4GH8

Crystal structure of a 'humanized' E. coli dihydrofolate reductase

4GH8 の概要

• エントリーDOI: 10.2210/pdb4gh8/pdb
• 分子名称: Dihydrofolate reductase, METHOTREXATE, NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE, ... (5 entities in total)
• 機能のキーワード: tetrahydrofolate, enzyme catalysis, evolution, dihydrofolate reductase, oxidoreductase
• 由来する生物種: Escherichia coli
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 39229.42

構造登録者

French, J.B.,Liu, C.T.,Hanoian, P.,Pringle, T.H.,Hammes-Schiffer, S.,Benkovic, S.J. (登録日: 2012-08-07, 公開日: 2013-06-05, 最終更新日: 2024-02-28)

主引用文献

Liu, C.T.,Hanoian, P.,French, J.B.,Pringle, T.H.,Hammes-Schiffer, S.,Benkovic, S.J.
Functional significance of evolving protein sequence in dihydrofolate reductase from bacteria to humans.
Proc.Natl.Acad.Sci.USA, 110:10159-10164, 2013

PubMed Abstract: With the rapidly growing wealth of genomic data, experimental inquiries on the functional significance of important divergence sites in protein evolution are becoming more accessible. Here we trace the evolution of dihydrofolate reductase (DHFR) and identify multiple key divergence sites among 233 species between humans and bacteria. We connect these sites, experimentally and computationally, to changes in the enzyme's binding properties and catalytic efficiency. One of the identified evolutionarily important sites is the N23PP modification (∼mid-Devonian, 415-385 Mya), which alters the conformational states of the active site loop in Escherichia coli dihydrofolate reductase and negatively impacts catalysis. This enzyme activity was restored with the inclusion of an evolutionarily significant lid domain (G51PEKN in E. coli enzyme; ∼2.4 Gya). Guided by this evolutionary genomic analysis, we generated a human-like E. coli dihydrofolate reductase variant through three simple mutations despite only 26% sequence identity between native human and E. coli DHFRs. Molecular dynamics simulations indicate that the overall conformational motions of the protein within a common scaffold are retained throughout evolution, although subtle changes to the equilibrium conformational sampling altered the free energy barrier of the enzymatic reaction in some cases. The data presented here provide a glimpse into the evolutionary trajectory of functional DHFR through its protein sequence space that lead to the diverged binding and catalytic properties of the E. coli and human enzymes.

PubMed: 23733948
DOI: 10.1073/pnas.1307130110

実験手法

X-RAY DIFFRACTION (1.85 Å)