RCSB PDB - 9DQR: Crystal structure of HrmJ from Streptomyces sp. Ag109_G2-6 (HrmJ-ssa) complexed with vanadyl(IV)-oxo and succinate

 9DQR

Crystal structure of HrmJ from Streptomyces sp. Ag109_G2-6 (HrmJ-ssa) complexed with vanadyl(IV)-oxo and succinate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.211 (Depositor), 0.209 (DCC) 
  • R-Value Work: 
    0.176 (Depositor), 0.176 (DCC) 
  • R-Value Observed: 
    0.178 (Depositor) 

Starting Model: experimental
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Literature

Comparison of a Nonheme Iron Cyclopropanase with a Homologous Hydroxylase Reveals Mechanistic Features Associated with Distinct Reaction Outcomes.

Zheng, Y.C.Li, X.Cha, L.Paris, J.C.Michael, C.Ushimaru, R.Ogasawara, Y.Abe, I.Guo, Y.Chang, W.C.

(2025) J Am Chem Soc 

  • DOI: https://doi.org/10.1021/jacs.4c17741
  • Primary Citation of Related Structures:  
    9DQ0, 9DQ1, 9DQ2, 9DQP, 9DQQ, 9DQR

  • PubMed Abstract: 

    Despite the diversity of reactions catalyzed by mononuclear iron and 2-oxoglutarate-dependent enzymes, the factors that lead to diverse reaction outcomes beyond canonical hydroxylation remain elusive. Cyclopropanation reactions are of particular interest not only due to the prevalence of cyclopropane moieties in pharmaceuticals but also due to the chemistry that allows cyclopropanation to outcompete oxygen rebound. HrmJ is one such cyclopropanase from the biosynthetic pathway of hormaomycin; however, a homologue is herein discovered that instead catalyzes C -hydroxylation of the same nitro enolate substrate. These enzymes were reconstituted with Mn(II) and V(IV)═O as mimics of the resting (Fe(II)) and reactive (Fe(IV)═O) intermediate states, respectively. Corresponding crystal structures of the cyclopropanase bound with a substrate imply H atom transfer via an offline π-pathway. In contrast, analogous structural analysis of the hydroxylase implies H atom abstraction likely proceeds through a σ-pathway. Preparation of isotopically labeled substrates and stopped-flow kinetic analyses indicate that while the pro-S hydrogen of C4 is abstracted in both enzymes, the Fe(IV)═O intermediate reacts ca. 17-fold faster in the active site of the hydroxylase, consistent with the mechanistic assignments. These results also support a correlation between the mechanism of H atom transfer and the subsequent fate of the substrate radical once generated. A subtle difference in substrate positioning not only affects the H atom abstraction pathway but also allows the nitro enolate moiety to intercept the resulting substrate radical in the active site of the cyclopropase, thereby facilitating intramolecular C-C bond formation in a stereoselective manner.


  • Organizational Affiliation

    Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
2OG-Fe dioxygenase family protein
A, B
253Streptomyces sp. Ag109_G2-6Mutation(s): 0 
Gene Names: EDD96_7010
UniProt
Find proteins for A0A3N4ZHX0 (Streptomyces sp. Ag109_G2-6)
Explore A0A3N4ZHX0 
Go to UniProtKB:  A0A3N4ZHX0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A3N4ZHX0
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.211 (Depositor), 0.209 (DCC) 
  • R-Value Work:  0.176 (Depositor), 0.176 (DCC) 
  • R-Value Observed: 0.178 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.622α = 90
b = 44.668β = 107.111
c = 126.433γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted SINClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2025-02-12
    Type: Initial release