4k4c

X-ray crystal structure of E. coli YbdB complexed with phenacyl-CoAX-ray crystal structure of E. coli YbdB complexed with phenacyl-CoA

Structural highlights

4k4c is a 4 chain structure with sequence from Escherichia coli K-12. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.85Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

ENTH_ECOLI Required for optimal enterobactin synthesis. Acts as a proofreading enzyme that prevents EntB misacylation by hydrolyzing the thioester bound existing between EntB and wrongly charged molecules. Displays esterase activity toward a wide range of substrates, including acyl-CoAs and aryl-CoAs.^[1] ^[2] ^[3] ^[4]

Publication Abstract from PubMed

Herein, the structural determinants for substrate recognition and catalysis in two hotdog-fold thioesterase paralogs, YbdB and YdiI from Escherichia coli, are identified and analyzed to provide insight into the evolution of biological function in the hotdog-fold enzyme superfamily. The X-ray crystal structures of YbdB and YdiI, in complex with inert substrate analogs, determined in this study revealed the locations of the respective thioester substrate binding sites and the identity of the residues positioned for substrate binding and catalysis. The importance of each of these residues was assessed through amino acid replacements followed by steady-state kinetic analyses of the corresponding site-directed mutants. Transient kinetic and solvent (18)O-labeling studies were then carried out to provide insight into the role of Glu63 posited to function as the nucleophile or general base in catalysis. Finally, the structure-function-mechanism profiles of the two paralogs, along with that of a more distant homolog, were compared to identify conserved elements of substrate recognition and catalysis, which define the core traits of the hotdog-fold thioesterase family, as well as structural features that are unique to each thioesterase. Founded on the insight gained from this analysis, we conclude that the promiscuity revealed by in vitro substrate activity determinations, and posited to facilitate the evolution of new biological function, is the product of intrinsic plasticity in substrate binding as well as in the catalytic mechanism.

Structure and Catalysis in the Escherichia coli Hotdog-fold Thioesterase Paralogs YdiI and YbdB.,Wu R, Latham JA, Chen D, Farelli J, Zhao H, Matthews K, Allen KN, Dunaway-Mariano D Biochemistry. 2014 Jul 29;53(29):4788-805. doi: 10.1021/bi500334v. Epub 2014 Jul , 18. PMID:25010423^[5]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Kuznetsova E, Proudfoot M, Sanders SA, Reinking J, Savchenko A, Arrowsmith CH, Edwards AM, Yakunin AF. Enzyme genomics: Application of general enzymatic screens to discover new enzymes. FEMS Microbiol Rev. 2005 Apr;29(2):263-79. PMID:15808744 doi:S0168-6445(05)00004-5
↑ Leduc D, Battesti A, Bouveret E. The hotdog thioesterase EntH (YbdB) plays a role in vivo in optimal enterobactin biosynthesis by interacting with the ArCP domain of EntB. J Bacteriol. 2007 Oct;189(19):7112-26. Epub 2007 Aug 3. PMID:17675380 doi:http://dx.doi.org/10.1128/JB.00755-07
↑ Chen D, Wu R, Bryan TL, Dunaway-Mariano D. In vitro kinetic analysis of substrate specificity in enterobactin biosynthetic lower pathway enzymes provides insight into the biochemical function of the hot dog-fold thioesterase EntH. Biochemistry. 2009 Jan 27;48(3):511-3. PMID:19119850 doi:http://dx.doi.org/10.1021/bi802207t
↑ Guo ZF, Sun Y, Zheng S, Guo Z. Preferential hydrolysis of aberrant intermediates by the type II thioesterase in Escherichia coli nonribosomal enterobactin synthesis: substrate specificities and mutagenic studies on the active-site residues. Biochemistry. 2009 Mar 3;48(8):1712-22. doi: 10.1021/bi802165x. PMID:19193103 doi:http://dx.doi.org/10.1021/bi802165x
↑ Wu R, Latham JA, Chen D, Farelli J, Zhao H, Matthews K, Allen KN, Dunaway-Mariano D. Structure and Catalysis in the Escherichia coli Hotdog-fold Thioesterase Paralogs YdiI and YbdB. Biochemistry. 2014 Jul 29;53(29):4788-805. doi: 10.1021/bi500334v. Epub 2014 Jul , 18. PMID:25010423 doi:http://dx.doi.org/10.1021/bi500334v

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OCA

[1] Kuznetsova E, Proudfoot M, Sanders SA, Reinking J, Savchenko A, Arrowsmith CH, Edwards AM, Yakunin AF. Enzyme genomics: Application of general enzymatic screens to discover new enzymes. FEMS Microbiol Rev. 2005 Apr;29(2):263-79. PMID:15808744 doi:S0168-6445(05)00004-5

[2] Leduc D, Battesti A, Bouveret E. The hotdog thioesterase EntH (YbdB) plays a role in vivo in optimal enterobactin biosynthesis by interacting with the ArCP domain of EntB. J Bacteriol. 2007 Oct;189(19):7112-26. Epub 2007 Aug 3. PMID:17675380 doi:http://dx.doi.org/10.1128/JB.00755-07

[3] Chen D, Wu R, Bryan TL, Dunaway-Mariano D. In vitro kinetic analysis of substrate specificity in enterobactin biosynthetic lower pathway enzymes provides insight into the biochemical function of the hot dog-fold thioesterase EntH. Biochemistry. 2009 Jan 27;48(3):511-3. PMID:19119850 doi:http://dx.doi.org/10.1021/bi802207t

[4] Guo ZF, Sun Y, Zheng S, Guo Z. Preferential hydrolysis of aberrant intermediates by the type II thioesterase in Escherichia coli nonribosomal enterobactin synthesis: substrate specificities and mutagenic studies on the active-site residues. Biochemistry. 2009 Mar 3;48(8):1712-22. doi: 10.1021/bi802165x. PMID:19193103 doi:http://dx.doi.org/10.1021/bi802165x

[5] Wu R, Latham JA, Chen D, Farelli J, Zhao H, Matthews K, Allen KN, Dunaway-Mariano D. Structure and Catalysis in the Escherichia coli Hotdog-fold Thioesterase Paralogs YdiI and YbdB. Biochemistry. 2014 Jul 29;53(29):4788-805. doi: 10.1021/bi500334v. Epub 2014 Jul , 18. PMID:25010423 doi:http://dx.doi.org/10.1021/bi500334v

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