2XHZ

Probing the active site of the sugar isomerase domain from E. coli arabinose-5-phosphate isomerase via X-ray crystallography

Summary for 2XHZ

• Entry DOI: 10.2210/pdb2xhz/pdb
• Descriptor: ARABINOSE 5-PHOSPHATE ISOMERASE (2 entities in total)
• Functional Keywords: isomerase, lipopolysaccharide biogenesis
• Biological source: ESCHERICHIA COLI
• Total number of polymer chains: 4
• Total formula weight: 77318.03

Authors

Gourlay, L.J.,Sommaruga, S.,Nardini, M.,Sperandeo, P.,Deho, G.,Polissi, A.,Bolognesi, M. (deposition date: 2010-06-24, release date: 2011-01-26, Last modification date: 2023-12-20)

Primary citation

Gourlay, L.J.,Sommaruga, S.,Nardini, M.,Sperandeo, P.,Deho, G.,Polissi, A.,Bolognesi, M.
Probing the Active Site of the Sugar Isomerase Domain from E. Coli Arabinose-5-Phosphate Isomerase Via X-Ray Crystallography.
Protein Sci., 19:2430-, 2010

PubMed Abstract: Lipopolysaccharide (LPS) biosynthesis represents an underexploited target pathway for novel antimicrobial development to combat the emergence of multidrug-resistant bacteria. A key player in LPS synthesis is the enzyme D-arabinose-5-phosphate isomerase (API), which catalyzes the reversible isomerization of D-ribulose-5-phosphate to D-arabinose-5-phosphate, a precursor of 3-deoxy-D-manno-octulosonate that is an essential residue of the LPS inner core. API is composed of two main domains: an N-terminal sugar isomerase domain (SIS) and a pair of cystathionine-β-synthase domains of unknown function. As the three-dimensional structure of an enzyme is a prerequisite for the rational development of novel inhibitors, we present here the crystal structure of the SIS domain of a catalytic mutant (K59A) of E. coli D-arabinose-5-phosphate isomerase at 2.6-Å resolution. Our structural analyses and comparisons made with other SIS domains highlight several potentially important active site residues. In particular, the crystal structure allowed us to identify a previously unpredicted His residue (H88) located at the mouth of the active site cavity as a possible catalytic residue. On the basis of such structural data, subsequently supported by biochemical and mutational experiments, we confirm the catalytic role of H88, which appears to be a generally conserved residue among two-domain isomerases.

PubMed: 20954237
DOI: 10.1002/PRO.525

Experimental method

X-RAY DIFFRACTION (2.6 Å)