5LDZ

Quadruple space group ambiguity due to rotational and translational non-crystallographic symmetry in human liver fructose-1,6-bisphosphatase

Summary for 5LDZ

• Entry DOI: 10.2210/pdb5ldz/pdb
• Descriptor: Fructose-1,6-bisphosphatase 1, ZINC ION, SULFATE ION, ... (5 entities in total)
• Functional Keywords: phosphoric monoester, allosteric enzyme, carbohydrate, metabolism, gluconeogenesis, hydrolase
• Biological source: Homo sapiens (Human)
• Total number of polymer chains: 6
• Total formula weight: 224805.47

Authors

Ruf, A.,Tetaz, T.,Schott, B.,Joseph, C.,Rudolph, M.G. (deposition date: 2016-06-29, release date: 2016-10-26, Last modification date: 2024-05-01)

Primary citation

Ruf, A.,Tetaz, T.,Schott, B.,Joseph, C.,Rudolph, M.G.
Quadruple space-group ambiguity owing to rotational and translational noncrystallographic symmetry in human liver fructose-1,6-bisphosphatase.
Acta Crystallogr D Struct Biol, 72:1212-1224, 2016

PubMed 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 P422, but structure determination was also possible in space groups P422, P422 and P422. All solutions have the same arrangement of three C-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 I422 with a c axis three times shorter and a single FBPase subunit in the asymmetric unit. I422 is a minimal, non-isomorphic supergroup of the four primitive tetragonal space groups, explaining the space-group ambiguity for this crystal.

PubMed: 27841754
DOI: 10.1107/S2059798316016715

Experimental method

X-RAY DIFFRACTION (2.2 Å)