5IQU | pdb_00005iqu

WelO5 G166D variant bound to Fe(II), 2-oxoglutarate, and 12-epifischerindole U

• PDB DOI: https://doi.org/10.2210/pdb5IQU/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Hapalosiphon welwitschii UTEX B 1830
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2016-03-11 Released: 2016-06-29 
• Deposition Author(s): Mitchell, A.J., Maggiolo, A.O., Boal, A.K.
• 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: 2.51 Å
• R-Value Free: 
  0.262 (Depositor), 0.277 (DCC) 
• R-Value Work: 
  0.223 (Depositor), 0.229 (DCC) 
• R-Value Observed: 
  0.225 (Depositor) 

Starting Model: experimental

Literature

Structural basis for halogenation by iron- and 2-oxo-glutarate-dependent enzyme WelO5.

Mitchell, A.J., Zhu, Q., Maggiolo, A.O., Ananth, N.R., Hillwig, M.L., Liu, X., Boal, A.K.

(2016) Nat Chem Biol 12: 636-640

• PubMed: 27348090 
• DOI: https://doi.org/10.1038/nchembio.2112
• Primary Citation Related Structures: 
  5IQS, 5IQT, 5IQU, 5IQV


• PubMed Abstract: 
  

  A 2.4-Å-resolution X-ray crystal structure of the carrier-protein-independent halogenase WelO5 in complex with its welwitindolinone precursor substrate, 12-epi-fischerindole U, reveals that the C13 chlorination target is proximal to the anticipated site of the oxo group in a presumptive cis-halo-oxo-iron(IV) (haloferryl) intermediate. Prior study of related halogenases forecasts substrate hydroxylation in this active-site configuration, but X-ray crystallographic verification of C13 halogenation in single crystals mandates that ligand dynamics must reposition the oxygen ligand to enable the observed outcome. S189A WelO5 produces a mixture of halogenation and hydroxylation products, showing that an outer-sphere hydrogen-bonding group orchestrates ligand movements to achieve a configuration that promotes halogen transfer.

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Organizational Affiliation: 
• Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, USA.
Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.
Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 36.1 kDa 
• Atom Count: 2,185 
• Modeled Residue Count: 267 
• Deposited Residue Count: 315 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
WelO5	A	315	Hapalosiphon welwitschii UTEX B 1830	Mutation(s): 1
UniProt
Find proteins for A0A067YX61 (Hapalosiphon welwitschii UTEX B 1830) Explore A0A067YX61  Go to UniProtKB:  A0A067YX61

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
6CU	D [auth A]	(6aS,9R,10R,10aS)-9-ethyl-10-isocyano-6,6,9-trimethyl-5,6,6a,7,8,9,10,10a-octahydroindeno[2,1-b]indole C21 H26 N2 BWQHHWNHLMXCLS-QBGRRASTSA-N
AKG	C [auth A]	2-OXOGLUTARIC ACID C5 H6 O5 KPGXRSRHYNQIFN-UHFFFAOYSA-N
FE2	B [auth A]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.51 Å
• R-Value Free:  0.262 (Depositor), 0.277 (DCC) 
• R-Value Work:  0.223 (Depositor), 0.229 (DCC) 
• R-Value Observed: 0.225 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.107	α = 90
b = 54.127	β = 90.79
c = 74.639	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
PHASER	phasing
HKL-2000	data reduction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-06-29 
Deposition Author(s): Mitchell, A.J., Maggiolo, A.O., Boal, A.K.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM100011

Revision History  

• Version 1.0: 2016-06-29
  Type: Initial release
  
• Version 1.1: 2016-07-13
  Changes: Database references
• Version 1.2: 2016-07-27
  Changes: Database references
• Version 1.3: 2017-09-13
  Changes: Author supporting evidence, Derived calculations
• Version 1.4: 2022-04-13
  Changes: Author supporting evidence, Database references, Derived calculations
• Version 1.5: 2023-09-27
  Changes: Data collection, Refinement description