1emj: Difference between revisions

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[[Image:1emj.png|left|200px]]


{{STRUCTURE_1emj|  PDB=1emj  |  SCENE=  }}
==URACIL-DNA GLYCOSYLASE BOUND TO DNA CONTAINING A 4'-THIO-2'DEOXYURIDINE ANALOG PRODUCT==
 
<StructureSection load='1emj' size='340' side='right'caption='[[1emj]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
===URACIL-DNA GLYCOSYLASE BOUND TO DNA CONTAINING A 4'-THIO-2'DEOXYURIDINE ANALOG PRODUCT===
== Structural highlights ==
 
<table><tr><td colspan='2'>[[1emj]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EMJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1EMJ FirstGlance]. <br>
{{ABSTRACT_PUBMED_10805771}}
</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&#8491;</td></tr>
 
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ASU:4-THIO-24-DIDEOXYRIBOFURANOSE-5-PHOSPHATE'>ASU</scene>, <scene name='pdbligand=URA:URACIL'>URA</scene></td></tr>
==About this Structure==
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1emj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1emj OCA], [https://pdbe.org/1emj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1emj RCSB], [https://www.ebi.ac.uk/pdbsum/1emj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1emj ProSAT]</span></td></tr>
[[1emj]] is a 3 chain structure of [[DNA glycosylate]] with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EMJ OCA].  
</table>
== Disease ==
[https://www.uniprot.org/uniprot/UNG_HUMAN UNG_HUMAN] Defects in UNG are a cause of immunodeficiency with hyper-IgM type 5 (HIGM5) [MIM:[https://omim.org/entry/608106 608106]. A rare immunodeficiency syndrome characterized by normal or elevated serum IgM levels with absence of IgG, IgA, and IgE. It results in a profound susceptibility to bacterial infections.<ref>PMID:12958596</ref> <ref>PMID:15967827</ref>
== Function ==
[https://www.uniprot.org/uniprot/UNG_HUMAN UNG_HUMAN] Excises uracil residues from the DNA which can arise as a result of misincorporation of dUMP residues by DNA polymerase or due to deamination of cytosine.
== 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/em/1emj_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=1emj ConSurf].
<div style="clear:both"></div>


==See Also==
==See Also==
*[[DNA glycosylate|DNA glycosylate]]
*[[DNA glycosylase 3D structures|DNA glycosylase 3D structures]]
 
== References ==
==Reference==
<references/>
<ref group="xtra">PMID:010805771</ref><ref group="xtra">PMID:010926503</ref><references group="xtra"/>
__TOC__
</StructureSection>
[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
[[Category: Uridine nucleosidase]]
[[Category: Large Structures]]
[[Category: Blackburn, G M.]]
[[Category: Blackburn GM]]
[[Category: Jones, G D.]]
[[Category: Jones GD]]
[[Category: Krokan, H E.]]
[[Category: Krokan HE]]
[[Category: Parikh, S S.]]
[[Category: Parikh SS]]
[[Category: Slupphaug, G.]]
[[Category: Slupphaug G]]
[[Category: Tainer, J A.]]
[[Category: Tainer JA]]
[[Category: Walcher, G.]]
[[Category: Walcher G]]
[[Category: Alpha/beta fold]]
[[Category: Hydrolase-dna complex]]
[[Category: Protein/dna]]
[[Category: Uracil-dna glycosylase]]

Latest revision as of 10:04, 7 February 2024

URACIL-DNA GLYCOSYLASE BOUND TO DNA CONTAINING A 4'-THIO-2'DEOXYURIDINE ANALOG PRODUCTURACIL-DNA GLYCOSYLASE BOUND TO DNA CONTAINING A 4'-THIO-2'DEOXYURIDINE ANALOG PRODUCT

Structural highlights

1emj is a 3 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Disease

UNG_HUMAN Defects in UNG are a cause of immunodeficiency with hyper-IgM type 5 (HIGM5) [MIM:608106. A rare immunodeficiency syndrome characterized by normal or elevated serum IgM levels with absence of IgG, IgA, and IgE. It results in a profound susceptibility to bacterial infections.[1] [2]

Function

UNG_HUMAN Excises uracil residues from the DNA which can arise as a result of misincorporation of dUMP residues by DNA polymerase or due to deamination of cytosine.

Evolutionary Conservation

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

See Also

References

  1. ↑ Imai K, Slupphaug G, Lee WI, Revy P, Nonoyama S, Catalan N, Yel L, Forveille M, Kavli B, Krokan HE, Ochs HD, Fischer A, Durandy A. Human uracil-DNA glycosylase deficiency associated with profoundly impaired immunoglobulin class-switch recombination. Nat Immunol. 2003 Oct;4(10):1023-8. Epub 2003 Sep 7. PMID:12958596 doi:http://dx.doi.org/10.1038/ni974
  2. ↑ Kavli B, Andersen S, Otterlei M, Liabakk NB, Imai K, Fischer A, Durandy A, Krokan HE, Slupphaug G. B cells from hyper-IgM patients carrying UNG mutations lack ability to remove uracil from ssDNA and have elevated genomic uracil. J Exp Med. 2005 Jun 20;201(12):2011-21. PMID:15967827 doi:10.1084/jem.20050042

1emj, resolution 2.00Å

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