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PDBsum entry 1v8z

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protein ligands metals Protein-protein interface(s) links
Lyase PDB id
1v8z
Jmol
Contents
Protein chains
386 a.a. *
Ligands
PLP ×4
Metals
_NA ×3
Waters ×251
* Residue conservation analysis
PDB id:
1v8z
Name: Lyase
Title: X-ray crystal structure of the tryptophan synthase b2 subuni hyperthermophile, pyrococcus furiosus
Structure: Tryptophan synthase beta chain 1. Chain: a, b, c, d. Synonym: tryptophan synthase b2 subunit. Engineered: yes
Source: Pyrococcus furiosus. Organism_taxid: 2261. Gene: trpb. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PDB file)
Resolution:
2.21Å     R-factor:   0.208     R-free:   0.263
Authors: Y.Hioki,K.Ogasahara,S.J.Lee,J.Ma,M.Ishida,Y.Yamagata,Y.Matsu M.Ota,S.Kuramitsu,K.Yutani,Riken Structural Genomics/proteo Initiative (Rsgi)
Key ref:
Y.Hioki et al. (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. PubMed id: 15206928 DOI: 10.1111/j.1432-1033.2004.04191.x
Date:
15-Jan-04     Release date:   22-Feb-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q8U093  (TRPB1_PYRFU) -  Tryptophan synthase beta chain 1
Seq:
Struc:
388 a.a.
386 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: 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     cellular amino acid biosynthetic process   4 terms 
  Biochemical function     lyase activity     2 terms  

 

 
    reference    
 
 
DOI no: 10.1111/j.1432-1033.2004.04191.x Eur J Biochem 271:2624-2635 (2004)
PubMed id: 15206928  
 
 
The crystal structure of the tryptophan synthase beta subunit from the hyperthermophile Pyrococcus furiosus. Investigation of stabilization factors.
Y.Hioki, K.Ogasahara, S.J.Lee, J.Ma, M.Ishida, Y.Yamagata, Y.Matsuura, M.Ota, M.Ikeguchi, S.Kuramitsu, K.Yutani.
 
  ABSTRACT  
 
The structure of the tryptophan synthase beta2 subunit (Pfbeta2) from the hyperthermophile, Pyrococcus furiosus, was determined by X-ray crystallographic analysis at 2.2 A resolution, and its stability was examined by DSC. This is the first report of the X-ray structure of the tryptophan synthase beta2 subunit alone, although the structure of the tryptophan synthase alpha2beta2 complex from Salmonella typhimurium has already been reported. The structure of Pfbeta2 was essentially similar to that of the beta2 subunit (Stbeta2) in the alpha2beta2 complex from S. typhimurium. The sequence alignment with secondary structures of Pfbeta and Stbeta in monomeric form showed that six residues in the N-terminal region and three residues in the C-terminal region were deleted in Pfbeta, and one residue at Pro366 of Stbeta and at Ile63 of Pfbeta was inserted. The denaturation temperature of Pfbeta2 was higher by 35 degrees C than the reported values from mesophiles at approximately pH 8. On the basis of structural information on both proteins, the analyses of the contributions of each stabilization factor indicate that: (a) the higher stability of Pfbeta2 is not caused by either a hydrophobic interaction or an increase in ion pairs; (b) the number of hydrogen bonds involved in the main chains of Pfbeta is greater by about 10% than that of Stbeta, indicating that the secondary structures of Pfbeta are more stabilized than those of Stbeta and (c) the sequence of Pfbeta seems to be better fitted to an ideally stable structure than that of Stbeta, as assessed from X-ray structure data.
 
  Selected figure(s)  
 
Figure 3.
Fig. 3. Crystal structure of [2] subunit alone of tryptophan synthase from P. furiosus. (A) The overall structure of the tryptophan synthase [2] dimer from P. furiosus. The N-terminal (1–200) and the C-terminal (201–388) residues are coloured red and blue, respectively. Arrows point to the first two strands and one helical structure (residue 58–64) that intrude into the C domain. The PLP molecule is represented as a CPK model, coloured gold. Drawings were prepared using MOLSCRIPT[71]. (B) Two similar N and C domains of Pf were superimposed using 69 C pairs fitted well among the 73 residues of St , which are reported to deviate by less than 4.0 Å between both domains [3]. The N and C domains are depicted in gold and green, respectively. Fitting used program LSQKAB[72].
Figure 5.
Fig. 5. Schematic stereo view of the superimposed monomer structures of the tryptophan synthase [2] from P. furiosus and S. typhimurium. Blue and red lines represent the coordinates of Pf and St (1BKS), respectively. Drawings were prepared using MOLSCRIPT[71]. Residual numbers are shown with an increase of 10 for the Pf . An arrow indicates the most different part between the proteins around position 60 of Pf .
 
  The above figures are reprinted by permission from the Federation of European Biochemical Societies: Eur J Biochem (2004, 271, 2624-2635) copyright 2004.  
  Figures were selected by an automated process.  

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.  
17425797 R.Merkl (2007).
Modelling the evolution of the archeal tryptophan synthase.
  BMC Evol Biol, 7, 59.  
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.