8UIQ | pdb_00008uiq

H47Q NicC with 2-mercaptopyridine ligand

• PDB DOI: https://doi.org/10.2210/pdb8UIQ/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Pseudomonas putida KT2440
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2023-10-10 Released: 2024-02-21 
• Deposition Author(s): Hicks, K.A., Perry, K., Turlington, Z.R., Vaz Ferreira de Macedo, S.
• Funding Organization(s): National Science Foundation (NSF, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.17 Å
• R-Value Free: 
  0.283 (Depositor), 0.255 (DCC) 
• R-Value Work: 
  0.245 (Depositor) 
• R-Value Observed: 
  0.247 (Depositor) 

Starting Model: experimental

Literature

Ligand bound structure of a 6-hydroxynicotinic acid 3-monooxygenase provides mechanistic insights.

Turlington, Z.R., Vaz Ferreira de Macedo, S., Perry, K., Belsky, S.L., Faust, J.A., Snider, M.J., Hicks, K.A.

(2024) Arch Biochem Biophys 752: 109859-109859

• PubMed: 38104959 
• DOI: https://doi.org/10.1016/j.abb.2023.109859
• Primary Citation Related Structures: 
  8UIQ, 8UIV


• PubMed Abstract: 
  

  6-Hydroxynicotinic acid 3-monooxygenase (NicC) is a bacterial enzyme involved in the degradation of nicotinic acid. This enzyme is a Class A flavin-dependent monooxygenase that catalyzes a unique decarboxylative hydroxylation. The unliganded structure of this enzyme has previously been reported and studied using steady- and transient-state kinetics to support a comprehensive kinetic mechanism. Here we report the crystal structure of the H47Q NicC variant in both a ligand-bound (solved to 2.17 Å resolution) and unliganded (1.51 Å resolution) form. Interestingly, in the liganded form, H47Q NicC is bound to 2-mercaptopyridine (2-MP), a contaminant present in the commercial stock of 6-mercaptopyridine-3-carboxylic acid(6-MNA), a substrate analogue. 2-MP binds weakly to H47Q NicC and is not a substrate for the enzyme. Based on kinetic and thermodynamic characterization, we have fortuitously captured a catalytically inactive H47Q NicC•2-MP complex in our crystal structure. This complex reveals interesting mechanistic details about the reaction catalyzed by 6-hydroxynicotinic acid 3-monooxygenase.

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Organizational Affiliation: 
• Department of Chemistry, State University of New York at Cortland, Cortland, NY, 13045, United States.
NE-CAT and Department of Chemistry and Chemical Biology, Cornell University, Argonne National Laboratory, Argonne, IL, United States.
Department of Chemistry, The College of Wooster, Wooster, OH, 44691, United States.
Department of Chemistry, State University of New York at Cortland, Cortland, NY, 13045, United States. Electronic address: [e-mail].

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 46.32 kDa 
• Atom Count: 3,012 
• Modeled Residue Count: 373 
• Deposited Residue Count: 405 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
6-hydroxynicotinate 3-monooxygenase	A	405	Pseudomonas putida KT2440	Mutation(s): 1  Gene Names: nicC EC: 1.14.13.114
UniProt
Find proteins for Q88FY2 (Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)) Explore Q88FY2  Go to UniProtKB:  Q88FY2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD (Subject of Investigation/LOI)	B [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
PYS (Subject of Investigation/LOI)	C [auth A]	2-PYRIDINETHIOL C5 H5 N S WHMDPDGBKYUEMW-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.17 Å
• R-Value Free:  0.283 (Depositor), 0.255 (DCC) 
• R-Value Work:  0.245 (Depositor) 
• R-Value Observed: 0.247 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.376	α = 90
b = 69.244	β = 90
c = 115.27	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-02-21 
Deposition Author(s): Hicks, K.A., Perry, K., Turlington, Z.R., Vaz Ferreira de Macedo, S.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	1817633

Revision History  

• Version 1.0: 2024-02-21
  Type: Initial release