7Y5F

Crystal structure of CmnC in complex with L-homoarginine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.52 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.181 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

Crystal structure of the alpha-ketoglutarate-dependent non-heme iron oxygenase CmnC in capreomycin biosynthesis and its engineering to catalyze hydroxylation of the substrate enantiomer.

Hsiao, Y.H.Huang, S.J.Lin, E.C.Hsiao, P.Y.Toh, S.I.Chen, I.H.Xu, Z.Lin, Y.P.Liu, H.J.Chang, C.Y.

(2022) Front Chem 10: 1001311-1001311

  • DOI: https://doi.org/10.3389/fchem.2022.1001311
  • Primary Citation of Related Structures:  
    7VGL, 7VGN, 7Y5F, 7Y5I, 7Y5P, 7YHE, 7YW9

  • PubMed Abstract: 

    CmnC is an α-ketoglutarate (α-KG)-dependent non-heme iron oxygenase involved in the formation of the l-capreomycidine (l-Cap) moiety in capreomycin (CMN) biosynthesis. CmnC and its homologues, VioC in viomycin (VIO) biosynthesis and OrfP in streptothricin (STT) biosynthesis, catalyze hydroxylation of l-Arg to form β-hydroxy l-Arg (CmnC and VioC) or β,γ-dihydroxy l-Arg (OrfP). In this study, a combination of biochemical characterization and structural determination was performed to understand the substrate binding environment and substrate specificity of CmnC. Interestingly, despite having a high conservation of the substrate binding environment among CmnC, VioC, and OrfP, only OrfP can hydroxylate the substrate enantiomer d-Arg. Superposition of the structures of CmnC, VioC, and OrfP revealed a similar folds and overall structures. The active site residues of CmnC, VioC, and OrfP are almost conserved; however Leu136, Ser138, and Asp249 around the substrate binding pocket in CmnC are replaced by Gln, Gly, and Tyr in OrfP, respectively. These residues may play important roles for the substrate binding. The mutagenesis analysis revealed that the triple mutant CmnC L136Q,S138G,D249Y switches the substrate stereoselectivity from l-Arg to d-Arg with ∼6% relative activity. The crystal structure of CmnC L136Q,S138G,D249Y in complex with d-Arg revealed that the substrate loses partial interactions and adopts a different orientation in the binding site. This study provides insights into the enzyme engineering to α-KG non-heme iron oxygenases for adjustment to the substrate stereoselectivity and development of biocatalysts.


  • Organizational Affiliation

    Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CmnC
A, B
358Saccharothrix mutabilis subsp. capreolusMutation(s): 0 
Gene Names: cmnC
UniProt
Find proteins for A6YEH4 (Saccharothrix mutabilis subsp. capreolus)
Explore A6YEH4 
Go to UniProtKB:  A6YEH4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA6YEH4
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.52 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.181 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.344α = 90
b = 127.514β = 90
c = 139.034γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, Taiwan)Taiwan110-2113-M-A49 -026 -MY3

Revision History  (Full details and data files)

  • Version 1.0: 2023-07-05
    Type: Initial release
  • Version 1.1: 2023-10-04
    Changes: Data collection, Database references
  • Version 1.2: 2023-11-15
    Changes: Data collection
  • Version 1.3: 2023-11-29
    Changes: Refinement description