PDBsum entry 1a5a

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protein ligands metals Protein-protein interface(s) links
Lyase PDB id
Protein chains
255 a.a. *
389 a.a. *
Waters ×394
* Residue conservation analysis
PDB id:
Name: Lyase
Title: Cryo-crystallography of a true substrate, indole-3-glycerol bound to a mutant (alphad60n) tryptophan synthase alpha2bet reveals the correct orientation of active site alpha glu 49
Structure: Tryptophan synthase (alpha chain). Chain: a. Engineered: yes. Mutation: yes. Tryptophan synthase (beta chain). Chain: b. Engineered: yes
Source: Salmonella typhimurium. Organism_taxid: 602. Cell_line: cb149. Gene: trpa/trpb. Expressed in: escherichia coli. Expression_system_taxid: 562. Expression_system_cell_line: cb149.
Biol. unit: Tetramer (from PDB file)
1.90Å     R-factor:   0.238     R-free:   0.298
Authors: S.Rhee,E.W.Miles,D.R.Davies
Key ref:
S.Rhee et al. (1998). Cryo-crystallography of a true substrate, indole-3-glycerol phosphate, bound to a mutant (alphaD60N) tryptophan synthase alpha2beta2 complex reveals the correct orientation of active site alphaGlu49. J Biol Chem, 273, 8553-8555. PubMed id: 9535826 DOI: 10.1074/jbc.273.15.8553
12-Feb-98     Release date:   27-May-98    
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Protein chain
Pfam   ArchSchema ?
P00929  (TRPA_SALTY) -  Tryptophan synthase alpha chain
268 a.a.
255 a.a.*
Protein chain
Pfam   ArchSchema ?
P0A2K1  (TRPB_SALTY) -  Tryptophan synthase beta chain
397 a.a.
389 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: Chains A, B: E.C.  - Tryptophan synthase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

Tryptophan Biosynthesis
      Reaction: L-serine + 1-C-(indol-3-yl)glycerol 3-phosphate = L-tryptophan + D-glyceraldehyde 3-phosphate + H2O
+ 1-C-(indol-3-yl)glycerol 3-phosphate
= L-tryptophan
+ D-glyceraldehyde 3-phosphate
+ H(2)O
      Cofactor: Pyridoxal 5'-phosphate
Pyridoxal 5'-phosphate
Bound ligand (Het Group name = PLP) matches with 93.75% similarity
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   5 terms 
  Biochemical function     catalytic activity     4 terms  


DOI no: 10.1074/jbc.273.15.8553 J Biol Chem 273:8553-8555 (1998)
PubMed id: 9535826  
Cryo-crystallography of a true substrate, indole-3-glycerol phosphate, bound to a mutant (alphaD60N) tryptophan synthase alpha2beta2 complex reveals the correct orientation of active site alphaGlu49.
S.Rhee, E.W.Miles, D.R.Davies.
The reversible cleavage of indole-3-glycerol by the alpha-subunit of tryptophan synthase has been proposed to be catalyzed by alphaGlu49 and alphaAsp60. Although previous x-ray crystallographic structures of the tryptophan synthase alpha2beta2 complex showed an interaction between the carboxylate of alphaAsp60 and the bound inhibitor indole-3-propanol phosphate, the carboxylate of alphaGlu49 was too distant to play its proposed role. To clarify the structural and functional roles of alphaGlu49, we have determined crystal structures of a mutant (alphaD60N) alpha2beta2 complex in the presence and absence of the true substrate, indole-3-glycerol phosphate. The enzyme in the crystal cleaves indole-3-glycerol phosphate very slowly at room temperature but not under cryo-conditions of 95 K. The structure of the complex with the true substrate obtained by cryo-crystallography reveals that indole-3-glycerol phosphate and indole-3-propanol phosphate have similar binding modes but different torsion angles. Most importantly, the side chain of alphaGlu49 interacts with 3-hydroxyl group of indole-3-glycerol phosphate as proposed. The movement of the side chain of alphaGlu49 into an extended conformation upon binding the true substrate provides evidence for an induced fit mechanism. Our results demonstrate how cryo-crystallography and mutagenesis can provide insight into enzyme mechanism.
  Selected figure(s)  
Figure 1.
Fig. 1. A, the final 2F[o] F[c] map overlaid on the models of IGP and residues Glu49 and Tyr175 in the D60N-IGP complex. The map was contoured at 0.6 . B, superposition between IGP (open circles) in the D60N-IGP and IPP (filled circles) in the K87T-Ser-IPP complex (7). The carboxylate of Asp60 is shown near the indole nitrogen of IPP and of IGP.
  The above figure is reprinted by permission from the ASBMB: J Biol Chem (1998, 273, 8553-8555) copyright 1998.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20370823 K.Nishio, K.Ogasahara, Y.Morimoto, T.Tsukihara, S.J.Lee, and K.Yutani (2010).
Large conformational changes in the Escherichia coli tryptophan synthase beta(2) subunit upon pyridoxal 5'-phosphate binding.
  FEBS J, 277, 2157-2170.
PDB codes: 2dh5 2dh6
18486479 M.F.Dunn, D.Niks, H.Ngo, T.R.Barends, and I.Schlichting (2008).
Tryptophan synthase: the workings of a channeling nanomachine.
  Trends Biochem Sci, 33, 254-264.  
18675375 T.R.Barends, M.F.Dunn, and I.Schlichting (2008).
Tryptophan synthase, an allosteric molecular factory.
  Curr Opin Chem Biol, 12, 593-600.  
11893063 E.W.Miles (2001).
Tryptophan synthase: a multienzyme complex with an intramolecular tunnel.
  Chem Rec, 1, 140-151.  
11297416 E.Weber-Ban, O.Hur, C.Bagwell, U.Banik, L.H.Yang, E.W.Miles, and M.F.Dunn (2001).
Investigation of allosteric linkages in the regulation of tryptophan synthase: the roles of salt bridges and monovalent cations probed by site-directed mutation, optical spectroscopy, and kinetics.
  Biochemistry, 40, 3497-3511.  
11395407 J.A.Gerlt, and P.C.Babbitt (2001).
Divergent evolution of enzymatic function: mechanistically diverse superfamilies and functionally distinct suprafamilies.
  Annu Rev Biochem, 70, 209-246.  
11209753 P.Rondard, and H.Bedouelle (2000).
Mutational scanning of a hairpin loop in the tryptophan synthase beta-subunit implicated in allostery and substrate channeling.
  Biol Chem, 381, 1185-1193.  
10769125 Y.X.Fan, P.McPhie, and E.W.Miles (2000).
Regulation of tryptophan synthase by temperature, monovalent cations, and an allosteric ligand. Evidence from Arrhenius plots, absorption spectra, and primary kinetic isotope effects.
  Biochemistry, 39, 4692-4703.  
10353822 E.Woehl, and M.F.Dunn (1999).
Mechanisms of monovalent cation action in enzyme catalysis: the first stage of the tryptophan synthase beta-reaction.
  Biochemistry, 38, 7118-7130.  
10090734 I.Bahar, and R.L.Jernigan (1999).
Cooperative fluctuations and subunit communication in tryptophan synthase.
  Biochemistry, 38, 3478-3490.  
10223296 K.A.Denessiouk, A.I.Denesyuk, J.V.Lehtonen, T.Korpela, and M.S.Johnson (1999).
Common structural elements in the architecture of the cofactor-binding domains in unrelated families of pyridoxal phosphate-dependent enzymes.
  Proteins, 35, 250-261.  
10600108 M.Weyand, and I.Schlichting (1999).
Crystal structure of wild-type tryptophan synthase complexed with the natural substrate indole-3-glycerol phosphate.
  Biochemistry, 38, 16469-16480.
PDB codes: 1qop 1qoq
9818266 B.L.Stoddard (1998).
New results using Laue diffraction and time-resolved crystallography.
  Curr Opin Struct Biol, 8, 612-618.  
9914259 J.N.Jansonius (1998).
Structure, evolution and action of vitamin B6-dependent enzymes.
  Curr Opin Struct Biol, 8, 759-769.  
9692955 S.Rhee, E.W.Miles, A.Mozzarelli, and D.R.Davies (1998).
Cryocrystallography and microspectrophotometry of a mutant (alpha D60N) tryptophan synthase alpha 2 beta 2 complex reveals allosteric roles of alpha Asp60.
  Biochemistry, 37, 10653-10659.
PDB code: 1beu
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.