9JEW | pdb_00009jew

Crystal structure of a cupin protein (tm1459, C106V mutant) in iron (Fe) substituted form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.08 Å
  • R-Value Free: 
    0.168 (Depositor), 0.167 (DCC) 
  • R-Value Work: 
    0.134 (Depositor), 0.141 (DCC) 
  • R-Value Observed: 
    0.135 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


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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 : e202401191-e202401191

  • DOI: https://doi.org/10.1002/asia.202401191
  • Primary Citation of 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.


  • 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cupin type-2 domain-containing protein
A, B
118Thermotoga maritimaMutation(s): 1 
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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9X1H0
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.08 Å
  • R-Value Free:  0.168 (Depositor), 0.167 (DCC) 
  • R-Value Work:  0.134 (Depositor), 0.141 (DCC) 
  • R-Value Observed: 0.135 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.55α = 90
b = 57.866β = 90
c = 74.93γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling
PHASERphasing
SHELXLrefinement

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)JapanJSPS KAKENHI 21H01954

Revision History  (Full details and data files)

  • Version 1.0: 2025-05-07
    Type: Initial release