1m3h: Difference between revisions

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New page: left|200px<br /> <applet load="1m3h" size="450" color="white" frame="true" align="right" spinBox="true" caption="1m3h, resolution 2.05Å" /> '''Crystal Structure o...
 
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[[Image:1m3h.gif|left|200px]]<br />
<applet load="1m3h" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1m3h, resolution 2.05&Aring;" />
'''Crystal Structure of Hogg1 D268E Mutant with Product Oligonucleotide'''<br />


==Overview==
==Crystal Structure of Hogg1 D268E Mutant with Product Oligonucleotide==
DNA glycosylase/lyases initiate the repair of damaged nucleobases in the, genome by catalyzing excision of aberrant nucleobases and nicking of the, lesion-containing DNA strand. Nearly all of these proteins have the, unusual property of remaining tightly bound in vitro to the end products, of the reaction cascade. We have taken advantage of this property to, crystallize and structurally characterize the end product resulting from, complete DNA processing by a catalytically active mutant form of human, 8-oxoguanine DNA glycosylase (D268E hOgg1). The resulting structure is, consistent with the currently accepted catalytic mechanism for the, protein. Unexpectedly, however, soaking of a nucleobase analog into the, crystals results in religation of the DNA backbone in situ.
<StructureSection load='1m3h' size='340' side='right'caption='[[1m3h]], [[Resolution|resolution]] 2.05&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1m3h]] is a 4 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=1M3H OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1M3H FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.05&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DDX:2,3-DEHYDRO-2,3-DIDEOXYRIBOFURANOSE-5-PHOSPHATE'>DDX</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=1m3h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m3h OCA], [https://pdbe.org/1m3h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1m3h RCSB], [https://www.ebi.ac.uk/pdbsum/1m3h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1m3h ProSAT]</span></td></tr>
</table>
== Disease ==
[https://www.uniprot.org/uniprot/OGG1_HUMAN OGG1_HUMAN] Defects in OGG1 may be a cause of renal cell carcinoma (RCC) [MIM:[https://omim.org/entry/144700 144700]. It is a heterogeneous group of sporadic or hereditary carcinoma derived from cells of the proximal renal tubular epithelium. It is subclassified into clear cell renal carcinoma (non-papillary carcinoma), papillary renal cell carcinoma, chromophobe renal cell carcinoma, collecting duct carcinoma with medullary carcinoma of the kidney, and unclassified renal cell carcinoma.
== Function ==
[https://www.uniprot.org/uniprot/OGG1_HUMAN OGG1_HUMAN] DNA repair enzyme that incises DNA at 8-oxoG residues. Excises 7,8-dihydro-8-oxoguanine and 2,6-diamino-4-hydroxy-5-N-methylformamidopyrimidine (FAPY) from damaged DNA. Has a beta-lyase activity that nicks DNA 3' to the lesion.
== 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/m3/1m3h_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=1m3h ConSurf].
<div style="clear:both"></div>


==Disease==
==See Also==
Known disease associated with this structure: Renal cell carcinoma, clear cell, somatic OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=601982 601982]]
*[[DNA glycosylase 3D structures|DNA glycosylase 3D structures]]
 
__TOC__
==About this Structure==
</StructureSection>
1M3H is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] with CA as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1M3H OCA].
 
==Reference==
Structures of end products resulting from lesion processing by a DNA glycosylase/lyase., Chung SJ, Verdine GL, Chem Biol. 2004 Dec;11(12):1643-9. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15610848 15610848]
[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
[[Category: Single protein]]
[[Category: Large Structures]]
[[Category: Chung, S.J.]]
[[Category: Chung SJ]]
[[Category: Verdine, G.L.]]
[[Category: Verdine GL]]
[[Category: CA]]
[[Category: dna glycosylase]]
[[Category: dna repair]]
[[Category: end product]]
[[Category: enzyme]]
[[Category: mutant]]
[[Category: protein-dna complex]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Mon Nov 12 18:06:46 2007''

Latest revision as of 10:39, 14 February 2024

Crystal Structure of Hogg1 D268E Mutant with Product OligonucleotideCrystal Structure of Hogg1 D268E Mutant with Product Oligonucleotide

Structural highlights

1m3h is a 4 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 2.05Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Disease

OGG1_HUMAN Defects in OGG1 may be a cause of renal cell carcinoma (RCC) [MIM:144700. It is a heterogeneous group of sporadic or hereditary carcinoma derived from cells of the proximal renal tubular epithelium. It is subclassified into clear cell renal carcinoma (non-papillary carcinoma), papillary renal cell carcinoma, chromophobe renal cell carcinoma, collecting duct carcinoma with medullary carcinoma of the kidney, and unclassified renal cell carcinoma.

Function

OGG1_HUMAN DNA repair enzyme that incises DNA at 8-oxoG residues. Excises 7,8-dihydro-8-oxoguanine and 2,6-diamino-4-hydroxy-5-N-methylformamidopyrimidine (FAPY) from damaged DNA. Has a beta-lyase activity that nicks DNA 3' to the lesion.

Evolutionary Conservation

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

See Also

1m3h, resolution 2.05Å

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