5H3B

Crystal Structure of SeMet-BioG from Haemophilus influenzae at 1.49 Angstroms resolution

Summary for 5H3B

• Entry DOI: 10.2210/pdb5h3b/pdb
• Descriptor: Uncharacterized protein HI_1552, GLYCEROL, ISOPROPYL ALCOHOL, ... (4 entities in total)
• Functional Keywords: alpha/beta-hydrolase fold, pimeloyl-acp methyl esterase, biotin biosynthesis, hydrolase
• Biological source: Haemophilus influenzae Rd KW20
• Total number of polymer chains: 2
• Total formula weight: 53039.04

Authors

Shi, J.,Guo, Z. (deposition date: 2016-10-21, release date: 2016-12-07, Last modification date: 2024-10-16)

Primary citation

Shi, J.,Cao, X.,Chen, Y.,Cronan, J.E.,Guo, Z.
An Atypical alpha / beta-Hydrolase Fold Revealed in the Crystal Structure of Pimeloyl-Acyl Carrier Protein Methyl Esterase BioG from Haemophilus influenzae
Biochemistry, 55:6705-6717, 2016

PubMed Abstract: Pimeloyl-acyl carrier protein (ACP) methyl esterase is an α/β-hydrolase that catalyzes the last biosynthetic step of pimeloyl-ACP, a key intermediate in biotin biosynthesis. Intriguingly, multiple nonhomologous isofunctional forms of this enzyme that lack significant sequence identity are present in diverse bacteria. One such esterase, Escherichia coli BioH, has been shown to be a typical α/β-hydrolase fold enzyme. To gain further insights into the role of this step in biotin biosynthesis, we have determined the crystal structure of another widely distributed pimeloyl-ACP methyl esterase, Haemophilus influenzae BioG, at 1.26 Å. The BioG structure is similar to the BioH structure and is composed of an α-helical lid domain and a core domain that contains a central seven-stranded β-pleated sheet. However, four of the six α-helices that flank both sides of the BioH core β-sheet are replaced with long loops in BioG, thus forming an unusual α/β-hydrolase fold. This structural variation results in a significantly decreased thermal stability of the enzyme. Nevertheless, the lid domain and the residues at the lid-core interface are well conserved between BioH and BioG, in which an analogous hydrophobic pocket for pimelate binding as well as similar ionic interactions with the ACP moiety are retained. Biochemical characterization of site-directed mutants of the residues hypothesized to interact with the ACP moiety supports a similar substrate interaction mode for the two enzymes. Consequently, these enzymes package the identical catalytic function under a considerably different protein surface.

PubMed: 27933801
DOI: 10.1021/acs.biochem.6b00818

Experimental method

X-RAY DIFFRACTION (1.492 Å)