8Q57

Crystal structure of class II SFP aldolase from Yersinia aldovae (YaSqiA-Zn-SO4) with bound sulfate ions

Summary for 8Q57

• Entry DOI: 10.2210/pdb8q57/pdb
• Descriptor: Tagatose-1,6-bisphosphate aldolase kbaY, SULFATE ION, ZINC ION, ... (6 entities in total)
• Functional Keywords: metal-dependent, aldolase, sulfoquinovose, sulfofructose phosphate, lyase
• Biological source: Yersinia aldovae
• Total number of polymer chains: 2
• Total formula weight: 68572.14

Authors

Sharma, M.,Davies, G.J. (deposition date: 2023-08-08, release date: 2023-10-25, Last modification date: 2023-11-22)

Primary citation

Sharma, M.,Kaur, A.,Madiedo Soler, N.,Lingford, J.P.,Epa, R.,Goddard-Borger, E.D.,Davies, G.J.,Williams, S.J.
Defining the molecular architecture, metal dependence, and distribution of metal-dependent class II sulfofructose-1-phosphate aldolases.
J.Biol.Chem., 299:105338-105338, 2023

PubMed Abstract: Sulfoquinovose (SQ, 6-deoxy-6-sulfoglucose) is a sulfosugar that is the anionic head group of plant, algal, and cyanobacterial sulfolipids: sulfoquinovosyl diacylglycerols. SQ is produced within photosynthetic tissues, forms a major terrestrial reservoir of biosulfur, and is an important species within the biogeochemical sulfur cycle. A major pathway for SQ breakdown is the sulfoglycolytic Embden-Meyerhof-Parnas pathway, which involves cleavage of the 6-carbon chain of the intermediate sulfofructose-1-phosphate (SFP) into dihydroxyacetone and sulfolactaldehyde, catalyzed by class I or II SFP aldolases. While the molecular basis of catalysis is understood for class I SFP aldolases, comparatively little is known about class II SFP aldolases. Here, we report the molecular architecture and biochemical basis of catalysis of two metal-dependent class II SFP aldolases from Hafnia paralvei and Yersinia aldovae. 3D X-ray structures of complexes with substrate SFP and product dihydroxyacetone phosphate reveal a dimer-of-dimers (tetrameric) assembly, the sulfonate-binding pocket, two metal-binding sites, and flexible loops that are implicated in catalysis. Both enzymes were metal-dependent and exhibited high K values for SFP, consistent with their role in a unidirectional nutrient acquisition pathway. Bioinformatic analysis identified a range of sulfoglycolytic Embden-Meyerhof-Parnas gene clusters containing class I/II SFP aldolases. The class I and II SFP aldolases have mututally exclusive occurrence within Actinobacteria and Firmicutes phyla, respectively, while both classes of enzyme occur within Proteobacteria. This work emphasizes the importance of SQ as a nutrient for diverse bacterial phyla and the different chemical strategies they use to harvest carbon from this sulfosugar.

PubMed: 37838169
DOI: 10.1016/j.jbc.2023.105338

Experimental method

X-RAY DIFFRACTION (1.7 Å)