3FQ7

Gabaculine complex of GSAM


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.214 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Absence of a catalytic water confers resistance to the neurotoxin gabaculine.

Orriss, G.L.Patel, T.R.Sorensen, J.Stetefeld, J.

(2010) Faseb J. 24: 404-414

  • DOI: 10.1096/fj.09-138297
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Gabaculine is a potent inhibitor of the vitamin B6-dependent key enzyme in chlorophyll biosynthesis, glutamate-1-semialdehyde aminomutase (GSAM). The inhibition effect is caused by an enzymatic deprotonation of the neurotoxin and requires the aldimin ...

    Gabaculine is a potent inhibitor of the vitamin B6-dependent key enzyme in chlorophyll biosynthesis, glutamate-1-semialdehyde aminomutase (GSAM). The inhibition effect is caused by an enzymatic deprotonation of the neurotoxin and requires the aldimine (PLP) form of the cofactor at the active site. In this study, we show that a single-point mutation confers resistance to gabaculine. A combined functional and structural analysis of wild-type GSAM in complex with gabaculine and the GSAM(M248I) form allowed us to decipher in atomic detail the molecular basis of this unique resistance. Interestingly, the gabaculine tolerance is caused by the absence of an essential water molecule that has a dual functional role. It serves as a nucleophilic shuttle for the hydroxyl anion along the reaction pathway and holds active-site Lys273 in a catalytically competent conformation. The single-point mutant is not able to fix this catalytic water between the beta-branched side chain of Ile248 and Lys273. As a consequence, the mutant enzyme is trapped in a gabaculine-insensitive but still enzymatically active amine (PMP) form.


    Organizational Affiliation

    Department of Chemistry, University of Manitoba, 144 Dysart Rd, Winnipeg, R3T 2N2, Manitoba, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glutamate-1-semialdehyde 2,1-aminomutase
A, B
427Synechococcus sp. (strain ATCC 27144 / PCC 6301 / SAUG 1402/1)Mutation(s): 0 
Gene Names: hemL (gsa)
EC: 5.4.3.8
Find proteins for P24630 (Synechococcus sp. (strain ATCC 27144 / PCC 6301 / SAUG 1402/1))
Go to UniProtKB:  P24630
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PXG
Query on PXG

Download SDF File 
Download CCD File 
A, B
3-[O-PHOSPHONOPYRIDOXYL]--AMINO-BENZOIC ACID
C15 H17 N2 O7 P
WSOQXCGRIUHULI-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
PXGIC50: 3000000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.214 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 66.372α = 90.00
b = 107.025β = 90.00
c = 121.752γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
SCALAdata scaling
CNSrefinement
MOSFLMdata reduction
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2009-01-07 
  • Released Date: 2009-11-24 
  • Deposition Author(s): Stetefeld, J.

Revision History 

  • Version 1.0: 2009-11-24
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance