6VDP | pdb_00006vdp

Crystal structure of SfmD truncated variant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.244 (Depositor), 0.240 (DCC) 
  • R-Value Work: 
    0.196 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 
    0.200 (Depositor) 

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Ligand Structure Quality Assessment 

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Literature

A novel catalytic heme cofactor in SfmD with a single thioether bond and a bis -His ligand set revealed by a de novo crystal structural and spectroscopic study.

Shin, I.Davis, I.Nieves-Merced, K.Wang, Y.McHardy, S.Liu, A.

(2021) Chem Sci 12: 3984-3998

  • DOI: https://doi.org/10.1039/d0sc06369j
  • Primary Citation of Related Structures:  
    6VDP, 6VDQ, 6VDZ, 6VE0

  • PubMed Abstract: 

    SfmD is a heme-dependent enzyme in the biosynthetic pathway of saframycin A. Here, we present a 1.78 Å resolution de novo crystal structure of SfmD, which unveils a novel heme cofactor attached to the protein with an unusual H x n H xxx C motif ( n ∼ 38). This heme cofactor is unique in two respects. It contains a single thioether bond in a cysteine-vinyl link with Cys317, and the ferric heme has two axial protein ligands, i.e. , His274 and His313. We demonstrated that SfmD heme is catalytically active and can utilize dioxygen and ascorbate for a single-oxygen insertion into 3-methyl-l-tyrosine. Catalytic assays using ascorbate derivatives revealed the functional groups of ascorbate essential to its function as a cosubstrate. Abolishing the thioether linkage through mutation of Cys317 resulted in catalytically inactive SfmD variants. EPR and optical data revealed that the heme center undergoes a substantial conformational change with one axial histidine ligand dissociating from the iron ion in response to substrate 3-methyl-l-tyrosine binding or chemical reduction by a reducing agent, such as the cosubstrate ascorbate. The labile axial ligand was identified as His274 through redox-linked structural determinations. Together, identifying an unusual heme cofactor with a previously unknown heme-binding motif for a monooxygenase activity and the structural similarity of SfmD to the members of the heme-based tryptophan dioxygenase superfamily will broaden understanding of heme chemistry.


  • Organizational Affiliation

    Department of Chemistry, The University of Texas at San Antonio One UTSA Circle Texas 78249 USA Feradical@utsa.edu.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3-methyl-L-tyrosine peroxygenase365Streptomyces lavendulaeMutation(s): 0 
Gene Names: sfmD
EC: 1.11.2.5
UniProt
Find proteins for B0CN28 (Streptomyces lavendulae)
Explore B0CN28 
Go to UniProtKB:  B0CN28
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB0CN28
Sequence Annotations
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.244 (Depositor), 0.240 (DCC) 
  • R-Value Work:  0.196 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 0.200 (Depositor) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.863α = 90
b = 59.863β = 90
c = 155.848γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
SOLVEphasing

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 HECClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2021-03-10
    Type: Initial release
  • Version 1.1: 2021-07-14
    Changes: Database references
  • Version 1.2: 2024-10-23
    Changes: Data collection, Database references, Structure summary