1lwv

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
(New page: 200px<br /> <applet load="1lwv" size="450" color="white" frame="true" align="right" spinBox="true" caption="1lwv, resolution 2.3&Aring;" /> '''Borohydride-trapped ...)
Current revision (08:37, 6 November 2024) (edit) (undo)
 
(17 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1lwv.gif|left|200px]]<br />
 
-
<applet load="1lwv" size="450" color="white" frame="true" align="right" spinBox="true"
 
-
caption="1lwv, resolution 2.3&Aring;" />
 
-
'''Borohydride-trapped hOgg1 Intermediate Structure Co-Crystallized with 8-aminoguanine'''<br />
 
-
==Overview==
+
==Borohydride-trapped hOgg1 Intermediate Structure Co-Crystallized with 8-aminoguanine==
-
Most spontaneous damage to bases in DNA is corrected through the action of, the base-excision DNA repair pathway. Base excision repair is initiated by, DNA glycosylases, lesion-specific enzymes that intercept aberrant bases in, DNA and catalyze their excision. How such proteins accomplish the feat of, catalyzing no fewer than five sequential reaction steps using a single, active site has been unknown. To help answer this, we report the structure, of a trapped catalytic intermediate in DNA repair by human 8-oxoguanine, DNA glycosylase. This structure and supporting biochemical results reveal, that the enzyme sequesters the excised lesion base and exploits it as a, cofactor to participate in catalysis. To our knowledge, the present, example represents the first documented case of product-assisted catalysis, in an enzyme-catalyzed reaction.
+
<StructureSection load='1lwv' size='340' side='right'caption='[[1lwv]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
 +
== Structural highlights ==
 +
<table><tr><td colspan='2'>[[1lwv]] 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=1LWV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1LWV 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]] 2.3&#8491;</td></tr>
 +
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ANG:8-AMINOGUANINE'>ANG</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=PED:PENTANE-3,4-DIOL-5-PHOSPHATE'>PED</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=1lwv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lwv OCA], [https://pdbe.org/1lwv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1lwv RCSB], [https://www.ebi.ac.uk/pdbsum/1lwv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1lwv 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/lw/1lwv_consurf.spt"</scriptWhenChecked>
 +
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=1lwv ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
Most spontaneous damage to bases in DNA is corrected through the action of the base-excision DNA repair pathway. Base excision repair is initiated by DNA glycosylases, lesion-specific enzymes that intercept aberrant bases in DNA and catalyze their excision. How such proteins accomplish the feat of catalyzing no fewer than five sequential reaction steps using a single active site has been unknown. To help answer this, we report the structure of a trapped catalytic intermediate in DNA repair by human 8-oxoguanine DNA glycosylase. This structure and supporting biochemical results reveal that the enzyme sequesters the excised lesion base and exploits it as a cofactor to participate in catalysis. To our knowledge, the present example represents the first documented case of product-assisted catalysis in an enzyme-catalyzed reaction.
-
==Disease==
+
Product-assisted catalysis in base-excision DNA repair.,Fromme JC, Bruner SD, Yang W, Karplus M, Verdine GL Nat Struct Biol. 2003 Mar;10(3):204-11. PMID:12592398<ref>PMID:12592398</ref>
-
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]]
+
-
==About this Structure==
+
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-
1LWV 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 and ANG as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1LWV OCA].
+
</div>
 +
<div class="pdbe-citations 1lwv" style="background-color:#fffaf0;"></div>
-
==Reference==
+
==See Also==
-
Product-assisted catalysis in base-excision DNA repair., Fromme JC, Bruner SD, Yang W, Karplus M, Verdine GL, Nat Struct Biol. 2003 Mar;10(3):204-11. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12592398 12592398]
+
*[[DNA glycosylase 3D structures|DNA glycosylase 3D structures]]
 +
== References ==
 +
<references/>
 +
__TOC__
 +
</StructureSection>
[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
-
[[Category: Single protein]]
+
[[Category: Large Structures]]
-
[[Category: Bruner, S.D.]]
+
[[Category: Bruner SD]]
-
[[Category: Fromme, J.C.]]
+
[[Category: Fromme JC]]
-
[[Category: Karplus, M.]]
+
[[Category: Karplus M]]
-
[[Category: Verdine, G.L.]]
+
[[Category: Verdine GL]]
-
[[Category: Yang, W.]]
+
[[Category: Yang W]]
-
[[Category: ANG]]
+
-
[[Category: CA]]
+
-
[[Category: borohydride]]
+
-
[[Category: covalent trapping]]
+
-
[[Category: dna glycosylase]]
+
-
[[Category: dna repair]]
+
-
[[Category: product-assisted catalysis]]
+
-
[[Category: protein/dna]]
+
-
[[Category: reaction intermediate]]
+
-
 
+
-
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Mon Nov 12 18:04:42 2007''
+

Current revision

Borohydride-trapped hOgg1 Intermediate Structure Co-Crystallized with 8-aminoguanine

PDB ID 1lwv

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1lwv"
Personal tools