9IVE image
Deposition Date 2024-07-23
Release Date 2024-12-25
Last Version Date 2024-12-25
Entry Detail
PDB ID:
9IVE
Keywords:
Title:
Structure of wild-type aminotransferase from Mycolicibacterium neoaurum in complex with LLP and ALA
Biological Source:
Method Details:
Experimental Method:
Resolution:
1.93 Å
R-Value Free:
0.21
R-Value Work:
0.18
R-Value Observed:
0.18
Space Group:
P 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Branched-chain amino acid transferase
Gene (Uniprot):D174_04695
Chain IDs:A, B, C, D
Chain Length:335
Number of Molecules:4
Biological Source:Mycolicibacterium neoaurum VKM Ac-1815D
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
LLP A LYS modified residue
Ligand Molecules
Primary Citation
Structure-guided engineering an (R)-transaminase from Mycobacterium neoaurum for efficient synthesis of chiral N-heterocyclic amines.
Int.J.Biol.Macromol. 287 138591 138591 (2024)
PMID: 39667461 DOI: 10.1016/j.ijbiomac.2024.138591

Abstact

(R)-selective amine transaminases (R-ATAs) show considerable potential for the asymmetric synthesis of chiral drug intermediates. However, the low catalytic efficiency of natural R-ATAs toward bulky ketone substrates, such as N-heterocyclic compounds, severely limits its industrial application. In this study, five putative (R)-ATAs were mined from NCBI database, among which MnTA showed the highest activity for N-Boc-3-pyrrolidinone (1a) and N-Boc-3-piperidone (2a), and its crystal structure was performed. Furthermore, a structure-guided engineering strategy combined with directed evolution and in silico design was executed. Four key sites for substrate binding were identified based on alanine scanning. Then, a saturated mutation library was constructed, and residues G66 and F127 were found to be the key sites affecting substrate binding. By further combining mutation and iterative saturation mutation, variants with markedly improved activity were obtained. The optimal mutant MnTA-M1 (F127M) and MnTA-M5 (G66L/H67N/F127M/L160I) also displayed significantly enhanced activity toward various cyclic ketones or bulky N-heterocyclic ketone analogs. Finally, the gram-scale synthesis of (R)-3-amino-N-Boc-pyrrolidin (1b) and (R)-3-amino-N-Boc-piperidine (2b) was performed by the best mutants, achieving the space-time yields (STY) of 108 and 214 g/L·d, respectively. This research provides efficient biocatalysts for the synthesis of various chiral N-heterocyclic amines, along with a structural insight into the molecular mechanism for enhanced catalytic performance.

Legend

Protein

Chemical

Disease

Primary Citation of related structures