5ZTX | pdb_00005ztx

co-factor free Transaminase

• PDB DOI: https://doi.org/10.2210/pdb5ZTX/pdb

• Classification: TRANSFERASE
• Organism(s): Vibrio fluvialis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-05-05 Released: 2018-08-29 
• Deposition Author(s): Park, H.H., Shin, Y.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.230 (Depositor), 0.221 (DCC) 
• R-Value Work: 
  0.177 (Depositor) 
• R-Value Observed: 
  0.180 (Depositor) 

Literature

Structural dynamics of the transaminase active site revealed by the crystal structure of a co-factor free omega-transaminase from Vibrio fluvialis JS17

Shin, Y.C., Yun, H., Park, H.H.

(2018) Sci Rep 8: 11454-11454

• PubMed: 30061559 
• DOI: https://doi.org/10.1038/s41598-018-29846-0
• Primary Citation Related Structures: 
  5ZTX


• PubMed Abstract: 
  

  Omega (ω)-transaminase catalyzes the transfer of an amino group from a non-α position amino acid, or an amine compound with no carboxylic group, to an amino acceptor, and has been studied intensively because of its high potential utility in industry and pharmatheutics. The ω-transaminase from Vibrio fluvialis JS17 (Vfat) is an amine:pyruvate transaminase capable of the stereo-selective transamination of arylic chiral amines. This enzyme exhibits extraordinary enantio-selectivity, and has a rapid reaction rate for chiral amine substrates. In this study, we report the crystal structure of the apo form of Vfat. The overall structure of Vfat was typical of other class III aminotransferase exhibiting an N-terminal helical domain, a small domain, and a large domain. Interestingly, the two subunits of apo Vfat in the asymmetric unit had different structures. A comparison of the overall structure to other transaminases, revealed that the structures of the N-terminal helical domain and the large domain can be affected by cofactor occupancy, but the structural rearrangement in these regions can occur independently.

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Organizational Affiliation: 
• Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, 02115, USA.
Department of Bioscience & Biotechnology, Konkuk University, Seoul, 143-701, Republic of Korea.
College of Pharmacy, Chung-Ang University, Seoul, 06974, Republic of Korea. [e-mail].

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: 103.48 kDa 
• Atom Count: 7,304 
• Modeled Residue Count: 859 
• Deposited Residue Count: 938 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
transaminase	A, B	469	Vibrio fluvialis	Mutation(s): 0
UniProt
Find proteins for F2XBU9 (Vibrio fluvialis) Explore F2XBU9  Go to UniProtKB:  F2XBU9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.230 (Depositor), 0.221 (DCC) 
• R-Value Work:  0.177 (Depositor) 
• R-Value Observed: 0.180 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.279	α = 90
b = 95.305	β = 90
c = 123.027	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-08-29 
Deposition Author(s): Park, H.H., Shin, Y.C.

Revision History  

• Version 1.0: 2018-08-29
  Type: Initial release
  
• Version 2.0: 2018-12-05
  Changes: Atomic model, Data collection, Database references, Source and taxonomy, Structure summary
• Version 2.1: 2024-03-27
  Changes: Data collection, Database references