3THI

THIAMINASE I FROM BACILLUS THIAMINOLYTICUS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of thiaminase-I from Bacillus thiaminolyticus at 2.0 A resolution.

Campobasso, N.Costello, C.A.Kinsland, C.Begley, T.P.Ealick, S.E.

(1998) Biochemistry 37: 15981-15989

  • DOI: 10.1021/bi981673l
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Thiaminase-I catalyzes the replacement of the thiazole moiety of thiamin with a wide variety of nucleophiles, such as pyridine, aniline, catechols, quinoline, and cysteine. The crystal structure of the enzyme from Bacillus thiaminolyticus was determi ...

    Thiaminase-I catalyzes the replacement of the thiazole moiety of thiamin with a wide variety of nucleophiles, such as pyridine, aniline, catechols, quinoline, and cysteine. The crystal structure of the enzyme from Bacillus thiaminolyticus was determined at 2.5 A resolution by multiple isomorphous replacement and refined to an R factor of 0.195 (Rfree = 0.272). Two other structures, one native and one containing a covalently bound inhibitor, were determined at 2.0 A resolution by molecular replacement from a second crystal form and were refined to R factors of 0.205 and 0.217 (Rfree = 0.255 and 0.263), respectively. The overall structure contains two alpha/beta-type domains separated by a large cleft. At the base of the cleft lies Cys113, previously identified as a key active site nucleophile. The structure with a covalently bound thiamin analogue, which functions as a mechanism-based inactivating agent, confirms the location of the active site. Glu241 appears to function as an active site base to increase the nucleophilicity of Cys113. The mutant Glu241Gln was made and shows no activity. Thiaminase-I shows no sequence identity to other proteins in the sequence databases, but the three-dimensional structure shows very high structural homology to the periplasmic binding proteins and the transferrins.


    Related Citations: 
    • Crystallization and Preliminary X-Ray Analysis of Thiaminase I from Bacillus Thiaminolyticus: Space Group Change Upon Freezing of Crystals
      Campobasso, N.,Begun, J.,Costello, C.A.,Begley, T.P.,Ealick, S.E.
      (1998) Acta Crystallogr.,Sect.D 54: 448


    Organizational Affiliation

    Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (THIAMINASE I)
A
371Paenibacillus thiaminolyticusMutation(s): 0 
EC: 2.5.1.2
Find proteins for P45741 (Paenibacillus thiaminolyticus)
Go to UniProtKB:  P45741
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.205 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 85.500α = 90.00
b = 117.500β = 90.00
c = 36.600γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
X-PLORrefinement
SCALEPACKdata scaling
X-PLORmodel building
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-10-14
    Type: Initial release
  • Version 1.1: 2007-10-16
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance