4Q31

The crystal structure of cystathione gamma lyase (CalE6) from Micromonospora echinospora

Summary for 4Q31

• Entry DOI: 10.2210/pdb4q31/pdb
• Descriptor: cystathione gamma lyase CalE6, 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, CHLORIDE ION, ... (6 entities in total)
• Functional Keywords: structural genomics, psi-biology, protein structure initiative, midwest center for structural genomics, mcsg, enzyme discovery for natural product biosynthesis, natpro, lyase
• Biological source: Micromonospora echinospora
• Total number of polymer chains: 8
• Total formula weight: 335292.09

Authors

Tan, K.,Bigelow, L.,Jedrzejczak, R.,Babnigg, G.,Bingman, C.A.,Yennamalli, R.M.,Singh, S.,Kharel, M.K.,Thorson, J.S.,Phillips Jr., G.N.,Joachimiak, A.,Midwest Center for Structural Genomics (MCSG),Enzyme Discovery for Natural Product Biosynthesis (NatPro) (deposition date: 2014-04-10, release date: 2014-05-07, Last modification date: 2025-03-26)

Primary citation

Cao, H.,Tan, K.,Wang, F.,Bigelow, L.,Yennamalli, R.M.,Jedrzejczak, R.,Babnigg, G.,Bingman, C.A.,Joachimiak, A.,Kharel, M.K.,Singh, S.,Thorson, J.S.,Phillips, G.N.
Structural dynamics of a methionine gamma-lyase for calicheamicin biosynthesis: Rotation of the conserved tyrosine stacking with pyridoxal phosphate.
Struct Dyn, 3:034702-034702, 2016

PubMed 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.

PubMed: 27191010
DOI: 10.1063/1.4948539

Experimental method

X-RAY DIFFRACTION (2.099 Å)