1uug: Difference between revisions

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New page: left|200px<br /><applet load="1uug" size="450" color="white" frame="true" align="right" spinBox="true" caption="1uug, resolution 2.4Å" /> '''ESCHERICHIA COLI URAC...
 
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[[Image:1uug.jpg|left|200px]]<br /><applet load="1uug" size="450" color="white" frame="true" align="right" spinBox="true"
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'''ESCHERICHIA COLI URACIL-DNA GLYCOSYLASE:INHIBITOR COMPLEX WITH WILD-TYPE UDG AND WILD-TYPE UGI'''<br />


==Overview==
==ESCHERICHIA COLI URACIL-DNA GLYCOSYLASE:INHIBITOR COMPLEX WITH WILD-TYPE UDG AND WILD-TYPE UGI==
Uracil-DNA glycosylase (UDG), which is a critical enzyme in DNA, base-excision repair that recognizes and removes uracil from DNA, is, specifically and irreversably inhibited by the thermostable uracil-DNA, glycosylase inhibitor protein (Ugi). A paradox for the highly specific Ugi, inhibition of UDG is how Ugi can successfully mimic DNA backbone, interactions for UDG without resulting in significant cross-reactivity, with numerous other enzymes that possess DNA backbone binding affinity., High-resolution X-ray crystal structures of Ugi both free and in complex, with wild-type and the functionally defective His187Asp mutant Escherichia, coli UDGs reveal the detailed molecular basis for duplex DNA backbone, mimicry by Ugi. The overall shape and charge distribution of Ugi most, closely resembles a midpoint in a trajectory between B-form DNA and the, kinked DNA observed in UDG:DNA product complexes. Thus, Ugi targets the, mechanism of uracil flipping by UDG and appears to be a transition-state, mimic for UDG-flipping of uracil nucleotides from DNA. Essentially all the, exquisite shape, electrostatic and hydrophobic complementarity for the, high-affinity UDG-Ugi interaction is pre-existing, except for a key flip, of the Ugi Gln19 carbonyl group and Glu20 side-chain, which is triggered, by the formation of the complex. Conformational changes between unbound, Ugi and Ugi complexed with UDG involve the beta-zipper structural motif, which we have named for the reversible pairing observed between, intramolecular beta-strands. A similar beta-zipper is observed in the, conversion between the open and closed forms of UDG. The combination of, extremely high levels of pre-existing structural complementarity to DNA, binding features specific to UDG with key local conformational changes in, Ugi resolves the UDG-Ugi paradox and suggests a potentially general, structural solution to the formation of very high affinity DNA, enzyme-inhibitor complexes that avoid cross- reactivity.
<StructureSection load='1uug' size='340' side='right'caption='[[1uug]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1uug]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_phage_PBS2 Bacillus phage PBS2] and [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UUG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1UUG 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]] 2.4&#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=1uug FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1uug OCA], [https://pdbe.org/1uug PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1uug RCSB], [https://www.ebi.ac.uk/pdbsum/1uug PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1uug ProSAT]</span></td></tr>
</table>
== Function ==
[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]
== 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/uu/1uug_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=1uug ConSurf].
<div style="clear:both"></div>


==About this Structure==
==See Also==
1UUG is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] and [http://en.wikipedia.org/wiki/Phage_pbs1 Phage pbs1]. 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=1UUG OCA].
*[[DNA glycosylase 3D structures|DNA glycosylase 3D structures]]
 
*[[Uracil glycosylase inhibitor|Uracil glycosylase inhibitor]]
==Reference==
__TOC__
Protein mimicry of DNA from crystal structures of the uracil-DNA glycosylase inhibitor protein and its complex with Escherichia coli uracil-DNA glycosylase., Putnam CD, Shroyer MJ, Lundquist AJ, Mol CD, Arvai AS, Mosbaugh DW, Tainer JA, J Mol Biol. 1999 Mar 26;287(2):331-46. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10080896 10080896]
</StructureSection>
[[Category: Escherichia coli]]
[[Category: Bacillus phage PBS2]]
[[Category: Phage pbs1]]
[[Category: Escherichia coli K-12]]
[[Category: Protein complex]]
[[Category: Large Structures]]
[[Category: Uridine nucleosidase]]
[[Category: Arvai AS]]
[[Category: Arvai, A.S.]]
[[Category: Mol CD]]
[[Category: Mol, C.D.]]
[[Category: Putnam CD]]
[[Category: Putnam, C.D.]]
[[Category: Tainer JA]]
[[Category: Tainer, J.A.]]
[[Category: dna base excision repair]]
[[Category: protein inhibitor]]
[[Category: protein mimicry of dna]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 04:19:51 2007''

Latest revision as of 09:17, 3 April 2024

ESCHERICHIA COLI URACIL-DNA GLYCOSYLASE:INHIBITOR COMPLEX WITH WILD-TYPE UDG AND WILD-TYPE UGIESCHERICHIA COLI URACIL-DNA GLYCOSYLASE:INHIBITOR COMPLEX WITH WILD-TYPE UDG AND WILD-TYPE UGI

Structural highlights

1uug is a 4 chain structure with sequence from Bacillus phage PBS2 and Escherichia coli K-12. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.4Å
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.

See Also

1uug, resolution 2.40Å

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