9DQ2

Crystal structure of HrmJ from Streptomyces sp. CFMR 7 (HrmJ-ssc) complexed with vanadyl(IV)-oxo, succinate and 6-nitronorleucine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 
    0.211 (Depositor), 0.210 (DCC) 
  • R-Value Work: 
    0.196 (Depositor), 0.195 (DCC) 
  • R-Value Observed: 
    0.197 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 6HNClick on this verticalbar to view detailsBest fitted SINClick on this verticalbar to view details

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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
BsmA domain containing protein
A, B
236Streptomyces sp. CFMR 7Mutation(s): 0 
Gene Names: ABE83_05625
UniProt
Find proteins for A0A0M5J3M0 (Streptomyces sp. CFMR 7)
Explore A0A0M5J3M0 
Go to UniProtKB:  A0A0M5J3M0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0M5J3M0
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
6HN (Subject of Investigation/LOI)
Query on 6HN

Download Ideal Coordinates CCD File 
C [auth A],
K [auth B]
6-nitro-L-norleucine
C6 H12 N2 O4
LMSAJWJHQUHKSX-YFKPBYRVSA-N
SIN (Subject of Investigation/LOI)
Query on SIN

Download Ideal Coordinates CCD File 
E [auth A],
M [auth B]
SUCCINIC ACID
C4 H6 O4
KDYFGRWQOYBRFD-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
N [auth B],
O [auth B],
P [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
BR
Query on BR

Download Ideal Coordinates CCD File 
H [auth A],
I [auth A],
J [auth A],
Q [auth B]
BROMIDE ION
Br
CPELXLSAUQHCOX-UHFFFAOYSA-M
VVO (Subject of Investigation/LOI)
Query on VVO

Download Ideal Coordinates CCD File 
D [auth A],
L [auth B]
oxovanadium(2+)
O V
MHHDXUNFNAZUGB-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free:  0.211 (Depositor), 0.210 (DCC) 
  • R-Value Work:  0.196 (Depositor), 0.195 (DCC) 
  • R-Value Observed: 0.197 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.113α = 90
b = 78.836β = 90
c = 97.166γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 6HNClick on this verticalbar to view detailsBest 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