2J9Z

Tryptophan Synthase T110 mutant complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.187 

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This is version 1.2 of the entry. See complete history. 


Literature

Betaq114N and Betat110V Mutations Reveal a Critically Important Role of the Substrate Alpha-Carboxylate Site in the Reaction Specificity of Tryptophan Synthase.

Blumenstein, L., Domratcheva, T., Niks, D., Ngo, H., Seidel, R., Dunn, M.F., Schlichting, I.

(2007) Biochemistry 46: 14100

  • DOI: 10.1021/bi7008568
  • Primary Citation of Related Structures:  
    2J9Z, 2J9Y

  • PubMed Abstract: 

    • In the PLP-requiring alpha2beta2 tryptophan synthase complex, recognition of the substrate l-Ser at the beta-site includes a loop structure (residues beta110-115) extensively H-bonded to the substrate alpha-carboxylate. To investigate the relationship of this subsite to catalytic function and to the regulation of substrate channeling, two loop mutants were constructed: betaThr110 --> Val, and betaGln114 --> Asn ...

    In the PLP-requiring alpha2beta2 tryptophan synthase complex, recognition of the substrate l-Ser at the beta-site includes a loop structure (residues beta110-115) extensively H-bonded to the substrate alpha-carboxylate. To investigate the relationship of this subsite to catalytic function and to the regulation of substrate channeling, two loop mutants were constructed: betaThr110 --> Val, and betaGln114 --> Asn. The betaT110V mutation greatly impairs both catalytic activity in the beta-reaction, and allosteric communication between the alpha- and beta-sites. The crystal structure of the betaT110V mutant shows that the modified l-Ser carboxylate subsite has altered protein interactions that impair beta-site catalysis and the communication of allosteric signals between the alpha- and beta-sites. Purified betaQ114N consists of two species of mutant protein, one with a reddish color (lambdamax = 506 nm). The reddish species is unable to react with l-Ser. The second betaQ114N species displays significant catalytic activities; however, intermediates obtained on reaction with substrate l-Ser and substrate analogues exhibit perturbed UV/vis absorption spectra. Incubation with l-Ser results in the formation of an inactive species during the first 15 min with lambdamax approximately 320 nm, followed by a slower conversion over 24 h to the species with lambdamax = 506 nm. The 320 and 506 nm species originate from conversion of the alpha-aminoacrylate external aldimine to the internal aldimine and alpha-aminoacrylate, followed by the nucleophilic attack of alpha-aminoacrylate on C-4' of the internal aldimine to give a covalent adduct with PLP. Subsequent treatment with sodium hydroxide releases a modified coenzyme consisting of a vinylglyoxylic acid moiety linked through C-4' to the 4-position of the pyridine ring. We conclude that the shortening of the side chain accompanying the replacement of beta114-Gln by Asn relaxes the steric constraints that prevent this reaction in the wild-type enzyme. This study reveals a new layer of structure-function interactions essential for reaction specificity in tryptophan synthase.

    Organizational Affiliation: 

    Max Planck Institute for Medical Research, Department of Biomolecular Mechanisms, Heidelberg, Germany.



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
TRYPTOPHAN SYNTHASE ALPHA CHAIN A268Salmonella enterica subsp. enterica serovar TyphimuriumMutation(s): 0 
EC: 4.2.1.20
Find proteins for P00929 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
Explore P00929 
Go to UniProtKB:  P00929
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
TRYPTOPHAN SYNTHASE BETA CHAIN B397Salmonella enterica subsp. enterica serovar TyphimuriumMutation(s): 1 
EC: 4.2.1.20
Find proteins for P0A2K1 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
Explore P0A2K1 
Go to UniProtKB:  P0A2K1
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PLP
Query on PLP
Download Ideal Coordinates CCD File 
B
PYRIDOXAL-5'-PHOSPHATE
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N		 Ligand Interaction
NA
Query on NA
Download Ideal Coordinates CCD File 
B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.187 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 182.8α = 90
b = 59.9β = 94.4
c = 67.6γ = 90
Software Package:
Software NamePurpose
CNSrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-12-04
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance