PDBsum entry 1s2l

Go to PDB code: 
protein Protein-protein interface(s) links
Transferase PDB id
Protein chains
165 a.a. *
153 a.a. *
Waters ×391
* Residue conservation analysis
PDB id:
Name: Transferase
Title: Purine 2'deoxyribosyltransferase native structure
Structure: Purine trans deoxyribosylase. Chain: a, b, c. Fragment: purine 2'-deoxyribosyltansferase. Engineered: yes
Source: Lactobacillus helveticus. Organism_taxid: 1587. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Hexamer (from PDB file)
2.10Å     R-factor:   0.231     R-free:   0.275
Authors: R.Anand,P.A.Kaminski,S.E.Ealick
Key ref:
R.Anand et al. (2004). Structures of purine 2'-deoxyribosyltransferase, substrate complexes, and the ribosylated enzyme intermediate at 2.0 A resolution. Biochemistry, 43, 2384-2393. PubMed id: 14992575 DOI: 10.1021/bi035723k
08-Jan-04     Release date:   30-Mar-04    
Go to PROCHECK summary

Protein chains
No UniProt id for this chain
Struc: 165 a.a.
Protein chain
Pfam   ArchSchema ?
Q8RLY5  (Q8RLY5_LACHE) -  Nucleoside deoxyribosyltransferase-I
167 a.a.
153 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: Chains B, C: E.C.  - Nucleoside deoxyribosyltransferase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: 2-deoxy-D-ribosyl-base1 + base2 = 2-deoxy-D-ribosyl-base2 + base1
+ base(2)
= 2-deoxy-D-ribosyl-base(2)
+ base(1)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     deoxyribonucleoside monophosphate catabolic process   1 term 
  Biochemical function     transferase activity     4 terms  


    Added reference    
DOI no: 10.1021/bi035723k Biochemistry 43:2384-2393 (2004)
PubMed id: 14992575  
Structures of purine 2'-deoxyribosyltransferase, substrate complexes, and the ribosylated enzyme intermediate at 2.0 A resolution.
R.Anand, P.A.Kaminski, S.E.Ealick.
The structure of class I N-deoxyribosyltransferase from Lactobacillus helveticus was determined by X-ray crystallography. Unlike class II N-deoxyribosyltransferases, which accept either purine or pyrimidine deoxynucleosides, class I enzymes are specific for purines as both the donor and acceptor base. Both class I and class II enzymes are highly specific for deoxynucleosides. The class I structure reveals similarities with the previously determined class II enzyme from Lactobacillus leichmanni [Armstrong, S. A., Cook, W. J., Short, S. A., and Ealick, S. E. (1996) Structure 4, 97-107]. The specificity of the class I enzyme for purine deoxynucleosides can be traced to a loop (residues 48-62), which shields the active site in the class II enzyme. In the class I enzyme, the purine base itself shields the active site from the solvent, while the smaller pyrimidine base cannot. The structure of the enzyme with a bound ribonucleoside shows that the nucleophilic oxygen atom of Glu101 hydrogen bonds to the O2' atom, rendering it unreactive and thus explaining the specificity for 2'-deoxynucleosides. The structure of a ribosylated enzyme intermediate reveals movements that occur during cleavage of the N-glycosidic bond. The structures of complexes with substrates and substrate analogues show that the purine base can bind in several different orientations, thus explaining the ability of the enzyme to catalyze alternate deoxyribosylation at the N3 or N7 position.

Literature references that cite this PDB file's key reference

  PubMed id Reference
  20944218 A.Kumar, A.Lomize, K.K.Jin, D.Carlton, M.D.Miller, L.Jaroszewski, P.Abdubek, T.Astakhova, H.L.Axelrod, H.J.Chiu, T.Clayton, D.Das, M.C.Deller, L.Duan, J.Feuerhelm, J.C.Grant, A.Grzechnik, G.W.Han, H.E.Klock, M.W.Knuth, P.Kozbial, S.S.Krishna, D.Marciano, D.McMullan, A.T.Morse, E.Nigoghossian, L.Okach, R.Reyes, C.L.Rife, N.Sefcovic, H.J.Tien, C.B.Trame, H.van den Bedem, D.Weekes, Q.Xu, K.O.Hodgson, J.Wooley, M.A.Elsliger, A.M.Deacon, A.Godzik, S.A.Lesley, and I.A.Wilson (2010).
Open and closed conformations of two SpoIIAA-like proteins (YP_749275.1 and YP_001095227.1) provide insights into membrane association and ligand binding.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 66, 1245-1253.
PDB codes: 2ook 2q3l
20048065 J.Fernández-Lucas, C.Acebal, J.V.Sinisterra, M.Arroyo, and la Mata (2010).
Lactobacillus reuteri 2'-deoxyribosyltransferase, a novel biocatalyst for tailoring of nucleosides.
  Appl Environ Microbiol, 76, 1462-1470.  
19929835 C.L.Verlinde, E.Fan, S.Shibata, Z.Zhang, Z.Sun, W.Deng, J.Ross, J.Kim, L.Xiao, T.L.Arakaki, J.Bosch, J.M.Caruthers, E.T.Larson, I.Letrong, A.Napuli, A.Kelly, N.Mueller, F.Zucker, W.C.Van Voorhis, E.A.Merritt, and W.G.Hol (2009).
Fragment-based cocktail crystallography by the medical structural genomics of pathogenic protozoa consortium.
  Curr Top Med Chem, 9, 1678-1687.  
19460093 K.A.Lawrence, M.W.Jewett, P.A.Rosa, and F.C.Gherardini (2009).
Borrelia burgdorferi bb0426 encodes a 2'-deoxyribosyltransferase that plays a central role in purine salvage.
  Mol Microbiol, 72, 1517-1529.  
18487606 P.A.Kaminski, P.Dacher, L.Dugué, and S.Pochet (2008).
In vivo reshaping the catalytic site of nucleoside 2'-deoxyribosyltransferase for dideoxy- and didehydronucleosides via a single amino acid substitution.
  J Biol Chem, 283, 20053-20059.  
17502392 J.Pettersson, M.E.Schrumpf, S.J.Raffel, S.F.Porcella, C.Guyard, K.Lawrence, F.C.Gherardini, and T.G.Schwan (2007).
Purine salvage pathways among Borrelia species.
  Infect Immun, 75, 3877-3884.  
17234634 Y.K.Ghiorghi, K.I.Zeller, C.V.Dang, and P.A.Kaminski (2007).
The c-Myc target gene Rcl (C6orf108) encodes a novel enzyme, deoxynucleoside 5'-monophosphate N-glycosidase.
  J Biol Chem, 282, 8150-8156.  
16642528 L.L.Grochowski, and T.M.Zabriskie (2006).
Characterization of BlsM, a nucleotide hydrolase involved in cytosine production for the biosynthesis of blasticidin S.
  Chembiochem, 7, 957-964.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.