9LFT | pdb_00009lft

Biochemical and structural characterization of a novel 4-hydroxyphenylacetate-3-monooxygenase from Geobacillus mahadii Geo-05


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 
    0.250 (Depositor), 0.249 (DCC) 
  • R-Value Work: 
    0.184 (Depositor), 0.189 (DCC) 
  • R-Value Observed: 
    0.187 (Depositor) 

Starting Model: in silico
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Biochemical and structural insights into GMHpaB: A thermostable 4-Hydroxyphenylacetate-3-monooxygenase with dual cofactor versatility.

Che Husain, N.A.Padzil, A.M.Taib, A.Z.M.Zain, N.C.Bakar, M.F.A.Gregory, K.S.Acharya, K.R.Jonet, M.A.Jamaluddin, H.

(2025) Int J Biol Macromol 321: 146065-146065

  • DOI: https://doi.org/10.1016/j.ijbiomac.2025.146065
  • Primary Citation of Related Structures:  
    9LFT

  • PubMed Abstract: 

    4-Hydroxyphenylacetate-3-monooxygenase from the thermophilic bacterium Geobacillus mahadii Geo-05 catalyzes the hydroxylation of 4-hydroxyphenylacetate (4-HPA) to 3,4-dihydroxyphenylacetate (3,4-DHPA), marking the initial step of the 4-HPA degradation pathway. This enzyme comprises of two components: an oxygenase and reductase. In this study, the gene encoding the oxygenase component, GMHpaB was successfully cloned, overexpressed in Escherichia coli BL21 (DE3) and purified to homogeneity. Purified GMHpaB was shown to bind reduced chromogenic cofactors, evidenced by maximal absorbance peaks at 375 nm. GMHpaB is optimally active at 55 °C and demonstrates thermostability, retaining 96 % of its catalytic activity after 30 min of incubation at its optimum temperature. Furthermore, GMHpaB displays versatility, showing high enzymatic activity with both FMN and FAD as cofactors, with relative activity increases by 250 % and 383 %, respectively, compared to the cofactor-free control. The overall fold classifies GMHpaB as group D flavin-dependent monooxygenase, but distinct loop conformations set it apart from homologs within the group. Notably, residue Glu212, positioned on the substrate binding loop of GMHpaB plays a critical role in anchoring and stabilizing the flavin binding loop, potentially contributing to the enzymes dual cofactor compatibility. These biochemical and structural insights lay the groundwork for future applications, particularly in high-temperature biocatalysis.


  • Organizational Affiliation
    • Department of Bioscience, Faculty of Science, Universiti Teknologi Malaysia, 81310 Johor Bahru, Johor, Malaysia; Structural Biology and Functional Omics, Malaysia Genome and Vaccine Institute, National Institutes of Biotechnology Malaysia, 43000 Kajang, Selangor, Malaysia.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
4-Hydroxyphenylacetate-3-monooxygenase
A, B, C, D
518Geobacillus mahadiaMutation(s): 0 
EC: 1.14.14.9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PEU (Subject of Investigation/LOI)
Query on PEU

Download Ideal Coordinates CCD File 
E [auth B]2,5,8,11,14,17,20,23,26,29,32,35,38,41,44,47,50,53,56,59,62,65,68,71,74,77,80-HEPTACOSAOXADOOCTACONTAN-82-OL
C55 H112 O28
ISGUIIHZEJGUGQ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free:  0.250 (Depositor), 0.249 (DCC) 
  • R-Value Work:  0.184 (Depositor), 0.189 (DCC) 
  • R-Value Observed: 0.187 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.571α = 90
b = 108.202β = 99.46
c = 99.055γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
DIALSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentMalaysiaFRGS/1/2019/STG05/MOSTI/02/1

Revision History  (Full details and data files)

  • Version 1.0: 2025-09-10
    Type: Initial release