9EBR | pdb_00009ebr

The structure of NiaR from Thermotoga maritima bound to nicotinic acid

• PDB DOI: https://doi.org/10.2210/pdb9EBR/pdb
• Entry: 9EBR supersedes: 9BUL

• Classification: DNA BINDING PROTEIN
• Organism(s): Thermotoga maritima
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-11-13 Released: 2025-01-22 
• Deposition Author(s): Glasfeld, A., Cheng, D.W.C., Li, Y.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.260 (Depositor), 0.259 (DCC) 
• R-Value Work: 
  0.217 (Depositor), 0.217 (DCC) 
• R-Value Observed: 
  0.220 (Depositor) 

Starting Model: experimental

Literature

The activation of the metal-containing regulatory protein NiaR from Thermotoga maritima by its effector, nicotinic acid.

Cheng, W.C.D., Li, Y., Nakashima, M., Moenne-Loccoz, P., Rush, K.W., Glasfeld, A.

(2025) J Biol Inorg Chem 30: 169-179

• PubMed: 39899144 
• DOI: https://doi.org/10.1007/s00775-025-02096-y
• Primary Citation Related Structures: 
  9EBR


• PubMed Abstract: 
  

  NiaR is a regulatory protein that represses the expression of proteins involved in the de novo biosynthesis and uptake of nicotinic acid (NA), with NA acting as a co-repressor. The previously published structure of NiaR from Thermotoga maritima (TmNiaR) identified it as a functional homodimer containing a transition metal ion in a suspected NA-binding pocket. Here, we present the crystal structure of NA bound to the iron-metalated form of TmNiaR. Supported by spectroscopic and solution studies, this structure shows that NA binds to a protein-bound ferrous ion via its ring nitrogen. In addition, the carboxylate group on NA interacts with Tyr108 from the dyad-related subunit, repositioning the likely DNA-binding domains of the dimer to promote high-affinity interactions with DNA operators. The specificity of TmNiaR for NA can be explained by the hydrogen bonding scheme within the NA-binding pocket.

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Organizational Affiliation: 
• Department of Chemistry, Reed College, Portland, OR, 97202, USA.
Department of Biochemistry, Duke University School of Medicine, Durham, NC, 27710, USA.
Department of Chemical Physiology and Biochemistry, School of Medicine, Oregon Health and Science University, Portland, OR, 97239, USA.
Department of Chemistry and Biochemistry, Auburn University, Auburn, AL, 36849, USA.
Department of Chemistry, Reed College, Portland, OR, 97202, USA. [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: 19.88 kDa 
• Atom Count: 1,347 
• Modeled Residue Count: 168 
• Deposited Residue Count: 175 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable transcription repressor NiaR	A	175	Thermotoga maritima	Mutation(s): 0  Gene Names: niaR, TM_1602
UniProt
Find proteins for Q9X1T8 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9X1T8  Go to UniProtKB:  Q9X1T8

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NIO (Subject of Investigation/LOI)	C [auth A]	NICOTINIC ACID C6 H5 N O2 PVNIIMVLHYAWGP-UHFFFAOYSA-N
PRO	D [auth A]	PROLINE C5 H9 N O2 ONIBWKKTOPOVIA-BYPYZUCNSA-N
FE2 (Subject of Investigation/LOI)	B [auth A]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.260 (Depositor), 0.259 (DCC) 
• R-Value Work:  0.217 (Depositor), 0.217 (DCC) 
• R-Value Observed: 0.220 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.243	α = 90
b = 83.243	β = 90
c = 66.838	γ = 120

Software Package:

Software Name	Purpose
Coot	model building
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-01-22 
Deposition Author(s): Glasfeld, A., Cheng, D.W.C., Li, Y.
• This entry supersedes: 9BUL

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-01-22
  Type: Initial release
  
• Version 1.1: 2025-02-19
  Changes: Database references
• Version 1.2: 2025-04-02
  Changes: Database references