1f8y: Difference between revisions

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New page: left|200px<br /><applet load="1f8y" size="450" color="white" frame="true" align="right" spinBox="true" caption="1f8y, resolution 2.40Å" /> '''CRYSTAL STRUCTURE AN...
 
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[[Image:1f8y.jpg|left|200px]]<br /><applet load="1f8y" size="450" color="white" frame="true" align="right" spinBox="true"
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'''CRYSTAL STRUCTURE ANALYSIS OF NUCLEOSIDE 2-DEOXYRIBOSYLTRANSFERASE COMPLEXED WITH 5-METHYL-2'-DEOXYPSEUDOURIDINE'''<br />


==Overview==
==CRYSTAL STRUCTURE ANALYSIS OF NUCLEOSIDE 2-DEOXYRIBOSYLTRANSFERASE COMPLEXED WITH 5-METHYL-2'-DEOXYPSEUDOURIDINE==
BACKGROUND: Nucleoside 2-deoxyribosyltransferase plays an important role, in the salvage pathway of nucleotide metabolism in certain organisms, catalyzing the cleavage of beta-2'-deoxyribonucleosides and the subsequent, transfer of the deoxyribosyl moiety to an acceptor purine or pyrimidine, base. The kinetics describe a ping-pong-bi-bi pathway involving the, formation of a covalent enzyme-deoxyribose intermediate. The enzyme is, produced by a limited number of microorganisms and its functions have been, exploited in its use as a biocatalyst to synthesize nucleoside analogs of, therapeutic interest. RESULTS: We describe the crystal structure of the, enzyme with and without bound ligand. The native structure was solved by, the single isomorphous replacement with anomalous scattering method, (SIRAS) and refined to 2.5 A resolution resulting in a crystallographic R, factor of 16.6%. The enzyme comprises a single domain that belongs to the, general class of doubly-wound alpha/beta proteins; it also exhibits a, unique nucleoside-binding motif. X-ray analysis of enzyme-purine and, enzyme-pyrimidine complexes presented here reveals that the active site, lies in a cleft formed by the edge of the beta sheet and two alpha helices, and contains side chains from two subunits. CONCLUSIONS: These results, indicate residues that may be important in substrate binding and catalysis, and thus may serve as a framework for elucidating the mechanism of enzyme, activity. In particular, the proposed nucleophile, Glu98, lies in the, nucleoside-binding pocket at an appropriate position for nucleophilic, attack. A comparison of the enzyme interactions with both a purine and, pyrimidine ligand provides some insight into the structural basis for, enzyme specificity.
<StructureSection load='1f8y' size='340' side='right'caption='[[1f8y]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
 
== Structural highlights ==
==About this Structure==
<table><tr><td colspan='2'>[[1f8y]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Lactobacillus_leichmannii Lactobacillus leichmannii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1F8Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1F8Y FirstGlance]. <br>
1F8Y is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Lactobacillus_leichmannii Lactobacillus leichmannii] with 5MD 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=1F8Y 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]] 2.4&#8491;</td></tr>
 
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5MD:5-METHYL-2-DEOXYPSEUDOURIDINE'>5MD</scene></td></tr>
==Reference==
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1f8y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f8y OCA], [https://pdbe.org/1f8y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1f8y RCSB], [https://www.ebi.ac.uk/pdbsum/1f8y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1f8y ProSAT]</span></td></tr>
Crystal structures of nucleoside 2-deoxyribosyltransferase in native and ligand-bound forms reveal architecture of the active site., Armstrong SR, Cook WJ, Short SA, Ealick SE, Structure. 1996 Jan 15;4(1):97-107. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=8805514 8805514]
</table>
== Function ==
[https://www.uniprot.org/uniprot/NTD_LACLE NTD_LACLE] Catalyzes the cleavage of the glycosidic bond of 2'-deoxyribonucleosides and the transfer of the deoxyribosyl moiety to an acceptor purine or pyrimidine base.<ref>PMID:7797550</ref> <ref>PMID:8805514</ref>
== 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/f8/1f8y_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=1f8y ConSurf].
<div style="clear:both"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Lactobacillus leichmannii]]
[[Category: Lactobacillus leichmannii]]
[[Category: Nucleoside deoxyribosyltransferase]]
[[Category: Large Structures]]
[[Category: Single protein]]
[[Category: Armstrong SR]]
[[Category: Armstrong, S.R.]]
[[Category: Cook WJ]]
[[Category: Cook, W.J.]]
[[Category: Ealick SE]]
[[Category: Ealick, S.E.]]
[[Category: Short SA]]
[[Category: Short, S.A.]]
[[Category: 5MD]]
[[Category: active site]]
[[Category: alpha/beta protein]]
[[Category: biocatalyst]]
[[Category: nucleoside]]
[[Category: x-ray crystallography]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 14:43:11 2007''

Latest revision as of 10:12, 7 February 2024

CRYSTAL STRUCTURE ANALYSIS OF NUCLEOSIDE 2-DEOXYRIBOSYLTRANSFERASE COMPLEXED WITH 5-METHYL-2'-DEOXYPSEUDOURIDINECRYSTAL STRUCTURE ANALYSIS OF NUCLEOSIDE 2-DEOXYRIBOSYLTRANSFERASE COMPLEXED WITH 5-METHYL-2'-DEOXYPSEUDOURIDINE

Structural highlights

1f8y is a 2 chain structure with sequence from Lactobacillus leichmannii. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.4Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

NTD_LACLE Catalyzes the cleavage of the glycosidic bond of 2'-deoxyribonucleosides and the transfer of the deoxyribosyl moiety to an acceptor purine or pyrimidine base.[1] [2]

Evolutionary Conservation

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

References

  1. ↑ Porter DJ, Merrill BM, Short SA. Identification of the active site nucleophile in nucleoside 2-deoxyribosyltransferase as glutamic acid 98. J Biol Chem. 1995 Jun 30;270(26):15551-6. PMID:7797550
  2. ↑ Armstrong SR, Cook WJ, Short SA, Ealick SE. Crystal structures of nucleoside 2-deoxyribosyltransferase in native and ligand-bound forms reveal architecture of the active site. Structure. 1996 Jan 15;4(1):97-107. PMID:8805514

1f8y, resolution 2.40Å

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