4ATQ

GABA-transaminase A1R958 in complex with external aldimine PLP-GABA adduct

• PDB DOI:  https://doi.org/10.2210/pdb4ATQ/pdb

• Classification: TRANSFERASE
• Organism(s): Paenarthrobacter aurescens TC1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-05-09 Released: 2012-10-10 
• Deposition Author(s): Bruce, H., Tuan, A.N., Mangas Sanchez, J., Hart, S., Turkenburg, J.P., Grogan, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 0.248 
• R-Value Work: 0.202 
• R-Value Observed: 0.204 

Literature

Structures of a Gamma-Aminobutyrate (Gaba) Transaminase from the S-Triazine-Degrading Organism Arthrobacter Aurescens Tc1 in Complex with Plp and with its External Aldimine Plp- Gaba Adduct.

Bruce, H., Nguyen Tuan, A., Mangas Sanchez, J., Leese, C., Hopwood, J., Hyde, R., Hart, S., Turkenburg, J.P., Grogan, G.

(2012) Acta Crystallogr Sect F Struct Biol Cryst Commun 68: 1175

• PubMed: 23027742 
• DOI: https://doi.org/10.1107/S1744309112030023
• Primary Citation of Related Structures:  
  4ATP, 4ATQ


• PubMed Abstract: 
  

Two complex structures of the γ-aminobutyrate (GABA) transaminase A1R958 from Arthrobacter aurescens TC1 are presented. The first, determined to a resolution of 2.80 Å, features the internal aldimine formed by reaction between the ℇ-amino group of Lys295 and the cofactor pyridoxal phosphate (PLP); the second, determined to a resolution of 2.75 Å, features the external aldimine adduct formed between PLP and GABA in the first half-reaction. This is the first structure of a microbial GABA transaminase in complex with its natural external aldimine and reveals the molecular determinants of GABA binding in this enzyme.

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Organizational Affiliation: 

York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5DD, England.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

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

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 575.81 kDa 
• Atom Count: 38,709 
• Modelled Residue Count: 5,284 
• Deposited Residue Count: 5,472 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
4-AMINOBUTYRATE TRANSAMINASE	A, B, C, D, E, F, G, H, I, J, K, L	456	Paenarthrobacter aurescens TC1	Mutation(s): 0  Gene Names: gabT, AAur_3069 EC: 2.6.1.19
UniProt
Find proteins for A1R958 (Paenarthrobacter aurescens (strain TC1)) Explore A1R958  Go to UniProtKB:  A1R958

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLP	AA [auth H], CA [auth I], EA [auth J], GA [auth K], IA [auth L], M [auth A], O [auth B], Q [auth C], S [auth D], U [auth E], W [auth F], Y [auth G]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N
ABU	BA [auth H], DA [auth I], FA [auth J], HA [auth K], JA [auth L], N [auth A], P [auth B], R [auth C], T [auth D], V [auth E], X [auth F], Z [auth G]	GAMMA-AMINO-BUTANOIC ACID C4 H9 N O2 BTCSSZJGUNDROE-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 0.248 
• R-Value Work: 0.202 
• R-Value Observed: 0.204 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 176.71	α = 90
b = 292.83	β = 90
c = 105.96	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-10-10 
Deposition Author(s): Bruce, H., Tuan, A.N., Mangas Sanchez, J., Hart, S., Turkenburg, J.P., Grogan, G.

Revision History  

• Version 1.0: 2012-10-10
  Type: Initial release
  
• Version 1.1: 2012-10-17
  Changes: Database references