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PDBsum entry 1qop

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protein ligands metals Protein-protein interface(s) links
Lyase PDB id
1qop
Jmol
Contents
Protein chains
265 a.a. *
390 a.a. *
Ligands
IPL
PLP
Metals
_NA
Waters ×801
* Residue conservation analysis
PDB id:
1qop
Name: Lyase
Title: Crystal structure of wild-type tryptophan synthase complexed with indole propanol phosphate
Structure: Tryptophan synthase alpha chain. Chain: a. Engineered: yes. Other_details: inhibitor indole propanol phosphate bound to the alpha site. Tryptophan synthase beta chain. Chain: b. Engineered: yes
Source: Salmonella typhimurium. Organism_taxid: 602. Gene: trpa. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: trpb.
Biol. unit: Tetramer (from PDB file)
Resolution:
1.40Å     R-factor:   0.150     R-free:   0.177
Authors: M.Weyand,I.Schlichting
Key ref:
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. PubMed id: 10600108 DOI: 10.1021/bi9920533
Date:
15-Nov-99     Release date:   10-Nov-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P00929  (TRPA_SALTY) -  Tryptophan synthase alpha chain
Seq:
Struc:
268 a.a.
265 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
Bound ligand (Het Group name = IPL)
matches with 89.47% similarity
= 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: 10.1021/bi9920533 Biochemistry 38:16469-16480 (1999)
PubMed id: 10600108  
 
 
Crystal structure of wild-type tryptophan synthase complexed with the natural substrate indole-3-glycerol phosphate.
M.Weyand, I.Schlichting.
 
  ABSTRACT  
 
We used freeze trapping to stabilize the Michaelis complex of wild-type tryptophan synthase and the alpha-subunit substrate indole-3-glycerol phosphate (IGP) and determined its structure to 1. 8 A resolution. In addition, we determined the 1.4 A resolution structure of the complex with indole-3-propanole phosphate (IPP), a noncleavable IGP analogue. The interaction of the 3'-hydroxyl of IGP with the catalytic alphaGlu49 leads to a twisting of the propane chain and to a repositioning of the indole ring compared to IPP. Concomitantly, the catalytic alphaAsp60 rotates resulting in a translocation of the COMM domain [betaGly102-betaGly189, for definition see Schneider et al. (1998) Biochemistry 37, 5394-5406] in a direction opposite to the one in the IPP complex. This results in loss of the allosteric sodium ion bound at the beta-subunit and an opening of the beta-active site, thereby making the cofactor pyridoxal 5'-phosphate (PLP) accessible to solvent and thus serine binding. These findings form the structural basis for the information transfer from the alpha- to the beta-subunit and may explain the affinity increase of the beta-active site for serine upon IGP binding.
 

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
21085641 M.Q.Fatmi, and C.E.Chang (2010).
The role of oligomerization and cooperative regulation in protein function: the case of tryptophan synthase.
  PLoS Comput Biol, 6, e1000994.  
18675375 T.R.Barends, M.F.Dunn, and I.Schlichting (2008).
Tryptophan synthase, an allosteric molecular factory.
  Curr Opin Chem Biol, 12, 593-600.  
17208039 G.McClarty, H.D.Caldwell, and D.E.Nelson (2007).
Chlamydial interferon gamma immune evasion influences infection tropism.
  Curr Opin Microbiol, 10, 47-51.  
17206660 J.T.Huang, J.P.Cheng, and H.Chen (2007).
Secondary structure length as a determinant of folding rate of proteins with two- and three-state kinetics.
  Proteins, 67, 12-17.  
17425797 R.Merkl (2007).
Modelling the evolution of the archeal tryptophan synthase.
  BMC Evol Biol, 7, 59.  
16267046 E.Di Cera (2006).
A structural perspective on enzymes activated by monovalent cations.
  J Biol Chem, 281, 1305-1308.  
15101993 H.Wood, C.Roshick, and G.McClarty (2004).
Tryptophan recycling is responsible for the interferon-gamma resistance of Chlamydia psittaci GPIC in indoleamine dioxygenase-expressing host cells.
  Mol Microbiol, 52, 903-916.  
14534310 P.Storici, D.De Biase, F.Bossa, S.Bruno, A.Mozzarelli, C.Peneff, R.B.Silverman, and T.Schirmer (2004).
Structures of gamma-aminobutyric acid (GABA) aminotransferase, a pyridoxal 5'-phosphate, and [2Fe-2S] cluster-containing enzyme, complexed with gamma-ethynyl-GABA and with the antiepilepsy drug vigabatrin.
  J Biol Chem, 279, 363-373.
PDB codes: 1ohv 1ohw 1ohy
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
12939261 A.Osborne, Q.Teng, E.W.Miles, and R.S.Phillips (2003).
Detection of open and closed conformations of tryptophan synthase by 15N-heteronuclear single-quantum coherence nuclear magnetic resonance of bound 1-15N-L-tryptophan.
  J Biol Chem, 278, 44083-44090.  
12782678 H.D.Caldwell, H.Wood, D.Crane, R.Bailey, R.B.Jones, D.Mabey, I.Maclean, Z.Mohammed, R.Peeling, C.Roshick, J.Schachter, A.W.Solomon, W.E.Stamm, R.J.Suchland, L.Taylor, S.K.West, T.C.Quinn, R.J.Belland, and G.McClarty (2003).
Polymorphisms in Chlamydia trachomatis tryptophan synthase genes differentiate between genital and ocular isolates.
  J Clin Invest, 111, 1757-1769.  
12643278 K.Ogasahara, M.Ishida, and K.Yutani (2003).
Stimulated interaction between and subunits of tryptophan synthase from hyperthermophile enhances its thermal stability.
  J Biol Chem, 278, 8922-8928.  
12011099 C.Fehlner-Gardiner, C.Roshick, J.H.Carlson, S.Hughes, R.J.Belland, H.D.Caldwell, and G.McClarty (2002).
Molecular basis defining human Chlamydia trachomatis tissue tropism. A possible role for tryptophan synthase.
  J Biol Chem, 277, 26893-26903.  
  11806827 G.Xie, C.Forst, C.Bonner, and R.A.Jensen (2002).
Significance of two distinct types of tryptophan synthase beta chain in Bacteria, Archaea and higher plants.
  Genome Biol, 3, RESEARCH0004.  
11756456 M.Weyand, I.Schlichting, A.Marabotti, and A.Mozzarelli (2002).
Crystal structures of a new class of allosteric effectors complexed to tryptophan synthase.
  J Biol Chem, 277, 10647-10652.
PDB codes: 1k3u 1k7e 1k7f
11756454 M.Weyand, I.Schlichting, P.Herde, A.Marabotti, and A.Mozzarelli (2002).
Crystal structure of the beta Ser178--> Pro mutant of tryptophan synthase. A "knock-out" allosteric enzyme.
  J Biol Chem, 277, 10653-10660.
PDB codes: 1k7x 1k8y 1k8z
11756459 S.Hettwer, and R.Sterner (2002).
A novel tryptophan synthase beta-subunit from the hyperthermophile Thermotoga maritima. Quaternary structure, steady-state kinetics, and putative physiological role.
  J Biol Chem, 277, 8194-8201.  
11893063 E.W.Miles (2001).
Tryptophan synthase: a multienzyme complex with an intramolecular tunnel.
  Chem Rec, 1, 140-151.  
11106389 M.Frey, C.Stettner, P.W.Pare, E.A.Schmelz, J.H.Tumlinson, and A.Gierl (2000).
An herbivore elicitor activates the gene for indole emission in maize.
  Proc Natl Acad Sci U S A, 97, 14801-14806.  
10805771 S.S.Parikh, G.Walcher, G.D.Jones, G.Slupphaug, H.E.Krokan, G.M.Blackburn, and J.A.Tainer (2000).
Uracil-DNA glycosylase-DNA substrate and product structures: conformational strain promotes catalytic efficiency by coupled stereoelectronic effects.
  Proc Natl Acad Sci U S A, 97, 5083-5088.
PDB codes: 1emh 1emj
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.