1s2g: Difference between revisions

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[[Image:1s2g.jpg|left|200px]]


{{Structure
==Purine 2'deoxyribosyltransferase + 2'-deoxyadenosine==
|PDB= 1s2g |SIZE=350|CAPTION= <scene name='initialview01'>1s2g</scene>, resolution 2.10&Aring;
<StructureSection load='1s2g' size='340' side='right'caption='[[1s2g]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
|SITE=  
== Structural highlights ==
|LIGAND= <scene name='pdbligand=3D1:5-(6-AMINO-PURIN-9-YL)-2-HYDROXYMETHYL-TETRAHYDRO-FURAN-3-OL'>3D1</scene>
<table><tr><td colspan='2'>[[1s2g]] 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=1S2G OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1S2G FirstGlance]. <br>
|ACTIVITY= [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]  
</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>
|GENE=
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3D1:(2R,3S,5R)-5-(6-AMINO-9H-PURIN-9-YL)-TETRAHYDRO-2-(HYDROXYMETHYL)FURAN-3-OL'>3D1</scene></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=1s2g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1s2g OCA], [https://pdbe.org/1s2g PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1s2g RCSB], [https://www.ebi.ac.uk/pdbsum/1s2g PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1s2g ProSAT]</span></td></tr>
 
</table>
'''Purine 2'deoxyribosyltransferase + 2'-deoxyadenosine'''
== Function ==
 
[https://www.uniprot.org/uniprot/Q8RLY5_LACHE Q8RLY5_LACHE]  
 
== Evolutionary Conservation ==
==Overview==
[[Image:Consurf_key_small.gif|200px|right]]
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.
Check<jmol>
 
  <jmolCheckbox>
==About this Structure==
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/s2/1s2g_consurf.spt"</scriptWhenChecked>
1S2G is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Lactobacillus_helveticus Lactobacillus helveticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1S2G OCA].  
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
 
    <text>to colour the structure by Evolutionary Conservation</text>
==Reference==
  </jmolCheckbox>
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://www.ncbi.nlm.nih.gov/pubmed/14992575 14992575]
</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=1s2g 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: 3D1]]
[[Category: 2'-deoxyadenosine]]
[[Category: 2'-purine deoxyribosyltansferase]]
[[Category: ptd]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 13:59:33 2008''

Latest revision as of 11:27, 14 February 2024

Purine 2'deoxyribosyltransferase + 2'-deoxyadenosinePurine 2'deoxyribosyltransferase + 2'-deoxyadenosine

Structural highlights

1s2g 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
Ligands:
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.

1s2g, resolution 2.10Å

Drag the structure with the mouse to rotate

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