3VND

Crystal structure of tryptophan synthase alpha-subunit from the psychrophile Shewanella frigidimarina K14-2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.173 

wwPDB Validation 3D Report Full Report


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Literature

Strategy for cold adaptation of the tryptophan synthase alpha subunit from the psychrophile Shewanella frigidimarina K14-2: crystal structure and physicochemical properties

Mitsuya, D.Tanaka, S.Matsumura, H.Urano, N.Takano, K.Ogasahara, K.Takehira, M.Yutani, K.Ishida, M.

(2014) J.Biochem. 155: 73-82

  • DOI: 10.1093/jb/mvt098

  • PubMed Abstract: 
  • To investigate the molecular basis of cold adaptation of enzymes, we determined the crystal structure of the tryptophan synthase α subunit (SfTSA) from the psychrophile Shewanella frigidimarina K14-2 by X-ray analysis at 2.6-Å resolution and also exa ...

    To investigate the molecular basis of cold adaptation of enzymes, we determined the crystal structure of the tryptophan synthase α subunit (SfTSA) from the psychrophile Shewanella frigidimarina K14-2 by X-ray analysis at 2.6-Å resolution and also examined its physicochemical properties. SfTSA was found to have the following characteristics: (i) The stabilities against heat and denaturant of SfTSA were lower than those of an α subunit (EcTSA) from Escherichia coli. This lower equilibrium stability originated from both a faster unfolding rate and a slower refolding rate; (ii) the heat denaturation of SfTSA was completely reversible at pH 7.0 and the solubility of denatured SfTSA was higher than that of denatured EcTSA. The two-state transition of denaturation for SfTSA was highly cooperative, whereas the denaturation process of EcTSA was considerably more complex and (iii) the global structure of SfTSA was quite similar to those of α subunits from other species. Relative to those other proteins, SfTSA exhibited an increase in cavity volume and a decrease in the number of ion pairs. SfTSA also lacks a hydrogen bond near loop B, related to catalytic function. These characteristics of SfTSA might provide the conformational flexibility required for catalytic activity at low temperatures.


    Organizational Affiliation

    Department of Ocean Sciences, Graduate school of Marine Science and Technology, Tokyo University of Marine Science and Technology, 4-5-7, Konan, Minato, Tokyo 108-8477; Department of Material and Life Science, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871; Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871; Department of Biomolecular Chemistry, Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 1-5 Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522; Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871; Department of Life Science, University of Hyogo, 3-2-1, Kouto, Kamigori, Ako-gun, Hyogo 678-1297; and RIKEN SPring-8 Center, RIKEN Harima Institute, 1-1-1, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tryptophan synthase alpha chain
A, B, C, D, E, F, G, H
267Shewanella frigidimarinaGene Names: trpA
EC: 4.2.1.20
Find proteins for H1AFK5 (Shewanella frigidimarina)
Go to UniProtKB:  H1AFK5
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
PE8
Query on PE8

Download SDF File 
Download CCD File 
B, D, E, G
3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL
C16 H34 O9
GLZWNFNQMJAZGY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.173 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 181.136α = 90.00
b = 182.779β = 90.00
c = 181.795γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
MOLREPphasing
HKL-2000data reduction
HKL-2000data scaling
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-01-16
    Type: Initial release
  • Version 1.1: 2014-12-24
    Type: Database references