1s2l: Difference between revisions

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[[Image:1s2l.jpg|left|200px]]<br /><applet load="1s2l" size="350" color="white" frame="true" align="right" spinBox="true"
caption="1s2l, resolution 2.10&Aring;" />
'''Purine 2'deoxyribosyltransferase native structure'''<br />


==Overview==
==Purine 2'deoxyribosyltransferase native structure==
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.
<StructureSection load='1s2l' size='340' side='right'caption='[[1s2l]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
 
== Structural highlights ==
==About this Structure==
<table><tr><td colspan='2'>[[1s2l]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Lactobacillus_helveticus Lactobacillus helveticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1S2L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1S2L FirstGlance]. <br>
1S2L is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Lactobacillus_helveticus Lactobacillus helveticus]. 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=1S2L OCA].
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.1&#8491;</td></tr>
 
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1s2l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1s2l OCA], [https://pdbe.org/1s2l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1s2l RCSB], [https://www.ebi.ac.uk/pdbsum/1s2l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1s2l ProSAT]</span></td></tr>
==Reference==
</table>
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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=14992575 14992575]
== Function ==
[https://www.uniprot.org/uniprot/Q8RLY5_LACHE Q8RLY5_LACHE]
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/s2/1s2l_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1s2l ConSurf].
<div style="clear:both"></div>
__TOC__
</StructureSection>
[[Category: Lactobacillus helveticus]]
[[Category: Lactobacillus helveticus]]
[[Category: Nucleoside deoxyribosyltransferase]]
[[Category: Large Structures]]
[[Category: Single protein]]
[[Category: Anand R]]
[[Category: Anand, R.]]
[[Category: Ealick SE]]
[[Category: Ealick, S E.]]
[[Category: Kaminski PA]]
[[Category: Kaminski, P A.]]
[[Category: 2'-purine deoxyribosyltansferase]]
[[Category: native]]
[[Category: ptd]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 14:57:13 2008''

Latest revision as of 11:27, 14 February 2024

Purine 2'deoxyribosyltransferase native structurePurine 2'deoxyribosyltransferase native structure

Structural highlights

1s2l is a 3 chain structure with sequence from Lactobacillus helveticus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.1Å
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

Q8RLY5_LACHE

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

1s2l, resolution 2.10Å

Drag the structure with the mouse to rotate

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OCA
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