4HCW

Structure of a eukaryotic thiaminase-I


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.71 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.231 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure of a eukaryotic thiaminase I.

Kreinbring, C.A.Remillard, S.P.Hubbard, P.Brodkin, H.R.Leeper, F.J.Hawksley, D.Lai, E.Y.Fulton, C.Petsko, G.A.Ringe, D.

(2014) Proc Natl Acad Sci U S A 111: 137-142

  • DOI: https://doi.org/10.1073/pnas.1315882110
  • Primary Citation of Related Structures:  
    4HCW, 4HCY

  • PubMed Abstract: 

    Thiaminases, enzymes that cleave vitamin B1, are sporadically distributed among prokaryotes and eukaryotes. Thiaminase I enzymes catalyze the elimination of the thiazole ring moiety from thiamin through substitution of the methylene group with a nitrogenous base or sulfhydryl compound. In eukaryotic organisms, these enzymes are reported to have much higher molecular weights than their bacterial counterparts. A thiaminase I of the single-celled amoeboflagellate Naegleria gruberi is the only eukaryotic thiaminase I to have been cloned, sequenced, and expressed. Here, we present the crystal structure of N. gruberi thiaminase I to a resolution of 2.8 Å, solved by isomorphous replacement and pseudo-two-wavelength multiwavelength anomalous diffraction and refined to an R factor of 0.231 (Rfree, 0.265). This structure was used to solve the structure of the enzyme in complex with 3-deazathiamin, a noncleavable thiamin analog and enzyme inhibitor (2.7 Å; R, 0.233; Rfree, 0.267). These structures define the mode of thiamin binding to this class of thiaminases and indicate the involvement of Asp272 as the catalytic base. This enzyme is able to use thiamin as a substrate and is active with amines such as aniline and veratrylamine as well as sulfhydryl compounds such as l-cysteine and β-mercaptoethanol as cosubstrates. Despite significant differences in polypeptide sequence and length, we have shown that the N. gruberi thiaminase I is homologous in structure and activity to a previously characterized bacterial thiaminase I.


  • Organizational Affiliation

    Department of Biochemistry and Chemistry, Rosenstiel Basic Medical Sciences Research Center, and Department of Biology, Brandeis University, Waltham, MA 02454-9110.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
thiaminase-I
A, B, C, D, E
A, B, C, D, E, F
357Naegleria gruberiMutation(s): 0 
Gene Names: NAEGRDRAFT_78612
EC: 2.5.1.2
UniProt
Find proteins for D2V4Z5 (Naegleria gruberi)
Explore D2V4Z5 
Go to UniProtKB:  D2V4Z5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD2V4Z5
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.71 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.231 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.56α = 90
b = 203.05β = 90
c = 309.18γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SHARPphasing
PHENIXmodel building
PHENIXrefinement
DENZOdata reduction
SCALEPACKdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-10-02
    Type: Initial release
  • Version 1.1: 2013-10-30
    Changes: Database references
  • Version 1.2: 2014-02-05
    Changes: Database references
  • Version 1.3: 2024-02-28
    Changes: Data collection, Database references