Steve Ealick's Research Group


Purine 2′-Deoxyribosyltransferase


PDB files:

1S2L native enzyme

1S2I complex with 6-bromopurine

1S3F complex with 6-selenoinosine)

1S2D complex with arabinoside: ribosylated intermediate (Araa)

1S2G complex with 2′-deoxyadenosine

*4MEJ complex with 8,9-dihydro-9-oxoimidazo[2,1-b]purine (N2,3-ethenoguanine)

Description:

Purine 2′-deoxyribosyltransferase (PTD) is a class I N-deoxyribosyltransferases which is specific for the transfer of deoxyribose between two purines (Pur ⇔Pur) with a preference of deoxyinosine (dIno) > deoxyadenosine (dAdo) > deoxyguanosine (dGuo) as the donor substrate. Class II N-deoxyribosyltransferases such as nucleoside trans-deoxyribosylase (NTD) can also catalyze deoxyriboxe transfers between pyrimidines and/or purines. The structure of PTD from Lactobacillus helveticus was solved by molecular replacement using nucleoside 2-deoxyribosyltransferase, NTD, as a search model.

The PTD monomer is very similar to the structure of NTD and consists of a central core structure with a five-stranded parallel β-sheets, flanked by four α-helices.


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The active form of PTD is a hexamer that packs as a trimer of dimers. As in NTD, there is one active site per monomer and each catalytic site requires participation from a neighboring subunit.


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The active site of PTD shows bound substrate dAdo with key residues and hydrogen bonding patterns. In the paper we also show complexes of other species bound to the active site.

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Reference:

Anand R, Kaminski PA and Ealick SE. Structures of Purine 2′-Deoxyribosyltransferase, Substrate Complexes and the Ribosylated Enzyme Intermediate at 2.0 Å Resolution. Biochemistry 43:2384-2393 (2004).

*Ye W, Paul D, Gao L, Seckute J, Sangaiah R, Jayaraj K, Zhang Z, Kaminski PA, Ealick SE, Gold A, and Ball LM. Ethenoguanines Undergo Glycosylation by Nucleoside 2'-Deoxyribosyltransferases at Non-Natural Sites. PLoS One 9:e115082 (2014).



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