Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 89.48 kDa 
• Atom Count: 7088 
• Modelled Residue Count: 796 
• Deposited Residue Count: 796 
• Unique protein chains: 1

4RKC

Psychrophilic aromatic amino acids aminotransferase from Psychrobacter sp. B6

• PDB DOI: 10.2210/pdb4RKC/pdb

• Classification: TRANSFERASE
• Organism(s): Psychrobacter sp. B6
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-10-12 Released: 2015-03-11 
• Deposition Author(s): Bujacz, A., Rutkiewicz-Krotewicz, M., Bujacz, G., Nowakowska-Sapota, K., Turkiewicz, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.19 Å
• R-Value Free: 0.203 
• R-Value Work: 0.142 
• R-Value Observed: 0.145 

Literature

Crystal structure and enzymatic properties of a broad substrate-specificity psychrophilic aminotransferase from the Antarctic soil bacterium Psychrobacter sp. B6.

Bujacz, A., Rutkiewicz-Krotewicz, M., Nowakowska-Sapota, K., Turkiewicz, M.

(2015) Acta Crystallogr D Biol Crystallogr 71: 632-645

• PubMed: 25760611 
• DOI: 10.1107/S1399004714028016
• Primary Citation of Related Structures:  
  4RKC, 4RKD


• PubMed Abstract: 
  

Aminotransferases (ATs) are enzymes that are commonly used in the chemical and pharmaceutical industries for the synthesis of natural and non-natural amino acids by transamination reactions. Currently, the easily accessible enzymes from mesophilic organisms are most commonly used; however, for economical and ecological reasons the utilization of aminotransferases from psychrophiles would be more advantageous, as their optimum reaction temperature is usually significantly lower than for the mesophilic ATs. Here, gene isolation, protein expression, purification, enzymatic properties and structural studies are reported for the cold-active aromatic amino-acid aminotransferase (PsyArAT) from Psychrobacter sp. B6, a psychrotrophic, Gram-negative strain from Antarctic soil. Preliminary computational analysis indicated dual functionality of the enzyme through the ability to utilize both aromatic amino acids and aspartate as substrates. This postulation was confirmed by enzymatic activity tests, which showed that it belonged to the class EC 2.6.1.57. The first crystal structures of a psychrophilic aromatic amino-acid aminotransferase have been determined at resolutions of 2.19 Å for the native enzyme (PsyArAT) and 2.76 Å for its complex with aspartic acid (PsyArAT/D). Both types of crystals grew in the monoclinic space group P21 under slightly different crystallization conditions. The PsyArAT crystals contained a dimer (90 kDa) in the asymmetric unit, which corresponds to the active form of this enzyme, whereas the crystals of the PsyArAT/D complex included four dimers showing different stages of the transamination reaction.

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Organizational Affiliation: 

Institute of Technical Biochemistry, Lodz University of Technology, Stefanowskiego 4/10, 90-924 Lodz, Poland.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aromatic amino acid aminotransferase	A, B	398	Psychrobacter sp. B6	Mutation(s): 0  EC: 2.6.1.57 (PDB Primary Data), 2.6.1 (UniProt)
UniProt
Find proteins for C7E5X4 (Psychrobacter sp. B6) Explore C7E5X4  Go to UniProtKB:  C7E5X4

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PMP	K [auth A], P [auth B]	4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE C8 H13 N2 O5 P ZMJGSOSNSPKHNH-UHFFFAOYSA-N
NO3	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], M [auth B], N [auth B], O [auth B]	NITRATE ION N O3 NHNBFGGVMKEFGY-UHFFFAOYSA-N
MG	C [auth A], L [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.19 Å
• R-Value Free: 0.203 
• R-Value Work: 0.142 
• R-Value Observed: 0.145 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.687	α = 90
b = 62.106	β = 102.91
c = 85.895	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-10-12 
• Released Date: 2015-03-11 
Deposition Author(s): Bujacz, A., Rutkiewicz-Krotewicz, M., Bujacz, G., Nowakowska-Sapota, K., Turkiewicz, M.

Revision History  

• Version 1.0: 2015-03-11
  Type: Initial release
  
• Version 1.1: 2015-03-18
  Changes: Database references
• Version 1.2: 2018-10-10
  Changes: Data collection, Database references, Structure summary