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PDBsum entry 1kfk

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protein ligands metals Protein-protein interface(s) links
Lyase PDB id
1kfk
Jmol
Contents
Protein chains
251 a.a. *
392 a.a. *
Ligands
PLP
Metals
_NA
Waters ×336
* Residue conservation analysis
PDB id:
1kfk
Name: Lyase
Title: Crystal structure of tryptophan synthase from salmonella typ
Structure: Tryptophan synthase alpha chain. Chain: a. Synonym: trpa. Engineered: yes. Tryptophan synthase beta chain. Chain: b. Engineered: yes
Source: Salmonella typhimurium. Organism_taxid: 602. Expressed in: escherichia coli. Expression_system_taxid: 562. Organism_taxid: 99287. Strain: lt2.
Biol. unit: Tetramer (from PDB file)
Resolution:
2.40Å     R-factor:   0.183     R-free:   0.225
Authors: V.Kulik,M.Weyand,R.Seidel,D.Niks,D.Arac,M.F.Dunn,I.Schlichti
Key ref:
V.Kulik et al. (2002). On the role of alphaThr183 in the allosteric regulation and catalytic mechanism of tryptophan synthase. J Mol Biol, 324, 677-690. PubMed id: 12460570 DOI: 10.1016/S0022-2836(02)01109-9
Date:
21-Nov-01     Release date:   21-Oct-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P00929  (TRPA_SALTY) -  Tryptophan synthase alpha chain
Seq:
Struc:
268 a.a.
251 a.a.
Protein chain
Pfam   ArchSchema ?
P0A2K1  (TRPB_SALTY) -  Tryptophan synthase beta chain
Seq:
Struc:
397 a.a.
392 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
+ 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: 10.1016/S0022-2836(02)01109-9 J Mol Biol 324:677-690 (2002)
PubMed id: 12460570  
 
 
On the role of alphaThr183 in the allosteric regulation and catalytic mechanism of tryptophan synthase.
V.Kulik, M.Weyand, R.Seidel, D.Niks, D.Arac, M.F.Dunn, I.Schlichting.
 
  ABSTRACT  
 
The catalytic activity and substrate channeling of the pyridoxal 5'-phosphate-dependent tryptophan synthase alpha(2)beta(2) complex is regulated by allosteric interactions that modulate the switching of the enzyme between open, low activity and closed, high activity states during the catalytic cycle. The highly conserved alphaThr183 residue is part of loop alphaL6 and is located next to the alpha-active site and forms part of the alpha-beta subunit interface. The role of the interactions of alphaThr183 in alpha-site catalysis and allosteric regulation was investigated by analyzing the kinetics and crystal structures of the isosteric mutant alphaThr183Val. The mutant displays strongly impaired allosteric alpha-beta communication, and the catalytic activity of the alpha-reaction is reduced one hundred fold, whereas the beta-activity is not affected. The structural work establishes that the basis for the missing inter-subunit signaling is the lack of loop alphaL6 closure even in the presence of the alpha-subunit ligands, 3-indolyl-D-glycerol 3'-phosphate, or 3-indolylpropanol 3'-phosphate. The structural basis for the reduced alpha-activity has its origins in the missing hydrogen bond between alphaThr183 and the catalytic residue, alphaAsp60.
 
  Selected figure(s)  
 
Figure 7.
Figure 7. SigmaA-weighted 2Fo 2 Fc electron density maps contoured at 1s around the external aldimine bLys87 in aT183VSer. The Schiff-base linkage between PLP and bLys87 is broken. As can be seen from Figure 8, bLys87 interacts with the phosphoryl group of PLP. The Figure was prepared using ``BOBSCRIPT'', 41 MOLS- CRIPT 39 and RASTER3D. 40
 
  The above figure is reprinted by permission from Elsevier: J Mol Biol (2002, 324, 677-690) copyright 2002.  
  Figure was 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.  
18366663 R.Merkl, and M.Zwick (2008).
H2r: identification of evolutionary important residues by means of an entropy based analysis of multiple sequence alignments.
  BMC Bioinformatics, 9, 151.  
18675375 T.R.Barends, M.F.Dunn, and I.Schlichting (2008).
Tryptophan synthase, an allosteric molecular factory.
  Curr Opin Chem Biol, 12, 593-600.  
18351684 T.R.Barends, T.Domratcheva, V.Kulik, L.Blumenstein, D.Niks, M.F.Dunn, and I.Schlichting (2008).
Structure and mechanistic implications of a tryptophan synthase quinonoid intermediate.
  Chembiochem, 9, 1024-1028.
PDB code: 3cep
17084112 A.Hardin, C.F.Villalta, M.Doan, M.Jabri, V.Chockalingham, S.J.White, and R.G.Fowler (2007).
A molecular characterization of spontaneous frameshift mutagenesis within the trpA gene of Escherichia coli.
  DNA Repair (Amst), 6, 177-189.  
15691828 S.Raboni, S.Bettati, and A.Mozzarelli (2005).
Identification of the geometric requirements for allosteric communication between the alpha- and beta-subunits of tryptophan synthase.
  J Biol Chem, 280, 13450-13456.  
15117965 F.Schiaretti, S.Bettati, C.Viappiani, and A.Mozzarelli (2004).
pH dependence of tryptophan synthase catalytic mechanism: I. The first stage, the beta-elimination reaction.
  J Biol Chem, 279, 29572-29582.  
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
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 code is shown on the right.