4ZRB

Crystal Structure of Hypothetical Thioesterase Protein SP_1851 with Coenzyme A from Streptococcus pneumoniae TIGR4

Summary for 4ZRB

• Entry DOI: 10.2210/pdb4zrb/pdb
• Related: 4I82 4XY5 4XY6 4ZRF
• Descriptor: Hypothetical Thioesterase Protein SP_1851, COENZYME A (3 entities in total)
• Functional Keywords: paai thioesterase, hotdog fold, streptococcus pneumoniae, hydrolase
• Biological source: Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)
• Total number of polymer chains: 8
• Total formula weight: 124952.33

Authors

Khandokar, Y.B.,Srivastava, P.,Forwood, J.K. (deposition date: 2015-05-12, release date: 2015-05-27, Last modification date: 2023-09-27)

Primary citation

Khandokar, Y.B.,Srivastava, P.,Sarker, S.,Swarbrick, C.M.,Aragao, D.,Cowieson, N.,Forwood, J.K.
Structural and Functional Characterization of the PaaI Thioesterase from Streptococcus pneumoniae Reveals a Dual Specificity for Phenylacetyl-CoA and Medium-chain Fatty Acyl-CoAs and a Novel CoA-induced Fit Mechanism.
J.Biol.Chem., 291:1866-1876, 2016

PubMed Abstract: PaaI thioesterases are members of the TE13 thioesterase family that catalyze the hydrolysis of thioester bonds between coenzyme A and phenylacetyl-CoA. In this study we characterize the PaaI thioesterase from Streptococcus pneumoniae (SpPaaI), including structural analysis based on crystal diffraction data to 1.8-Å resolution, to reveal two double hotdog domains arranged in a back to back configuration. Consistent with the crystallography data, both size exclusion chromatography and small angle x-ray scattering data support a tetrameric arrangement of thioesterase domains in solution. Assessment of SpPaaI activity against a range of acyl-CoA substrates showed activity for both phenylacetyl-CoA and medium-chain fatty-acyl CoA substrates. Mutagenesis of putative active site residues reveals Asn(37), Asp(52), and Thr(68) are important for catalysis, and size exclusion chromatography analysis and x-ray crystallography confirm that these mutants retain the same tertiary and quaternary structures, establishing that the reduced activity is not a result of structural perturbations. Interestingly, the structure of SpPaaI in the presence of CoA provides a structural basis for the observed substrate specificity, accommodating a 10-carbon fatty acid chain, and a large conformational change of up to 38 Å in the N terminus, and a loop region involving Tyr(38)-Tyr(39). This is the first time PaaI thioesterases have displayed a dual specificity for medium-chain acyl-CoAs substrates and phenylacetyl-CoA substrates, and we provide a structural basis for this specificity, highlighting a novel induced fit mechanism that is likely to be conserved within members of this enzyme family.

PubMed: 26538563
DOI: 10.1074/jbc.M115.677484

Experimental method

X-RAY DIFFRACTION (2.2 Å)