7U6I | pdb_00007u6i

HalB with glycine and succinate

• PDB DOI: https://doi.org/10.2210/pdb7U6I/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Streptomyces wuyuanensis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2022-03-04 Released: 2023-03-15 
• Deposition Author(s): Neugebauer, M.E., Kissman, E.N., Chang, M.C.Y.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 
  0.223 (Depositor), 0.191 (DCC) 
• R-Value Work: 
  0.197 (Depositor) 
• R-Value Observed: 
  0.199 (Depositor) 

Starting Model: experimental

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

• PubMed: 36913566 
• 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.

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Organizational Affiliation: 
• Department of Chemistry, University of California, Berkeley, CA 94720.
Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720.
Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 57.67 kDa 
• Atom Count: 4,340 
• Modeled Residue Count: 481 
• Deposited Residue Count: 502 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Halogenase B	A, B	251	Streptomyces wuyuanensis	Mutation(s): 0  Gene Names: SAMN05444921_127108
UniProt
Find proteins for A0A1H0BKU7 (Streptomyces wuyuanensis) Explore A0A1H0BKU7  Go to UniProtKB:  A0A1H0BKU7

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SIN (Subject of Investigation/LOI)	C [auth A], E [auth B]	SUCCINIC ACID C4 H6 O4 KDYFGRWQOYBRFD-UHFFFAOYSA-N
GOL	F [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
GLY (Subject of Investigation/LOI)	D [auth A]	GLYCINE C2 H5 N O2 DHMQDGOQFOQNFH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free:  0.223 (Depositor), 0.191 (DCC) 
• R-Value Work:  0.197 (Depositor) 
• R-Value Observed: 0.199 (Depositor) 

Space Group: P 6₂ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 165.48	α = 90
b = 165.48	β = 90
c = 105.332	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
Aimless	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-03-15 
Deposition Author(s): Neugebauer, M.E., Kissman, E.N., Chang, M.C.Y.

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

Revision History  

• 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