7TQR | pdb_00007tqr

Crystal Structure of histidine ammonia lyase from Thermoplasma acidophilum

• PDB DOI: https://doi.org/10.2210/pdb7TQR/pdb

• Classification: LYASE
• Organism(s): Thermoplasma acidophilum
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2022-01-26 Released: 2022-04-06 
• Deposition Author(s): Wu, K., Dulchavsky, M., Bardwell, J.C.A.
• Funding Organization(s): Howard Hughes Medical Institute (HHMI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.183 (Depositor), 0.183 (DCC) 
• R-Value Work: 
  0.148 (Depositor), 0.148 (DCC) 
• R-Value Observed: 
  0.150 (Depositor) 

Starting Model: experimental

Literature

Microreactor equipped with naturally acid-resistant histidine ammonia lyase from an extremophile.

Ade, C., Marcelino, T.F., Dulchavsky, M., Wu, K., Bardwell, J.C.A., Stadler, B.

(2022) Mater Adv 3: 3649-3662

• PubMed: 36238657 
• DOI: https://doi.org/10.1039/d2ma00051b
• Primary Citation Related Structures: 
  7TQR


• PubMed Abstract: 
  

  Extremophile enzymes are useful in biotechnology and biomedicine due to their abilities to withstand harsh environments. The abilities of histidine ammonia lyases from different extremophiles to preserve their catalytic activities after exposure to acid were assessed. Thermoplasma acidophilum histidine ammonia lyase was identified as an enzyme with a promising catalytic profile following acid treatment. The fusion of this enzyme with the maltose-binding protein or co-incubation with the chaperone HdeA further helped Thermoplasma acidophilum histidine ammonia lyase to withstand acid treatments down to pH 2.8. The assembly of a microreactor by encapsulation of MBP- Thermoplasma acidophilum histidine ammonia lyase into a photocrosslinked poly(vinyl alcohol) hydrogel allowed the enzyme to recover over 50% of its enzymatic activity following exposure to simulated gastric and intestinal fluids. Our results show that using engineered proteins obtained from extremophiles in combination with polymer-based encapsulation can advance the oral formulations of biologicals.

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Organizational Affiliation: 
• Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, Aarhus, 8000, Denmark.
Sino-Danish Center for Education and Research, University of Chinese Academy of Sciences, China.
Department of Molecular, Cellular, and Developmental Biology and Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, 48109, USA.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 54.26 kDa 
• Atom Count: 3,807 
• Modeled Residue Count: 484 
• Deposited Residue Count: 495 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable histidine ammonia-lyase	A	495	Thermoplasma acidophilum	Mutation(s): 1  Gene Names: hutH, Ta0242 EC: 4.3.1.3
UniProt
Find proteins for Q9HLI6 (Thermoplasma acidophilum (strain ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165)) Explore Q9HLI6  Go to UniProtKB:  Q9HLI6

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MDO	A	L-PEPTIDE LINKING	C8 H11 N3 O3		ALA, SER, GLY

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.183 (Depositor), 0.183 (DCC) 
• R-Value Work:  0.148 (Depositor), 0.148 (DCC) 
• R-Value Observed: 0.150 (Depositor) 

Space Group: P 6 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 168.99	α = 90
b = 168.99	β = 90
c = 67.751	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
Aimless	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-04-06 
Deposition Author(s): Wu, K., Dulchavsky, M., Bardwell, J.C.A.

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Funding Organization	Location	Grant Number
Howard Hughes Medical Institute (HHMI)	United States	--

Revision History  

• Version 1.0: 2022-04-06
  Type: Initial release
  
• Version 1.1: 2022-10-26
  Changes: Database references
• Version 1.2: 2023-10-18
  Changes: Data collection, Refinement description
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection, Derived calculations
• Version 2.1: 2024-10-09
  Changes: Structure summary
• Version 3.0: 2026-03-18
  Changes: Polymer sequence