3L8E

Crystal Structure of apo form of D,D-heptose 1.7-bisphosphate phosphatase from E. Coli

Summary for 3L8E

• Entry DOI: 10.2210/pdb3l8e/pdb
• Related: 3L8F 3L8G 3L8H
• Descriptor: D,D-heptose 1,7-bisphosphate phosphatase, ZINC ION, ACETIC ACID, ... (4 entities in total)
• Functional Keywords: had superfamily, gmhb, d-glycero-d-manno-heptose-1, 7-bisphosphate phosphatase, carbohydrate metabolism, cytoplasm, hydrolase, lipopolysaccharide biosynthesis
• Biological source: Escherichia coli
• Cellular location: Cytoplasm : P63228
• Total number of polymer chains: 2
• Total formula weight: 42038.38

Authors

Nguyen, H.,Peisach, E.,Allen, K.N. (deposition date: 2009-12-31, release date: 2010-02-02, Last modification date: 2024-02-21)

Primary citation

Nguyen, H.H.,Wang, L.,Huang, H.,Peisach, E.,Dunaway-Mariano, D.,Allen, K.N.
Structural Determinants of Substrate Recognition in the HAD Superfamily Member d-glycero-d-manno-Heptose-1,7-bisphosphate Phosphatase (GmhB) .
Biochemistry, 49:1082-1092, 2010

PubMed Abstract: The haloalkanoic acid dehalogenase (HAD) enzyme superfamily is the largest family of phosphohydrolases. In HAD members, the structural elements that provide the binding interactions that support substrate specificity are separated from those that orchestrate catalysis. For most HAD phosphatases, a cap domain functions in substrate recognition. However, for the HAD phosphatases that lack a cap domain, an alternate strategy for substrate selection must be operative. One such HAD phosphatase, GmhB of the HisB subfamily, was selected for structure-function analysis. Herein, the X-ray crystallographic structures of Escherichia coli GmhB in the apo form (1.6 A resolution), in a complex with Mg(2+) and orthophosphate (1.8 A resolution), and in a complex with Mg(2+) and d-glycero-d-manno-heptose 1beta,7-bisphosphate (2.2 A resolution) were determined, in addition to the structure of Bordetella bronchiseptica GmhB bound to Mg(2+) and orthophosphate (1.7 A resolution). The structures show that in place of a cap domain, the GmhB catalytic site is elaborated by three peptide inserts or loops that pack to form a concave, semicircular surface around the substrate leaving group. Structure-guided kinetic analysis of site-directed mutants was conducted in parallel with a bioinformatics study of sequence diversification within the HisB subfamily to identify loop residues that serve as substrate recognition elements and that distinguish GmhB from its subfamily counterpart, the histidinol-phosphate phosphatase domain of HisB. We show that GmhB and the histidinol-phosphate phosphatase domain use the same design of three substrate recognition loops inserted into the cap domain yet, through selective residue usage on the loops, have achieved unique substrate specificity and thus novel biochemical function.

PubMed: 20050614
DOI: 10.1021/bi902019q

Experimental method

X-RAY DIFFRACTION (1.64 Å)