6Q1L | pdb_00006q1l

Crystal structure of oxidized iodotyrosine deiodinase (IYD) bound to FMN and 3-iodo-L-tyrosine

• PDB DOI: https://doi.org/10.2210/pdb6Q1L/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Thermotoga neapolitana DSM 4359
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-08-05 Released: 2021-04-07 
• Deposition Author(s): Sun, Z., Kavran, J.M., Rokita, S.E.
• Funding Organization(s): National Science Foundation (NSF, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.203 (Depositor), 0.203 (DCC) 
• R-Value Work: 
  0.171 (Depositor), 0.171 (DCC) 
• R-Value Observed: 
  0.172 (Depositor) 

Literature

The minimal structure for iodotyrosine deiodinase function is defined by an outlier protein from the thermophilic bacterium Thermotoga neapolitana.

Sun, Z., Xu, B., Spisak, S., Kavran, J.M., Rokita, S.E.

(2021) J Biological Chem 297: 101385-101385

• PubMed: 34748729 
• DOI: https://doi.org/10.1016/j.jbc.2021.101385
• Primary Citation Related Structures: 
  6PZ0, 6Q1L


• PubMed Abstract: 
  

  The nitroreductase superfamily of enzymes encompasses many flavin mononucleotide (FMN)-dependent catalysts promoting a wide range of reactions. All share a common core consisting of an FMN-binding domain, and individual subgroups additionally contain one to three sequence extensions radiating from defined positions within this core to support their unique catalytic properties. To identify the minimum structure required for activity in the iodotyrosine deiodinase subgroup of this superfamily, attention was directed to a representative from the thermophilic organism Thermotoga neapolitana (TnIYD). This representative was selected based on its status as an outlier of the subgroup arising from its deficiency in certain standard motifs evident in all homologues from mesophiles. We found that TnIYD lacked a typical N-terminal sequence and one of its two characteristic sequence extensions, neither of which was found to be necessary for activity. We also show that TnIYD efficiently promotes dehalogenation of iodo-, bromo-, and chlorotyrosine, analogous to related deiodinases (IYDs) from humans and other mesophiles. In addition, 2-iodophenol is a weak substrate for TnIYD as it was for all other IYDs characterized to date. Consistent with enzymes from thermophilic organisms, we observed that TnIYD adopts a compact fold and low surface area compared with IYDs from mesophilic organisms. The insights gained from our investigations on TnIYD demonstrate the advantages of focusing on sequences that diverge from conventional standards to uncover the minimum essentials for activity. We conclude that TnIYD now represents a superior starting structure for future efforts to engineer a stable dehalogenase targeting halophenols of environmental concern.

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Organizational Affiliation: 
• Department of Chemistry, Johns Hopkins University, Baltimore, Maryland, USA.
Chemistry-Biology Interface Graduate Program, Johns Hopkins University, Baltimore, Maryland, USA.
Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA; Department of Biophysics and Biophysical Chemistry, School of Medicine, Johns Hopkins University, Baltimore, Maryland, USA; Department of Oncology, School of Medicine, Johns Hopkins University, Baltimore, Maryland, USA.
Department of Chemistry, Johns Hopkins University, Baltimore, Maryland, USA. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 47.52 kDa 
• Atom Count: 3,517 
• Modeled Residue Count: 368 
• Deposited Residue Count: 384 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
iodotyrosine deiodinase	A, B	192	Thermotoga neapolitana DSM 4359	Mutation(s): 0  Gene Names: CTN_0569 EC: 1.21.1.1
UniProt
Find proteins for B9K712 (Thermotoga neapolitana (strain ATCC 49049 / DSM 4359 / NBRC 107923 / NS-E)) Explore B9K712  Go to UniProtKB:  B9K712

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMN (Subject of Investigation/LOI)	C [auth A], I [auth B]	FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N
IYR (Subject of Investigation/LOI)	D [auth A], J [auth B]	3-IODO-TYROSINE C9 H10 I N O3 UQTZMGFTRHFAAM-ZETCQYMHSA-N
CL	E [auth A], F [auth A], G [auth A], H [auth A], K [auth B], L [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.203 (Depositor), 0.203 (DCC) 
• R-Value Work:  0.171 (Depositor), 0.171 (DCC) 
• R-Value Observed: 0.172 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.861	α = 90
b = 81.232	β = 90
c = 103.9	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-04-07 
Deposition Author(s): Sun, Z., Kavran, J.M., Rokita, S.E.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	--

Revision History  

• Version 1.0: 2021-04-07
  Type: Initial release
  
• Version 2.0: 2021-10-20
  Type: Coordinate replacement
  Reason: Model completeness
  Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Other, Refinement description, Structure summary
• Version 2.1: 2022-04-20
  Changes: Database references
• Version 2.2: 2024-05-22
  Changes: Data collection