7U6H | pdb_00007u6h

HalD with ornithine and alpha-ketoglutarate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.213 (Depositor), 0.215 (DCC) 
  • R-Value Work: 
    0.177 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 
    0.179 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7U6H

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 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.

Macromolecule Content 

  • Total Structure Weight: 126.28 kDa 
  • Atom Count: 9,369 
  • Modeled Residue Count: 1,012 
  • Deposited Residue Count: 1,056 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Halogenase D
A, B, C, D
264Pseudomonas kilonensisMutation(s): 0 
Gene Names: VP02_10785
UniProt
Find proteins for A0A0F4XRB2 (Pseudomonas kilonensis)
Explore A0A0F4XRB2 
Go to UniProtKB:  A0A0F4XRB2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0F4XRB2
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PG4

Query on PG4



Download:Ideal Coordinates CCD File
O [auth B]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
PGE

Query on PGE



Download:Ideal Coordinates CCD File
DA [auth D]
EA [auth D]
H [auth A]
I [auth A]
J [auth A]
DA [auth D],
EA [auth D],
H [auth A],
I [auth A],
J [auth A],
R [auth B],
Y [auth C]
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
AKG
(Subject of Investigation/LOI)

Query on AKG



Download:Ideal Coordinates CCD File
FA [auth D],
K [auth A],
S [auth B],
Z [auth C]
2-OXOGLUTARIC ACID
C5 H6 O5
KPGXRSRHYNQIFN-UHFFFAOYSA-N
ORN
(Subject of Investigation/LOI)

Query on ORN



Download:Ideal Coordinates CCD File
CA [auth D],
G [auth A],
N [auth B],
V [auth C]
L-ornithine
C5 H12 N2 O2
AHLPHDHHMVZTML-BYPYZUCNSA-N
PEG

Query on PEG



Download:Ideal Coordinates CCD File
P [auth B],
Q [auth B],
W [auth C],
X [auth C]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
NI

Query on NI



Download:Ideal Coordinates CCD File
AA [auth D],
E [auth A],
L [auth B],
T [auth C]
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
BA [auth D],
F [auth A],
M [auth B],
U [auth C]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.213 (Depositor), 0.215 (DCC) 
  • R-Value Work:  0.177 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 0.179 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.05α = 66.24
b = 73.226β = 75.8
c = 73.176γ = 85.28
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

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