Quadruple space-group ambiguity owing to rotational and translational noncrystallographic symmetry in human liver fructose-1,6-bisphosphatase.

Armin Ruf,Markus G Rudolph,Brigitte Schott,Catherine Joseph,Tim Tetaz

doi:10.1107/s2059798316016715

Armin Ruf, Markus G Rudolph + Show 3 more

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https://doi.org/10.1107/s2059798316016715

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Abstract

Fructose-1,6-bisphosphatase (FBPase) is a key regulator of gluconeogenesis and a potential drug target for type 2 diabetes. FBPase is a homotetramer of 222 symmetry with a major and a minor dimer interface. The dimers connected via the minor interface can rotate with respect to each other, leading to the inactive T-state and active R-state conformations of FBPase. Here, the first crystal structure of human liver FBPase in the R-state conformation is presented, determined at a resolution of 2.2 Å in a tetragonal setting that exhibits an unusual arrangement of noncrystallographic symmetry (NCS) elements. Self-Patterson function analysis and various intensity statistics revealed the presence of pseudo-translation and the absence of twinning. The space group is P41212, but structure determination was also possible in space groups P43212, P4122 and P4322. All solutions have the same arrangement of three C2-symmetric dimers spaced by 1/3 along an NCS axis parallel to the c axis located at (1/4, 1/4, z), which is therefore invisible in a self-rotation function analysis. The solutions in the four space groups are related to one another and emulate a body-centred lattice. If all NCS elements were crystallographic, the space group would be I4122 with a c axis three times shorter and a single FBPase subunit in the asymmetric unit. I4122 is a minimal, non-isomorphic supergroup of the four primitive tetragonal space groups, explaining the space-group ambiguity for this crystal.

Highlights

Glucose is the main energy source for the brain
Alignment of molecular symmetry axes with crystallographic elements is quite common for FBPases from different organisms. 30 out of 90 structures in the PDB, including pig, rabbit and human FBPases, crystallized in five different space groups and contain only a single subunit in the asymmetric unit
The tetramer is constructed by crystallographic symmetry operations (Choe et al, 1998, 2000; Weeks et al, 1999; Choe, Iancu et al, 2003; Choe, Nelson et al, 2003; Iancu et al, 2005; Shi et al, 2013; Gao et al, 2013; Barciszewski et al, 2016). 50 more FBPase structures in three different space groups have a C1/C2 dimer in the asymmetric unit, and the tetramer is completed by crystallographic symmetry

Summary

Introduction

Blood glucose homeostasis is maintained mainly by the balance of catabolic glycolysis on the one hand and (with respect to glucose) anabolic glycogenolysis and gluconeogenesis on the other. High glucose levels arise from excessive gluconeogenesis in the liver rather than from glycogenolysis of hepatic glycogen stores. Fructose 1,6bisphosphatase (FBPase) is a major control point in gluconeogenesis, catalyzing the hydrolysis of fructose 1,6bisphosphate (F-1,6-P2) to fructose 6-phosphate (F6P) and inorganic phosphate (Fig. 1a). This step in gluconeogenesis is synergistically down-regulated by fructose 2,6-bisphosphate (F-2,6-P2) and AMP, which bind to the active site and an allosteric site of FBPase, respectively. While the cellular level of AMP seems to be constant (Xue et al, 1994), the concentration of F-2,6-P2 is controlled by the glucagon-sensitive enzyme 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase

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