Structural dynamics of a methionine γ-lyase for calicheamicin biosynthesis: Rotation of the conserved tyrosine stacking with pyridoxal phosphate.

Hongnan Cao,Robert Jedrzejczak,Gyorgy Babnigg,Jon S Thorson,Shanteri Singh,George N Phillips,Craig A Bingman,Madan K Kharel,Andrzej Joachimiak,Ragothaman M Yennamalli,Lance Bigelow,Fengbin Wang,Kemin Tan

doi:10.1063/1.4948539

Abstract

CalE6 from Micromonospora echinospora is a (pyridoxal 5′ phosphate) PLP-dependent methionine γ-lyase involved in the biosynthesis of calicheamicins. We report the crystal structure of a CalE6 2-(N-morpholino)ethanesulfonic acid complex showing ligand-induced rotation of Tyr100, which stacks with PLP, resembling the corresponding tyrosine rotation of true catalytic intermediates of CalE6 homologs. Elastic network modeling and crystallographic ensemble refinement reveal mobility of the N-terminal loop, which involves both tetrameric assembly and PLP binding. Modeling and comparative structural analysis of PLP-dependent enzymes involved in Cys/Met metabolism shine light on the functional implications of the intrinsic dynamic properties of CalE6 in catalysis and holoenzyme maturation.

Highlights

Structural dynamics on various time and length scales are inherent properties of biological macromolecules and are often related to their functions
Modeling and comparative structural analysis of PLP-dependent enzymes involved in Cys/Met metabolism shine light on the functional implications of the intrinsic dynamic properties of CalE6 in catalysis and holoenzyme maturation
We demonstrated through comparative structural analysis of CalE6 and its homologs that the conserved tyrosine residue stacking with PLP is subject to ligand-induced rotation

Summary

Introduction

Structural dynamics on various time and length scales are inherent properties of biological macromolecules and are often related to their functions. Protein dynamics can be probed by solution approaches like nucleic magnetic resonance (NMR) and other spectroscopies and by a combination of X-ray crystallography and computational modeling.. Recent advances in time-resolved serial femtosecond crystallography (TR-SFX) using pulsed ultra-bright X-ray free electron lasers (XFELs) show promise in capturing photoactive proteins in action at atomic level by taking data within a very short time courses (in the order of 100 fs) during which light-induced conformational changes have been previously initiated.. Among many a)Current address: Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Himachal Pradesh 173234, India. B)Current address: Department of Chemistry and Biochemistry, The University of Oklahoma, Norman, Oklahoma 73019, 2329-7778/2016/3(3)/034702/12 Author(s) 2016.

Methods

Results

Conclusion