6NIE | pdb_00006nie

BesD with Fe(II), chloride, and alpha-ketoglutarate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 
    0.216 (Depositor), 0.219 (DCC) 
  • R-Value Work: 
    0.177 (Depositor), 0.181 (DCC) 
  • R-Value Observed: 
    0.179 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 6NIE

This is version 1.3 of the entry. See complete history

Literature

A family of radical halogenases for the engineering of amino-acid-based products.

Neugebauer, M.E.Sumida, K.H.Pelton, J.G.McMurry, J.L.Marchand, J.A.Chang, M.C.Y.

(2019) Nat Chem Biol 15: 1009-1016

  • DOI: https://doi.org/10.1038/s41589-019-0355-x
  • Primary Citation Related Structures: 
    6NIE

  • PubMed Abstract: 

    The integration of synthetic and biological catalysis enables new approaches to the synthesis of small molecules by combining the high selectivity of enzymes with the reaction diversity offered by synthetic chemistry. While organohalogens are valued for their bioactivity and utility as synthetic building blocks, only a handful of enzymes that carry out the regioselective halogenation of unactivated [Formula: see text] bonds have previously been identified. In this context, we report the structural characterization of BesD, a recently discovered radical halogenase from the Fe II /α-ketogluturate-dependent family that chlorinates the free amino acid lysine. We also identify and characterize additional halogenases that produce mono- and dichlorinated, as well as brominated and azidated, amino acids. The substrate selectivity of this new family of radical halogenases takes advantage of the central role of amino acids in metabolism and enables engineering of biosynthetic pathways to afford a wide variety of compound classes, including heterocycles, diamines, α-keto acids and peptides.


  • Organizational Affiliation
    • Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, USA.

Macromolecule Content 

  • Total Structure Weight: 118.87 kDa 
  • Atom Count: 8,788 
  • Modeled Residue Count: 976 
  • Deposited Residue Count: 1,020 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
BesD, lysine halogenase
A, B, C, D
255Streptantibioticus cattleyicolor NRRL 8057 = DSM 46488Mutation(s): 0 
Gene Names: SCATT_p06880
EC: 1.14.20
UniProt
Find proteins for G8XHD5 (Streptantibioticus cattleyicolor (strain ATCC 35852 / DSM 46488 / JCM 4925 / NBRC 14057 / NRRL 8057))
Explore G8XHD5 
Go to UniProtKB:  G8XHD5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG8XHD5
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
LYS

Query on LYS



Download:Ideal Coordinates CCD File
E [auth A],
I [auth B],
N [auth C],
R [auth D]
LYSINE
C6 H15 N2 O2
KDXKERNSBIXSRK-YFKPBYRVSA-O
AKG

Query on AKG



Download:Ideal Coordinates CCD File
H [auth A],
L [auth B],
Q [auth C],
U [auth D]
2-OXOGLUTARIC ACID
C5 H6 O5
KPGXRSRHYNQIFN-UHFFFAOYSA-N
FE2

Query on FE2



Download:Ideal Coordinates CCD File
F [auth A],
J [auth B],
O [auth C],
S [auth D]
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
FE

Query on FE



Download:Ideal Coordinates CCD File
M [auth B]FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
G [auth A],
K [auth B],
P [auth C],
T [auth D]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free:  0.216 (Depositor), 0.219 (DCC) 
  • R-Value Work:  0.177 (Depositor), 0.181 (DCC) 
  • R-Value Observed: 0.179 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.358α = 115.36
b = 68.916β = 91.57
c = 79.702γ = 112.95
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
CRANK2phasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2019-10-02
    Type: Initial release
  • Version 1.1: 2019-10-09
    Changes: Data collection, Database references
  • Version 1.2: 2019-11-27
    Changes: Author supporting evidence
  • Version 1.3: 2024-03-13
    Changes: Data collection, Database references, Derived calculations