TODO:

Add model components

• O2
• NAG
• HOOH
• Ions

Pick more approx. CBGA pose

• Current pose has few clashes but is far from asite

Add impropers for FAD-His-Cys

• Use the LigParGen parameters

Fix nonstandard residues

• Curently all His residues are HIE including His114
• I think Cys176 needs to be CYX if it's ligand bound

Fix protons

• Protonate His292
• Deprotonate Tyr484
• Protonation states should reflect H-bonds
  • View ligand interaction

Replace the CHARMM-GUI 3VTE model

• Use the 3VTE PDB-REDO model
• Either delete the S-S fragments or add the crosslinks
  • Filling with modeled loops is a bad idea

Propsed FAD-dependent Oxidative Cyclization

Tyr484 abstracts a proton from CBGA to form an alkoxide nucleophile.
FAD accepts a hydride to form a tertiary carbocation that arranges the ring closure.

• Mutations at Tyr484 abolish catalysis (catalytic base)
• Mutations at His114 and Cys176 abolish catalysis (covalent FAD bound residues)
• Mutations at Tyr417 and His292 greatly reduce K_cat (non-covalent FAD bound residues)

BRENDA: EC 1.21.3.7

DOI: 10.1007/978-3-319-54564-6_8

Active-site + FAD + substrate