PDBsum entry 1v8z

Lyase

PDB id: 1v8z

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 subunit from 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.Matsuura, M.Ota,S.Kuramitsu,K.Yutani,Riken Structural Genomics/proteomics 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

Protein chains

Q8U093  (TRPB1_PYRFU) -  Tryptophan synthase beta chain 1 from Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)

Seq: 388 a.a.

Struc: 386 a.a.

Enzyme reactions

• Enzyme class: E.C.4.2.1.20 - tryptophan synthase.
• Pathway: Tryptophan Biosynthesis
• Reaction: (1S,2R)-1-C-(indol-3-yl)glycerol 3-phosphate + L-serine = D-glyceraldehyde 3-phosphate + L-tryptophan + H2O
• 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

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.