7U6I

HalB with glycine and succinate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Biocatalytic control of site-selectivity and chain length-selectivity in radical amino acid halogenases.

Kissman, E.N.Neugebauer, M.E.Sumida, K.H.Swenson, C.V.Sambold, N.A.Marchand, J.A.Millar, D.C.Chang, M.C.Y.

(2023) Proc Natl Acad Sci U S A 120: e2214512120-e2214512120

  • DOI: https://doi.org/10.1073/pnas.2214512120
  • Primary Citation of Related Structures:  
    7U6H, 7U6I, 7U6J

  • PubMed Abstract: 

    Biocatalytic C-H activation has the potential to merge enzymatic and synthetic strategies for bond formation. Fe II /αKG-dependent halogenases are particularly distinguished for their ability both to control selective C-H activation as well as to direct group transfer of a bound anion along a reaction axis separate from oxygen rebound, enabling the development of new transformations. In this context, we elucidate the basis for the selectivity of enzymes that perform selective halogenation to yield 4-Cl-lysine (BesD), 5-Cl-lysine (HalB), and 4-Cl-ornithine (HalD), allowing us to probe how site-selectivity and chain length selectivity are achieved. We now report the crystal structure of the HalB and HalD, revealing the key role of the substrate-binding lid in positioning the substrate for C 4 vs C 5 chlorination and recognition of lysine vs ornithine. Targeted engineering of the substrate-binding lid further demonstrates that these selectivities can be altered or switched, showcasing the potential to develop halogenases for biocatalytic applications.


  • Organizational Affiliation

    Department of Chemistry, University of California, Berkeley, CA 94720.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Halogenase B
A, B
251Streptomyces wuyuanensisMutation(s): 0 
Gene Names: SAMN05444921_127108
UniProt
Find proteins for A0A1H0BKU7 (Streptomyces wuyuanensis)
Explore A0A1H0BKU7 
Go to UniProtKB:  A0A1H0BKU7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1H0BKU7
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 
  • Space Group: P 62 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 165.48α = 90
b = 165.48β = 90
c = 105.332γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
Aimlessdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


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: 2023-03-15
    Type: Initial release
  • Version 1.1: 2023-03-22
    Changes: Database references
  • Version 1.2: 2023-10-25
    Changes: Data collection, Refinement description