9JEU | pdb_00009jeu

Crystal structure of a cupin protein (tm1459) in iron (Fe) substituted form

• PDB DOI: https://doi.org/10.2210/pdb9JEU/pdb

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


• Deposited: 2024-09-03 Released: 2025-05-07 
• Deposition Author(s): Fujieda, N., Ichihashi, H., Kurisu, G., Itoh, S.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.19 Å
• R-Value Free: 
  0.186 (Depositor), 0.179 (DCC) 
• R-Value Work: 
  0.151 (Depositor), 0.144 (DCC) 
• R-Value Observed: 
  0.151 (Depositor) 

Starting Model: experimental

Literature

Unusual Self-Hydroxylation in 4-Histidine Tetrad-Supporting Nonheme Iron Center.

Fujieda, N., Ishihama, K.I., Ichihashi, H., Yanagisawa, S., Kurisu, G., Itoh, S.

(2025) Chem Asian J 20: e202401191-e202401191

• PubMed: 40260495 
• DOI: https://doi.org/10.1002/asia.202401191
• Primary Citation Related Structures: 
  9JET, 9JEU, 9JEV, 9JEW


• PubMed Abstract: 
  

  The TM1459 protein from Thermotoga maritima is a member of the cupin protein superfamily and contains a mononuclear metal center. Structural information has been obtained using X-ray crystallography; however, its physiological role remains unknown. The metal-binding site has an octahedral coordination geometry ligated by four histidine imidazoles and two terminal water molecules present in the cis position. This protein had the ability to bind Mn, Fe, and Zn ions; additionally, a self-hydroxylation reaction occurred in the Fe-TM1459 C106V mutant. Namely, one of the tyrosine residues (Tyr7) was hydroxylated to generate the green form. Spectroscopic analyses using Vis-NIR, MALDI-TOF/MS, and resonance Raman spectroscopy confirmed that Tyr7 was hydroxylated to 3,4-dihydroxyphenylalanine giving an iron-catecholate complex. Because the Y7A/C106V mutant did not produce this green form, the mutation of Cys106 to Val was assumed to have induced a conformational change in Tyr7 that facilitated its approach to the metal center promoting the self-hydroxylation reaction. Thus, these results demonstrated that Fe-TM1459 protein has monooxygenase activity.

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Organizational Affiliation: 
• Department of Applied Biological Chemistry, Graduate School of Agriculture, Osaka Metropolitan University, 1-1 Gakuen-cho, Naka-ku, Sakai-shi, Osaka, 599-8531, Japan.
Department of Molecular Chemistry, Division of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamada-oka, Suita, Osaka, 565-0871, Japan.
Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori-cho, Ako-gun, Hyogo, 678-1297, Japan.
Institute for Protein Research, Osaka University, 3-2 Yamada-oka, Suita, Osaka, 565-0871, Japan.

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: 27.03 kDa 
• Atom Count: 2,183 
• Modeled Residue Count: 232 
• Deposited Residue Count: 236 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cupin type-2 domain-containing protein	A, B	118	Thermotoga maritima	Mutation(s): 0  Gene Names: TM_1459
UniProt
Find proteins for Q9X1H0 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9X1H0  Go to UniProtKB:  Q9X1H0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FE (Subject of Investigation/LOI)	C [auth A], D [auth B]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSD	A, B	L-PEPTIDE LINKING	C3 H7 N O4 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.19 Å
• R-Value Free:  0.186 (Depositor), 0.179 (DCC) 
• R-Value Work:  0.151 (Depositor), 0.144 (DCC) 
• R-Value Observed: 0.151 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.498	α = 90
b = 57.596	β = 90
c = 74.658	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing
SHELXL	refinement

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-05-07 
Deposition Author(s): Fujieda, N., Ichihashi, H., Kurisu, G., Itoh, S.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	JSPS KAKENHI 21H01954

Revision History  

• Version 1.0: 2025-05-07
  Type: Initial release
  
• Version 1.1: 2025-07-02
  Changes: Database references