1s2d: Difference between revisions

Revision as of 15:57, 21 February 2008

Purine 2'-Deoxyribosyl complex with arabinoside: Ribosylated Intermediate (AraA)

OverviewOverview

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.

About this StructureAbout this Structure

1S2D is a Single protein structure of sequence from Lactobacillus helveticus with as ligand. Active as Nucleoside deoxyribosyltransferase, with EC number 2.4.2.6 Full crystallographic information is available from OCA.

ReferenceReference

Structures of purine 2'-deoxyribosyltransferase, substrate complexes, and the ribosylated enzyme intermediate at 2.0 A resolution., Anand R, Kaminski PA, Ealick SE, Biochemistry. 2004 Mar 9;43(9):2384-93. PMID:14992575

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-[[Image:1s2d.jpg|left|200px]]<br /><applet load="1s2d" size="450" color="white" frame="true" align="right" spinBox="true"
+[[Image:1s2d.jpg|left|200px]]<br /><applet load="1s2d" size="350" color="white" frame="true" align="right" spinBox="true"
 caption="1s2d, resolution 2.10&Aring;" />
 '''Purine 2'-Deoxyribosyl complex with arabinoside: Ribosylated Intermediate (AraA)'''<br />
 ==Overview==
-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.
+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.
 ==About this Structure==
-S2D is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Lactobacillus_helveticus Lactobacillus helveticus] with ADE as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Nucleoside_deoxyribosyltransferase Nucleoside deoxyribosyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.2.6 2.4.2.6] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1S2D OCA].
+S2D is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Lactobacillus_helveticus Lactobacillus helveticus] with <scene name='pdbligand=ADE:'>ADE</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Nucleoside_deoxyribosyltransferase Nucleoside deoxyribosyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.2.6 2.4.2.6] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1S2D OCA].
 ==Reference==
@@ Line 15: / Line 15: @@
 [[Category: Single protein]]
 [[Category: Anand, R.]]
-[[Category: Ealick, S.E.]]
+[[Category: Ealick, S E.]]
-[[Category: Kaminski, P.A.]]
+[[Category: Kaminski, P A.]]
 [[Category: ADE]]
 [[Category: araa]]
@@ Line 22: / Line 22: @@
 [[Category: ribosylate intermediate]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sat Nov 24 23:44:52 2007''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 14:57:09 2008''