4eug: Difference between revisions

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New page: left|200px<br /><applet load="4eug" size="450" color="white" frame="true" align="right" spinBox="true" caption="4eug, resolution 1.40Å" /> '''CRYSTALLOGRAPHIC AND...
 
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'''CRYSTALLOGRAPHIC AND ENZYMATIC STUDIES OF AN ACTIVE SITE VARIANT H187Q OF ESCHERICHIA COLI URACIL DNA GLYCOSYLASE: CRYSTAL STRUCTURES OF MUTANT H187Q AND ITS URACIL COMPLEX'''<br />


==Overview==
==Crystallographic and Enzymatic Studies of an Active Site Variant H187Q of Escherichia Coli Uracil DNA Glycosylase: Crystal Structures of Mutant H187Q and its Uracil Complex==
The DNA repair enzyme uracil DNA glycosylase (UDG) catalyzes the, hydrolysis of premutagenic uracil residues from single-stranded or duplex, DNA, producing free uracil and abasic DNA. Here we report the, high-resolution crystal structures of free UDG from Escherichia coli, strain B (1.60 A), its complex with uracil (1.50 A), and a second, active-site complex with glycerol (1.43 A). These represent the first, high-resolution structures of a prokaryotic UDG to be reported. The, overall structure of the E. coli enzyme is more similar to the human UDG, than the herpes virus enzyme. Significant differences between the, bacterial and viral structures are seen in the side-chain positions of the, putative general-acid (His187) and base (Asp64), similar to differences, previously observed between the viral and human enzymes. In general, the, active-site loop that contains His187 appears preorganized in comparison, with the viral and human enzymes, requiring smaller substrate-induced, conformational changes to bring active-site groups into catalytic, position. These structural differences may be related to the large, differences in the mechanism of uracil recognition used by the E. coli and, viral enzymes. The pH dependence of k(cat) for wild-type UDG and the D64N, and H187Q mutant enzymes is consistent with general-base catalysis by, Asp64, but provides no evidence for a general-acid catalyst. The catalytic, mechanism of UDG is critically discussed with respect to these results.
<StructureSection load='4eug' size='340' side='right'caption='[[4eug]], [[Resolution|resolution]] 1.40&Aring;' scene=''>
 
== Structural highlights ==
==About this Structure==
<table><tr><td colspan='2'>[[4eug]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_B Escherichia coli B]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4EUG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4EUG FirstGlance]. <br>
4EUG is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Active as [http://en.wikipedia.org/wiki/Uridine_nucleosidase Uridine nucleosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.3 3.2.2.3] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=4EUG 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]] 1.4&#8491;</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=4eug FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4eug OCA], [https://pdbe.org/4eug PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4eug RCSB], [https://www.ebi.ac.uk/pdbsum/4eug PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4eug ProSAT]</span></td></tr>
==Reference==
</table>
Crystal structure of Escherichia coli uracil DNA glycosylase and its complexes with uracil and glycerol: structure and glycosylase mechanism revisited., Xiao G, Tordova M, Jagadeesh J, Drohat AC, Stivers JT, Gilliland GL, Proteins. 1999 Apr 1;35(1):13-24. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10090282 10090282]
== Function ==
[[Category: Escherichia coli]]
[https://www.uniprot.org/uniprot/UNG_ECOLI UNG_ECOLI] 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.[HAMAP-Rule:MF_00148]
[[Category: Single protein]]
== Evolutionary Conservation ==
[[Category: Uridine nucleosidase]]
[[Image:Consurf_key_small.gif|200px|right]]
[[Category: Drohat, A.C.]]
Check<jmol>
[[Category: Gilliland, G.L.]]
  <jmolCheckbox>
[[Category: Jagadeesh, J.]]
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/eu/4eug_consurf.spt"</scriptWhenChecked>
[[Category: Stivers, J.T.]]
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
[[Category: Tordova, M.]]
    <text>to colour the structure by Evolutionary Conservation</text>
[[Category: Xiao, G.]]
  </jmolCheckbox>
[[Category: glycosylase]]
</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=4eug ConSurf].
 
<div style="clear:both"></div>
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 19:34:47 2007''
__TOC__
</StructureSection>
[[Category: Escherichia coli B]]
[[Category: Large Structures]]
[[Category: Drohat AC]]
[[Category: Gilliland GL]]
[[Category: Jagadeesh J]]
[[Category: Stivers JT]]
[[Category: Tordova M]]
[[Category: Xiao G]]

Latest revision as of 18:09, 14 March 2024

Crystallographic and Enzymatic Studies of an Active Site Variant H187Q of Escherichia Coli Uracil DNA Glycosylase: Crystal Structures of Mutant H187Q and its Uracil ComplexCrystallographic and Enzymatic Studies of an Active Site Variant H187Q of Escherichia Coli Uracil DNA Glycosylase: Crystal Structures of Mutant H187Q and its Uracil Complex

Structural highlights

4eug is a 1 chain structure with sequence from Escherichia coli B. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.4Å
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

UNG_ECOLI 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.[HAMAP-Rule:MF_00148]

Evolutionary Conservation

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

4eug, resolution 1.40Å

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