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PDBsum entry 1k7f

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protein ligands Protein-protein interface(s) links
Lyase PDB id
1k7f
Jmol
Contents
Protein chains
253 a.a. *
380 a.a. *
Ligands
IAV
PLP
Waters ×150
* Residue conservation analysis
PDB id:
1k7f
Name: Lyase
Title: Crystal structure of wild-type tryptophan synthase complexed [1h-indol-3-yl-acetyl]valine acid
Structure: Tryptophan synthase alpha chain. Chain: a. Engineered: yes. Tryptophan synthase beta chain. Chain: b. Engineered: yes
Source: Salmonella typhimurium. Organism_taxid: 602. Gene: trpa/trpb. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Tetramer (from PDB file)
Resolution:
1.90Å     R-factor:   0.200     R-free:   0.251
Authors: M.Weyand,I.Schlichting,A.Marabotti,A.Mozzarelli
Key ref:
M.Weyand et al. (2002). Crystal structures of a new class of allosteric effectors complexed to tryptophan synthase. J Biol Chem, 277, 10647-10652. PubMed id: 11756456 DOI: 10.1074/jbc.M111285200
Date:
19-Oct-01     Release date:   10-Jul-02    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P00929  (TRPA_SALTY) -  Tryptophan synthase alpha chain
Seq:
Struc:
268 a.a.
253 a.a.
Protein chain
Pfam   ArchSchema ?
P0A2K1  (TRPB_SALTY) -  Tryptophan synthase beta chain
Seq:
Struc:
397 a.a.
380 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: Chains A, B: E.C.4.2.1.20  - Tryptophan synthase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
Tryptophan Biosynthesis
      Reaction: L-serine + 1-C-(indol-3-yl)glycerol 3-phosphate = L-tryptophan + D-glyceraldehyde 3-phosphate + H2O
L-serine
+ 1-C-(indol-3-yl)glycerol 3-phosphate
=
L-tryptophan
Bound ligand (Het Group name = IAV)
matches with 52.17% similarity
+ 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  

 

 
    reference    
 
 
DOI no: 10.1074/jbc.M111285200 J Biol Chem 277:10647-10652 (2002)
PubMed id: 11756456  
 
 
Crystal structures of a new class of allosteric effectors complexed to tryptophan synthase.
M.Weyand, I.Schlichting, A.Marabotti, A.Mozzarelli.
 
  ABSTRACT  
 
Tryptophan synthase is a bifunctional alpha(2)beta(2) complex catalyzing the last two steps of l-tryptophan biosynthesis. The natural substrates of the alpha-subunit indole- 3-glycerolphosphate and glyceraldehyde-3-phosphate, and the substrate analogs indole-3-propanolphosphate and dl-alpha-glycerol-3-phosphate are allosteric effectors of the beta-subunit activity. It has been shown recently, that the indole-3-acetyl amino acids indole-3-acetylglycine and indole-3-acetyl-l-aspartic acid are both alpha-subunit inhibitors and beta-subunit allosteric effectors, whereas indole-3-acetyl-l-valine is only an alpha-subunit inhibitor (Marabotti, A., Cozzini, P., and Mozzarelli, A. (2000) Biochim. Biophys. Acta 1476, 287-299). The crystal structures of tryptophan synthase complexed with indole-3-acetylglycine and indole-3-acetyl-l-aspartic acid show that both ligands bind to the active site such that the carboxylate moiety is positioned similarly as the phosphate group of the natural substrates. As a consequence, the residues of the alpha-active site that interact with the ligands are the same as observed in the indole 3-glycerolphosphate-enzyme complex. Ligand binding leads to closure of loop alphaL6 of the alpha-subunit, a key structural element of intersubunit communication. This is in keeping with the allosteric role played by these compounds. The structure of the enzyme complex with indole-3-acetyl-l-valine is quite different. Due to the hydrophobic lateral chain, this molecule adopts a new orientation in the alpha-active site. In this case, closure of loop alphaL6 is no longer observed, in agreement with its functioning only as an inhibitor of the alpha-subunit reaction.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. 2mF[o] DF[c] electron density for the TRPSIAAA structures at the -active site. The density is shown at 1 -contouring for the IAAA molecule, Glu49, Asp60, Thr183, and for water molecules, which form hydrogen bonds with the -ligand. The hydrogen bonds of the enzymatic important amino acids Glu49 and Asp60 are shown as dashed lines (see Table II). The figure was prepared using "BOBSCRIPT" (40), "MOLSCRIPT" (41), and "RASTER3D" (42, 43). A, TRPSIAD structure. B, TRPSIAG structure. The second conformation of Glu49 is shown in orange. C, TRPSIAV structure.
Figure 2.
Fig. 2. Stereo plot of the structure superposition of TRPSIPP , TRPSIAD, and TRPSIAV. The C[ ]-atom trace is shown for TRPSIPP; the -subunit is colored in gray, loops L2 and L6 in cyan, and the -subunit in pink. The IPP, IAD, and IAV ligand C-atoms are colored in yellow, green, or orange, respectively. Nitrogen atoms are colored in blue, oxygen atoms are colored in red, and phosphate atoms are colored in magenta. The figure was prepared using MOLSCRIPT (41) and RASTER3D (42).
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2002, 277, 10647-10652) copyright 2002.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19387555 S.Raboni, S.Bettati, and A.Mozzarelli (2009).
Tryptophan synthase: a mine for enzymologists.
  Cell Mol Life Sci, 66, 2391-2403.  
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.  
15206928 Y.Hioki, K.Ogasahara, S.J.Lee, J.Ma, M.Ishida, Y.Yamagata, Y.Matsuura, M.Ota, M.Ikeguchi, S.Kuramitsu, and K.Yutani (2004).
The crystal structure of the tryptophan synthase beta subunit from the hyperthermophile Pyrococcus furiosus. Investigation of stabilization factors.
  Eur J Biochem, 271, 2624-2635.
PDB code: 1v8z
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