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PDBsum entry 3pr2

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protein ligands metals Protein-protein interface(s) links
Lyase PDB id
3pr2
Jmol
Contents
Protein chains
266 a.a. *
391 a.a. *
Ligands
F9F
7MN
Metals
_CS ×3
Waters ×286
* Residue conservation analysis
PDB id:
3pr2
Name: Lyase
Title: Tryptophan synthase indoline quinonoid structure with f9 inh alpha site
Structure: Tryptophan synthase alpha chain. Chain: a. Engineered: yes. Tryptophan synthase beta chain. Chain: b. Engineered: yes
Source: Salmonella enterica subsp. Enterica se typhimurium. Organism_taxid: 90371. Gene: stm1727, trpa. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: stm1726, trpb.
Resolution:
1.85Å     R-factor:   0.200     R-free:   0.227
Authors: J.Lai,D.Niks,Y.Wang,T.Domratcheva,T.R.M.Barends,F.Schwarz,R. D.W.Elliott,M.Q.Fatmi,C.A.Chang,I.Schlichting,M.F.Dunn,L.J.
Key ref: J.Lai et al. (2011). X-ray and NMR crystallography in an enzyme active site: the indoline quinonoid intermediate in tryptophan synthase. J Am Chem Soc, 133, 4-7. PubMed id: 21142052 DOI: 10.1021/ja106555c
Date:
29-Nov-10     Release date:   09-Feb-11    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P00929  (TRPA_SALTY) -  Tryptophan synthase alpha chain
Seq:
Struc:
268 a.a.
266 a.a.
Protein chain
Pfam   ArchSchema ?
P0A2K1  (TRPB_SALTY) -  Tryptophan synthase beta chain
Seq:
Struc:
397 a.a.
391 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 = 7MN) matches with 48.39% 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: 10.1021/ja106555c J Am Chem Soc 133:4-7 (2011)
PubMed id: 21142052  
 
 
X-ray and NMR crystallography in an enzyme active site: the indoline quinonoid intermediate in tryptophan synthase.
J.Lai, D.Niks, Y.Wang, T.Domratcheva, T.R.Barends, F.Schwarz, R.A.Olsen, D.W.Elliott, M.Q.Fatmi, C.E.Chang, I.Schlichting, M.F.Dunn, L.J.Mueller.
 
  ABSTRACT  
 
Chemical-level details such as protonation and hybridization state are critical for understanding enzyme mechanism and function. Even at high resolution, these details are difficult to determine by X-ray crystallography alone. The chemical shift in NMR spectroscopy, however, is an extremely sensitive probe of the chemical environment, making solid-state NMR spectroscopy and X-ray crystallography a powerful combination for defining chemically detailed three-dimensional structures. Here we adopted this combined approach to determine the chemically rich crystal structure of the indoline quinonoid intermediate in the pyridoxal-5'-phosphate-dependent enzyme tryptophan synthase under conditions of active catalysis. Models of the active site were developed using a synergistic approach in which the structure of this reactive substrate analogue was optimized using ab initio computational chemistry in the presence of side-chain residues fixed at their crystallographically determined coordinates. Various models of charge and protonation state for the substrate and nearby catalytic residues could be uniquely distinguished by their calculated effects on the chemical shifts measured at specifically (13)C- and (15)N-labeled positions on the substrate. Our model suggests the importance of an equilibrium between tautomeric forms of the substrate, with the protonation state of the major isomer directing the next catalytic step.
 

 

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