Divergent evolution of ligand binding in the o -succinylbenzoate synthase family

Denis Odokonyero, Sugadev Ragumani, Mariana S. Lopez, Jeffrey B. Bonanno, Nicole D S Ozerova, Danae R. Woodard, Benjamin W. Machala, Subramanyam Swaminathan, Stephen K. Burley, Steven C. Almo, Margaret E. Glasner

Research output: Contribution to journalArticle

11 Citations (Scopus)

Abstract

Thermobifida fusca o-succinylbenzoate synthase (OSBS), a member of the enolase superfamily that catalyzes a step in menaquinone biosynthesis, has an amino acid sequence that is 22 and 28% identical with those of two previously characterized OSBS enzymes from Escherichia coli and Amycolatopsis sp. T-1-60, respectively. These values are considerably lower than typical levels of sequence identity among homologous proteins that have the same function. To determine how such divergent enzymes catalyze the same reaction, we determined the structure of T. fusca OSBS and identified amino acids that are important for ligand binding. We discovered significant differences in structure and conformational flexibility between T. fusca OSBS and other members of the enolase superfamily. In particular, the 20s loop, a flexible loop in the active site that permits ligand binding and release in most enolase superfamily proteins, has a four-amino acid deletion and is well-ordered in T. fusca OSBS. Instead, the flexibility of a different region allows the substrate to enter from the other side of the active site. T. fusca OSBS was more tolerant of mutations at residues that were critical for activity in E. coli OSBS. Also, replacing active site amino acids found in one protein with the amino acids that occur at the same place in the other protein reduces the catalytic efficiency. Thus, the extraordinary divergence between these proteins does not appear to reflect a higher tolerance of mutations. Instead, large deletions outside the active site were accompanied by alteration of active site size and electrostatic interactions, resulting in small but significant differences in ligand binding.

Original languageEnglish (US)
Pages (from-to)7512-7521
Number of pages10
JournalBiochemistry
Volume52
Issue number42
DOIs
StatePublished - 2013

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Ligands
Catalytic Domain
Phosphopyruvate Hydratase
Amino Acids
Proteins
Escherichia coli
Vitamin K 2
Mutation
Biosynthesis
Enzymes
Coulomb interactions
o-succinylbenzoic acid synthase
Static Electricity
Amino Acid Sequence
Substrates

ASJC Scopus subject areas

  • Biochemistry

Cite this

Odokonyero, D., Ragumani, S., Lopez, M. S., Bonanno, J. B., Ozerova, N. D. S., Woodard, D. R., ... Glasner, M. E. (2013). Divergent evolution of ligand binding in the o -succinylbenzoate synthase family. Biochemistry, 52(42), 7512-7521. https://doi.org/10.1021/bi401176d

Divergent evolution of ligand binding in the o -succinylbenzoate synthase family. / Odokonyero, Denis; Ragumani, Sugadev; Lopez, Mariana S.; Bonanno, Jeffrey B.; Ozerova, Nicole D S; Woodard, Danae R.; Machala, Benjamin W.; Swaminathan, Subramanyam; Burley, Stephen K.; Almo, Steven C.; Glasner, Margaret E.

In: Biochemistry, Vol. 52, No. 42, 2013, p. 7512-7521.

Research output: Contribution to journalArticle

Odokonyero, D, Ragumani, S, Lopez, MS, Bonanno, JB, Ozerova, NDS, Woodard, DR, Machala, BW, Swaminathan, S, Burley, SK, Almo, SC & Glasner, ME 2013, 'Divergent evolution of ligand binding in the o -succinylbenzoate synthase family', Biochemistry, vol. 52, no. 42, pp. 7512-7521. https://doi.org/10.1021/bi401176d
Odokonyero D, Ragumani S, Lopez MS, Bonanno JB, Ozerova NDS, Woodard DR et al. Divergent evolution of ligand binding in the o -succinylbenzoate synthase family. Biochemistry. 2013;52(42):7512-7521. https://doi.org/10.1021/bi401176d
Odokonyero, Denis ; Ragumani, Sugadev ; Lopez, Mariana S. ; Bonanno, Jeffrey B. ; Ozerova, Nicole D S ; Woodard, Danae R. ; Machala, Benjamin W. ; Swaminathan, Subramanyam ; Burley, Stephen K. ; Almo, Steven C. ; Glasner, Margaret E. / Divergent evolution of ligand binding in the o -succinylbenzoate synthase family. In: Biochemistry. 2013 ; Vol. 52, No. 42. pp. 7512-7521.
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