Crystal structures of aspartate aminotransferase reconstituted with 1-deazapyridoxal 5′-phosphate: Internal aldimine and stable l -aspartate external aldimine

Wait R. Griswold, Andrew J Fisher, Michael D. Toney

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The 1.8 Å resolution crystal structures of Escherichia coli aspartate aminotransferase reconstituted with 1-deazapyridoxal 5′-phosphate (deazaPLP; 2-formyl-3-hydroxy-4-methylbenzyl phosphate) in the internal aldimine and l-aspartate external aldimine forms are reported. The l- aspartate•deazaPLP external aldimine is extraordinarily stable (half-life of >20 days), allowing crystals of this intermediate to be grown by cocrystallization with l-aspartate. This structure is compared to that of the α-methyl-l-aspartate•PLP external aldimine. Overlays with the corresponding pyridoxal 5′-phosphate (PLP) aldimines show very similar orientations of deazaPLP with respect to PLP. The lack of a hydrogen bond between Asp222 and deazaPLP, which serves to "anchor" PLP in the active site, releases strain in the deazaPLP internal aldimine that is enforced in the PLP internal aldimine [Hayashi, H., Mizuguchi, H., Miyahara, I., Islam, M. M., Ikushiro, H., Nakajima, Y., Hirotsu, K., and Kagamiyama, H. (2003) Biochim. Biophys. Acta1647, 103] as evidenced by the planarity of the pyridine ring and the Schiff base linkage with Lys258. Additionally, loss of this anchor causes a 10° greater tilt of deazaPLP toward the substrate in the external aldimine. An important mechanistic difference between the l- aspartate•deazaPLP and α-methyl-l-aspartate•PLP external aldimines is a hydrogen bond between Gly38 and Lys258 in the former, positioning the catalytic base above and approximately equidistant between Cα and C4′. In contrast, in the α-methyl-l-aspartate•PLP external aldimine, the ε-amino group of Lys258 is rotated ∼70° to form a hydrogen bond to Tyr70 because of the steric bulk of the methyl group.

Original languageEnglish (US)
Pages (from-to)5918-5924
Number of pages7
Issue number26
StatePublished - Jul 5 2011


ASJC Scopus subject areas

  • Biochemistry

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