4HCY

Structure of a eukaryotic thiaminase-I bound to the thiamin analogue 3-deazathiamin

Summary for 4HCY

• Entry DOI: 10.2210/pdb4hcy/pdb
• Related: 4HCW
• Descriptor: thiaminase-I, 2-{4-[(4-amino-2-methylpyrimidin-5-yl)methyl]-3-methylthiophen-2-yl}ethanol (2 entities in total)
• Functional Keywords: transferase, thiamine pyridinylase
• Biological source: Naegleria gruberi (Amoeba)
• Total number of polymer chains: 6
• Total formula weight: 237290.81

Authors

Kreinbring, C.A.,Hubbard, P.A.,Leeper, F.J.,Hawksley, D.,Petsko, G.A.,Ringe, D. (deposition date: 2012-10-01, release date: 2013-10-02, Last modification date: 2023-09-20)

Primary citation

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.
Structure of a eukaryotic thiaminase I.
Proc.Natl.Acad.Sci.USA, 111:137-142, 2014

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.

PubMed: 24351929
DOI: 10.1073/pnas.1315882110

Experimental method

X-RAY DIFFRACTION (2.75 Å)