1SZS

The structure of gamma-aminobutyrate aminotransferase mutant: I50Q


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.170 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Kinetic and Crystallographic Analysis of Active Site Mutants of Escherichia coligamma-Aminobutyrate Aminotransferase.

Liu, W.Peterson, P.E.Langston, J.A.Jin, X.Zhou, X.Fisher, A.J.Toney, M.D.

(2005) Biochemistry 44: 2982-2992

  • DOI: 10.1021/bi048657a
  • Primary Citation of Related Structures:  
    1SZK, 1SZU, 1SZS

  • PubMed Abstract: 
  • The E. coli isozyme of gamma-aminobutyrate aminotransferase (GABA-AT) is a tetrameric pyridoxal phosphate-dependent enzyme that catalyzes transamination between primary amines and alpha-keto acids. The roles of the active site residues V241, E211, and I50 in the GABA-AT mechanism have been probed by site-directed mutagenesis ...

    The E. coli isozyme of gamma-aminobutyrate aminotransferase (GABA-AT) is a tetrameric pyridoxal phosphate-dependent enzyme that catalyzes transamination between primary amines and alpha-keto acids. The roles of the active site residues V241, E211, and I50 in the GABA-AT mechanism have been probed by site-directed mutagenesis. The beta-branched side chain of V241 facilitates formation of external aldimine intermediates with primary amine substrates, while E211 provides charge compensation of R398 selectively in the primary amine half-reaction and I50 forms a hydrophobic lid at the top of the substrate binding site. The structures of the I50Q, V241A, and E211S mutants were solved by X-ray crystallography to resolutions of 2.1, 2.5, and 2.52 A, respectively. The structure of GABA-AT is similar in overall fold and active site structure to that of dialkylglycine decarboxylase, which catalyzes both transamination and decarboxylation half-reactions in its normal catalytic cycle. Therefore, an attempt was made to convert GABA-AT into a decarboxylation-dependent aminotransferase similar to dialkylglycine decarboxylase by systematic mutation of E. coli GABA-AT active site residues. Two of the twelve mutants presented, E211S/I50G/C77K and E211S/I50H/V80D, have approximately 10-fold higher decarboxylation activities than the wild-type enzyme, and the E211S/I50H/V80D has formally changed the reaction specificity to that of a decarboxylase.


    Organizational Affiliation

    Department of Chemistry, University of California-Davis, Davis, California 95616, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
4-aminobutyrate aminotransferaseA, B, C, D426Escherichia coliMutation(s): 1 
Gene Names: gabTb2662
EC: 2.6.1.19 (PDB Primary Data), 2.6.1.48 (UniProt)
UniProt
Find proteins for P22256 (Escherichia coli (strain K12))
Explore P22256 
Go to UniProtKB:  P22256
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PMP (Subject of Investigation/LOI)
Query on PMP

Download Ideal Coordinates CCD File 
FA [auth C], O [auth A], RA [auth D], X [auth B]4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE
C8 H13 N2 O5 P
ZMJGSOSNSPKHNH-UHFFFAOYSA-N
 Ligand Interaction
PLP (Subject of Investigation/LOI)
Query on PLP

Download Ideal Coordinates CCD File 
EA [auth C], N [auth A], QA [auth D], W [auth B]PYRIDOXAL-5'-PHOSPHATE
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth C] , E [auth A] , F [auth A] , G [auth A] , GA [auth D] , H [auth A] , HA [auth D] , IA [auth D] , 
AA [auth C],  E [auth A],  F [auth A],  G [auth A],  GA [auth D],  H [auth A],  HA [auth D],  IA [auth D],  JA [auth D],  KA [auth D],  P [auth B],  Q [auth B],  R [auth B],  Y [auth C],  Z [auth C]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
BA [auth C] , CA [auth C] , DA [auth C] , I [auth A] , J [auth A] , K [auth A] , L [auth A] , LA [auth D] , 
BA [auth C],  CA [auth C],  DA [auth C],  I [auth A],  J [auth A],  K [auth A],  L [auth A],  LA [auth D],  M [auth A],  MA [auth D],  NA [auth D],  OA [auth D],  PA [auth D],  S [auth B],  T [auth B],  U [auth B],  V [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.170 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 108.1α = 90
b = 108.1β = 90
c = 301.7γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-03-01
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance