1RD5

Crystal structure of Tryptophan synthase alpha chain homolog BX1: a member of the chemical plant defense system


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.02 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.245 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

On the structural basis of the catalytic mechanism and the regulation of the alpha subunit of tryptophan synthase from Salmonella typhimurium and BX1 from maize, two evolutionarily related enzymes.

Kulik, V.Hartmann, E.Weyand, M.Frey, M.Gierl, A.Niks, D.Dunn, M.F.Schlichting, I.

(2005) J.Mol.Biol. 352: 608-620

  • DOI: 10.1016/j.jmb.2005.07.014
  • Primary Citation of Related Structures:  1TJP, 1TJR, 1WBJ

  • PubMed Abstract: 
  • Indole is a reaction intermediate in at least two biosynthetic pathways in maize seedlings. In the primary metabolism, the alpha-subunit (TSA) of the bifunctional tryptophan synthase (TRPS) catalyzes the cleavage of indole 3-glycerol phosphate (IGP) ...

    Indole is a reaction intermediate in at least two biosynthetic pathways in maize seedlings. In the primary metabolism, the alpha-subunit (TSA) of the bifunctional tryptophan synthase (TRPS) catalyzes the cleavage of indole 3-glycerol phosphate (IGP) to indole and d-glyceraldehyde 3-phosphate (G3P). Subsequently, indole diffuses through the connecting tunnel to the beta-active site where it is condensed with serine to form tryptophan and water. The maize enzyme, BX1, a homolog of TSA, also cleaves IGP to G3P and indole, and the indole is further converted to 2,4-dihydroxy-7-methoxy-2H-1,4-benzoxazin-3(4H)-one, a secondary plant metabolite. BX1 cleaves IGP significantly faster to G3P and indole than does TSA. In line with their different biological functions, these two evolutionary related enzymes differ significantly in their regulatory aspects while catalyzing the same chemistry. Here, the mechanism of IGP cleavage by TSA was analyzed using a novel transition state analogue generated in situ by reaction of 2-aminophenol and G3P. The crystal structure of the complex shows an sp3-hybridized atom corresponding to the C3 position of IGP. The catalytic alphaGlu49 rotates to interact with the sp3-hybridized atom and the 3' hydroxyl group suggesting that it serves both as proton donor and acceptor in the alpha-reaction. The second catalytic residue, alphaAsp60 interacts with the atom corresponding to the indolyl nitrogen, and the catalytically important loop alphaL6 is in the closed, high activity conformation. Comparison of the TSA and TSA-transition state analogue structures with the crystal structure of BX1 suggests that the faster catalytic rate of BX1 may be due to a stabilization of the active conformation: loop alphaL6 is closed and the catalytic glutamate is in the active conformation. The latter is caused by a substitution of the residues that stabilize the inactive conformation in TRPS.


    Related Citations: 
    • Analysis of a chemical plant defense mechanism in grasses
      Frey, M.,Chomet, P.,Glawischnig, E.,Stettner, C.,Grun, S.,Winklmair, A.,Eisenreich, W.,Bacher, A.,Meeley, R.B.,Briggs, S.P.,Simcox, K.,Gierl, A.
      (1997) Science 277: 696


    Organizational Affiliation

    Max Planck Institut fur medizinische Forschung, Abteilung fur Biomolekulare Mechanismen, Jahnstr. 29, 69120 Heidelberg, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tryptophan synthase alpha chain, chloroplast
A, B
262Zea maysGene Names: BX1
EC: 4.1.2.8, 4.2.1.20
Find proteins for P42390 (Zea mays)
Go to UniProtKB:  P42390
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MLA
Query on MLA

Download SDF File 
Download CCD File 
A, B
MALONIC ACID
DICARBOXYLIC ACID C3; PROPANEDIOLIC ACID; METHANEDICARBOXYLIC ACID
C3 H4 O4
OFOBLEOULBTSOW-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.02 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.245 
  • Space Group: F 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 91.094α = 90.00
b = 159.815β = 90.00
c = 162.877γ = 90.00
Software Package:
Software NamePurpose
XDSdata scaling
SHARPphasing
REFMACrefinement
MAR345data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-12-28
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Derived calculations, Version format compliance
  • Version 1.3: 2015-04-29
    Type: Non-polymer description
  • Version 1.4: 2017-10-11
    Type: Refinement description