1UBS

TRYPTOPHAN SYNTHASE (E.C.4.2.1.20) WITH A MUTATION OF LYS 87->THR IN THE B SUBUNIT AND IN THE PRESENCE OF LIGAND L-SERINE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structures of a mutant (betaK87T) tryptophan synthase alpha2beta2 complex with ligands bound to the active sites of the alpha- and beta-subunits reveal ligand-induced conformational changes.

Rhee, S.Parris, K.D.Hyde, C.C.Ahmed, S.A.Miles, E.W.Davies, D.R.

(1997) Biochemistry 36: 7664-7680

  • DOI: 10.1021/bi9700429
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Three-dimensional structures are reported for a mutant (betaK87T) tryptophan synthase alpha2beta2 complex with either the substrate L-serine (betaK87T-Ser) or product L-tryptophan (betaK87T-Trp) at the active site of the beta-subunit, in which both a ...

    Three-dimensional structures are reported for a mutant (betaK87T) tryptophan synthase alpha2beta2 complex with either the substrate L-serine (betaK87T-Ser) or product L-tryptophan (betaK87T-Trp) at the active site of the beta-subunit, in which both amino acids form external aldimines with the coenzyme, pyridoxal phosphate. We also present structures with L-serine bound to the beta site and either alpha-glycerol 3-phosphate (betaK87T-Ser-GP) or indole-3-propanol phosphate (betaK87T-Ser-IPP) bound to the active site of the alpha-subunit. The results further identify the substrate and product binding sites in each subunit and provide insight into conformational changes that occur upon formation of these complexes. The two structures having ligands at the active sites of both alpha- and beta-subunits reveal an important new feature, the ordering of alpha-subunit loop 6 (residues 179-187). Closure of loop 6 isolates the active site of the alpha-subunit from solvent and results in interaction between alphaThr183 and the catalytic residue alphaAsp60. Other conformational differences between the wild type and these two mutant structures include a rigid-body rotation of the alpha-subunit of approximately 5 degrees relative to the beta-subunit and large movements of part of the beta-subunit (residues 93-189) toward the rest of the beta-subunit. Much smaller differences are observed in the betaK87T-Ser structure. Remarkably, binding of tryptophan to the beta active site results in conformational changes very similar to those observed in the betaK87T-Ser-GP and betaK87T-Ser-IPP structures, with exception of the disordered alpha-subunit loop 6. These large-scale changes, the closure of loop 6, and the movements of a small number of side chains in the alpha-beta interaction site provide a structural base for interpreting the allosteric properties of tryptophan synthase.


    Related Citations: 
    • Three-Dimensional Structure of the Tryptophan Synthase Alpha2Beta2 Multienzyme Complex from Salmonella Typhimurium
      Hyde, C.C.,Ahmed, S.A.,Padlan, E.A.,Miles, E.W.,Davies, D.R.
      (1988) J.Biol.Chem. 263: 17857
    • Lysine87 in the B Subunit of Tryptophan Synthase that Forms an Internal Aldimine with Pyridoxal Phosphate Serves Critical Roles in Transimination, Catalysis, and Product Release
      Lu, Z.,Nagata, S.,Mcphie, P.,Miles, E.W.
      (1993) J.Biol.Chem. 268: 8727
    • Crystallization and Preliminary X-Ray Crystallographic Data of the Tryptophan Synthase Alpha2Beta2 Complex from Salmonella Typhimurium
      Ahmed, S.A.,Miles, E.W.,Davies, D.R.
      (1985) J.Biol.Chem. 260: 3716
    • The Tryptophan Synthase Multienzyme Complex: Exploring Structure-Function Relationships with X-Ray Crystallography and Mutagenesis
      Hyde, C.C.,Miles, E.W.
      (1990) Bio/Technology 8: 27


    Organizational Affiliation

    Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
TRYPTOPHAN SYNTHASE
A
268Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)Mutation(s): 0 
Gene Names: trpA
EC: 4.2.1.20
Find proteins for P00929 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
Go to UniProtKB:  P00929
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
TRYPTOPHAN SYNTHASE
B
397Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)Mutation(s): 1 
Gene Names: trpB
EC: 4.2.1.20
Find proteins for P0A2K1 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
Go to UniProtKB:  P0A2K1
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

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Download CCD File 
B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
SER
Query on SER

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Download CCD File 
B
SERINE
C3 H7 N O3
MTCFGRXMJLQNBG-REOHCLBHSA-N
 Ligand Interaction
PLP
Query on PLP

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Download CCD File 
B
PYRIDOXAL-5'-PHOSPHATE
VITAMIN B6 Phosphate
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 184.200α = 90.00
b = 61.800β = 94.80
c = 67.800γ = 90.00
Software Package:
Software NamePurpose
R-AXISIICdata collection
PROLSQrefinement
R-AXISdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1996-03-08
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance