3VND

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.175 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


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: https://doi.org/10.1093/jb/mvt098
  • Primary Citation of Related Structures:  
    3VND

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tryptophan synthase alpha chain
A, B, C, D, E
A, B, C, D, E, F, G, H
267Shewanella frigidimarinaMutation(s): 0 
Gene Names: trpA
EC: 4.2.1.20
UniProt
Find proteins for H1AFK5 (Shewanella frigidimarina)
Explore H1AFK5 
Go to UniProtKB:  H1AFK5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupH1AFK5
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PE8
Query on PE8

Download Ideal Coordinates CCD File 
BA [auth G],
N [auth B],
T [auth D],
W [auth E]
3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL
C16 H34 O9
GLZWNFNQMJAZGY-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth G]
CA [auth H]
DA [auth H]
I [auth A]
J [auth A]
AA [auth G],
CA [auth H],
DA [auth H],
I [auth A],
J [auth A],
K [auth A],
L [auth B],
M [auth B],
O [auth C],
P [auth C],
Q [auth D],
R [auth D],
S [auth D],
U [auth E],
V [auth E],
X [auth F],
Y [auth F],
Z [auth G]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.175 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 181.136α = 90
b = 182.779β = 90
c = 181.795γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-01-16
    Type: Initial release
  • Version 1.1: 2014-12-24
    Changes: Database references
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description