues, the G isoform (MSG) is ~730 residues, and this third isoform (MSH-halophilic) is ~430 residues in length. Both isoforms A and G have been structurally characterized in detail, but no structures have been reported for the H isoform which has been found thus far only in members of the halophilic Archaea.


We have solved the structure of a malate synthase H (MSH) isoform member from Haloferax volcanii in complex with glyoxylate at 2.51 Å resolution, and also as a ternary complex with acetyl-coenzyme A and pyruvate at 1.95 Å. Like the A and G isoforms, MSH is based on a β8/α8 (TIM) barrel. Unlike previously solved malate synthase structures which are all monomeric, this enzyme is found in the native state as a trimer/hexamer equilibrium. Compared to isoforms A and G, MSH displays deletion of an N-terminal domain and a smaller deletion at the C-terminus. The MSH active site is closely superimposable with those of MSA and MSG, with the ternary complex indicating a nucleophilic attack on pyruvate by the enolate intermediate of acetyl-coenzyme A.


The reported structures of MSH from Haloferax volcanii allow a detailed analysis and comparison with previously solved structures of isoforms A and G. These structural comparisons provide insight into evolutionary relationships among these isoforms, and also indicate that despite the size and sequence variation, and the truncated C-terminal domain of the H isoform, the catalytic mechanism is conserved. Sequence analysis in light of the structure indicates that additional members of isoform H likely exist in the databases but have been misannotated.