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PDBsum entry 1k7x

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protein ligands metals Protein-protein interface(s) links
Lyase PDB id
1k7x
Jmol
Contents
Protein chains
254 a.a. *
390 a.a. *
Ligands
PLP
Metals
_NA
Waters ×434
* Residue conservation analysis
PDB id:
1k7x
Name: Lyase
Title: Crystal structure of the beta-ser178pro mutant of tryptophan
Structure: Tryptophan synthase alpha chain. Chain: a. Engineered: yes. Tryptophan synthase beta chain. Chain: b. Engineered: yes. Mutation: 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:
1.70Å     R-factor:   0.189     R-free:   0.238
Authors: M.Weyand,I.Schlichting,A.Marabotti,A.Mozzarelli
Key ref:
M.Weyand et al. (2002). Crystal structure of the beta Ser178--> Pro mutant of tryptophan synthase. A "knock-out" allosteric enzyme. J Biol Chem, 277, 10653-10660. PubMed id: 11756454 DOI: 10.1074/jbc.M111031200
Date:
22-Oct-01     Release date:   19-Jun-02    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P00929  (TRPA_SALTY) -  Tryptophan synthase alpha chain
Seq:
Struc:
268 a.a.
254 a.a.
Protein chain
Pfam   ArchSchema ?
P0A2K1  (TRPB_SALTY) -  Tryptophan synthase beta chain
Seq:
Struc:
397 a.a.
390 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 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
+ 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.M111031200 J Biol Chem 277:10653-10660 (2002)
PubMed id: 11756454  
 
 
Crystal structure of the beta Ser178--> Pro mutant of tryptophan synthase. A "knock-out" allosteric enzyme.
M.Weyand, I.Schlichting, P.Herde, A.Marabotti, A.Mozzarelli.
 
  ABSTRACT  
 
The catalytic activity of the pyridoxal 5'-phosphate-dependent tryptophan synthase alpha(2)beta(2) complex is allosterically regulated. The hydrogen bond between the helix betaH6 residue betaSer(178) and the loop alphaL6 residue Gly(181) was shown to be critical in ligand-induced intersubunit signaling, with the alpha-beta communication being completely lost in the mutant betaSer(178) --> Pro (Marabotti, A., De Biase, D., Tramonti, A., Bettati, S., and Mozzarelli, A. (2001) J. Biol. Chem. 276, 17747-17753). The structural basis of the impaired allosteric regulation was investigated by determining the crystal structures of the mutant betaSer(178) --> Pro in the absence and presence of the alpha-subunit ligands indole-3-acetylglycine and glycerol 3-phosphate. The mutation causes local and distant conformational changes especially in the beta-subunit. The ligand-free structure exhibits larger differences at the N-terminal part of helix betaH6, whereas the enzyme ligand complexes show differences at the C-terminal side. In contrast to the wild-type enzyme loop alphaL6 remains in an open conformation even in the presence of alpha-ligands. This effects the equilibrium between active and inactive conformations of the alpha-active site, altering k(cat) and K(m), and forms the structural basis for the missing allosteric communication between the alpha- and beta-subunits.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. Stereo drawings of SigmaA-weighted 2mF[o] DF[c] maps contoured at 1 . A, the S178P mutation site showing the good definition of the new proline amino acid. B, the -active site of the final S178PIAG model. The hydrogen bonds involving indole-acetylglycine are shown as dashed lines. See Table II for the bond length. The hydrogen bond between the carboxylate of the active conformation of Glu49 and of IAG has also been observed in the TRPS IAG complex (24). C, the -active site of the final S178PGP model. The hydrogen bonds involving glycerol phosphate are shown as dashed lines. The figure was prepared using "BOBSCRIPT" (46), "MOLSCRIPT" (47), and "RASTER3D" (48, 49).
Figure 3.
Fig. 3. A, C[ ]-atom trace representation of the superposition of the wild-type and S178P mutant structures focused on the -active site, the mutation site and the / -subunit interface. The wild-type C[ ]-atom trace is colored in gray, and loops L2 and L6 of the -subunit are colored in cyan. The S178P mutant C -atom trace is colored in red for the -subunit and in yellow for the -subunit. The amino acids at position 178 are shown in ball-and-stick representation. B, C[ ]-atom trace representation of the superposition of the wild-type TRPSIAG and S178PIAG structures focused on the -active site, the mutation site, and the / -subunit interface. The wild-type C[ ]-atom trace is colored in gray, and loops L2 and L6 of the -subunit are colored in cyan. The S178P mutant C -atom trace is colored in red for the -subunit and in yellow for the -subunit. The IAG molecule of the S178PIAG structure and the amino acids at position 178 are shown in ball-and-stick representation. The figure was prepared using MOLSCRIPT (47) and RASTER3D (48, 49).
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2002, 277, 10653-10660) 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.  
18675375 T.R.Barends, M.F.Dunn, and I.Schlichting (2008).
Tryptophan synthase, an allosteric molecular factory.
  Curr Opin Chem Biol, 12, 593-600.  
17293883 P.G.Purohit, R.J.Tate, E.Pow, D.Hill, and J.G.Connolly (2007).
The role of the amino acid residue at alpha1:189 in the binding of neuromuscular blocking agents to mouse and human muscle nicotinic acetylcholine receptors.
  Br J Pharmacol, 150, 920-931.  
15883191 A.P.Dubnovitsky, R.B.Ravelli, A.N.Popov, and A.C.Papageorgiou (2005).
Strain relief at the active site of phosphoserine aminotransferase induced by radiation damage.
  Protein Sci, 14, 1498-1507.
PDB codes: 2bhx 2bi1 2bi2 2bi3 2bi5 2bi9 2bia 2bie 2big
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.