5BJ3 | pdb_00005bj3

THERMUS THERMOPHILUS ASPARTATE AMINOTRANSFERASE TETRA MUTANT 1

• PDB DOI: https://doi.org/10.2210/pdb5BJ3/pdb

• Classification: TRANSFERASE
• Organism(s): Thermus aquaticus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 1999-01-11 Released: 2003-09-02 
• Deposition Author(s): Ura, H., Nakai, T., Kawaguchi, S.I., Miyahara, I., Hirotsu, K., Kuramitsu, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.243 (Depositor) 
• R-Value Work: 
  0.215 (Depositor) 
• R-Value Observed: 
  0.215 (Depositor) 

Starting Model: experimental

Literature

Substrate recognition mechanism of thermophilic dual-substrate enzyme

Ura, H., Nakai, T., Kawaguchi, S.I., Miyahara, I., Hirotsu, K., Kuramitsu, S.

(2001) J Biochem 130: 89-98

• PubMed: 11432784 
• DOI: https://doi.org/10.1093/oxfordjournals.jbchem.a002966
• Primary Citation Related Structures: 
  1B5O, 1B5P, 1GC3, 1GC4, 1GCK, 5BJ3, 5BJ4


• PubMed Abstract: 
  

  Aspartate aminotransferase from an extremely thermophilic bacterium, Thermus thermophilus HB8 (ttAspAT), has been believed to be specific for an acidic substrate. However, stepwise introduction of mutations in the active-site residues finally changed its substrate specificity to that of a dual-substrate enzyme. The final mutant, [S15D, T17V, K109S, S292R] ttAspAT, is active toward both acidic and hydrophobic substrates. During the course of stepwise mutation, the activities toward acidic and hydrophobic substrates changed independently. The introduction of a mobile Arg292* residue into ttAspAT was the key step in the change to a "dual-substrate" enzyme. The substrate recognition mechanism of this thermostable "dual-substrate" enzyme was confirmed by X-ray crystallography. This work together with previous studies on various enzymes suggest that this unique "dual-substrate recognition" mechanism is a feature of not only aminotransferases but also other enzymes.

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Organizational Affiliation: 
• Department of Biology, Graduate School of Science, Osaka University, Machikaneyama-cho, Toyonaka, Osaka 560-0043, 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 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 169.61 kDa 
• Atom Count: 11,621 
• Modeled Residue Count: 1,452 
• Deposited Residue Count: 1,540 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (ASPARTATE AMINOTRANSFERASE)	A, B, C, D	385	Thermus aquaticus	Mutation(s): 4  EC: 2.6.1.1 (PDB Primary Data), 2.6.1.78 (UniProt)
UniProt
Find proteins for Q56232 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q56232  Go to UniProtKB:  Q56232

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLP	E [auth A], F [auth B], G [auth C], H [auth D]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.243 (Depositor) 
• R-Value Work:  0.215 (Depositor) 
• R-Value Observed: 0.215 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.44	α = 90
b = 62.25	β = 109.07
c = 154.77	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
X-PLOR	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-09-02 
Deposition Author(s): Ura, H., Nakai, T., Kawaguchi, S.I., Miyahara, I., Hirotsu, K., Kuramitsu, S.

Revision History  

• Version 1.0: 2003-09-02
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2021-11-03
  Changes: Database references, Derived calculations
• Version 1.4: 2023-09-20
  Changes: Data collection, Refinement description