9UBB

The structure of the AglA_K225E-Arg complex

Summary for 9UBB

• Entry DOI: 10.2210/pdb9ubb/pdb
• Descriptor: YqcI/YcgG family protein AglA, PROTOPORPHYRIN IX CONTAINING FE, ARGININE, ... (4 entities in total)
• Functional Keywords: hydroxylase, biosynthetic protein
• Biological source: Streptomyces monomycini
• Total number of polymer chains: 1
• Total formula weight: 28592.47

Authors

Sun, Y.,Dou, C.,Yan, W.,Zhou, D.,Zhu, X.,Cheng, W. (deposition date: 2025-04-02, release date: 2025-12-10)

Primary citation

Sun, Y.,Dou, C.,Yan, W.,Chen, P.,Zhang, L.,Zhou, D.,Zheng, Y.,Long, Z.,Li, S.,Xu, X.,Huang, Q.,Zhu, X.,Cheng, W.
A Dynamic Gate Enables Regioselective Hydroxylation of Free Arginine by a Non-Canonical Heme Enzyme.
Adv Sci, :e13032-e13032, 2025

PubMed Abstract: The YqcI/YcgG family of heme-dependent enzymes catalyzes guanidine N-H hydroxylation, a critical yet enigmatic step in bioactive natural product biosynthesis. Here, this mechanistic puzzle is resolved through high-resolution structural snapshots of AglA, a prototypical YqcI/YcgG member, revealing a non-canonical heme-binding "sandwich" fold. A dynamic regiochemical gating mechanism is uncovered: substrate-induced remodeling of loop L2 and key residues (Phe152, Arg179, Phe182) spatially constrains the guanidine group of aminomethylphosphonate-linked arginine (AMPn-Arg), enforcing exclusive internal N hydroxylation. Single-site mutations rewire hydrogen-bond networks to enable hydroxylation of free L-arginine with controllable regioselectivity (internal N vs terminal N) while preserving native internal N selectivity for AMPn-Arg. Crystal structures of engineered variants with free arginine, together with MD simulations, explain how subtle rearrangements of loop L2 and residues Phe152/Arg179/Phe182 pivot the guanidinium group relative to the heme Fe(IV) = O intermediate. Fusing AglA to its native PDR/VanB reductase yields a self-sufficient chimera with improved catalytic efficiency. This work establishes a structural blueprint for tuning guanidino N-H hydroxylation and demonstrates proof-of-principle control of regioselectivity in a non-canonical heme enzyme, thereby advancing the synthesis of arginine-based antibiotics and precision-functionalized therapeutics.

PubMed: 41221789
DOI: 10.1002/advs.202513032

Experimental method

X-RAY DIFFRACTION (1.41 Å)