1uug: Difference between revisions

← Older edit Newer edit →

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
-{{STRUCTURE_1uug|  PDB=1uug  |  SCENE=  }}
+==ESCHERICHIA COLI URACIL-DNA GLYCOSYLASE:INHIBITOR COMPLEX WITH WILD-TYPE UDG AND WILD-TYPE UGI==
-===ESCHERICHIA COLI URACIL-DNA GLYCOSYLASE:INHIBITOR COMPLEX WITH WILD-TYPE UDG AND WILD-TYPE UGI===
+<StructureSection load='1uug' size='340' side='right' caption='[[1uug]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
-{{ABSTRACT_PUBMED_10080896}}
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1uug]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_phage_pbs2 Bacillus phage pbs2] and [http://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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1UUG FirstGlance]. <br>
+</td></tr><tr><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">UNG ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 Escherichia coli K-12])</td></tr>
+<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[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] </span></td></tr>
+<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1uug FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1uug OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1uug RCSB], [http://www.ebi.ac.uk/pdbsum/1uug PDBsum]</span></td></tr>
+<table>
+== 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/chain_selection.php?pdb_ID=2ata ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+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.
-==About this Structure==
+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:10080896<ref>PMID:10080896</ref>
-[[1uug]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_phage_pbs2 Bacillus phage pbs2] and [http://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].
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
 ==See Also==
-*[[DNA glycosylate|DNA glycosylate]]
+*[[DNA glycosylase|DNA glycosylase]]
 *[[Uracil glycosylate inhibitor|Uracil glycosylate inhibitor]]
+*[[Uracil-DNA glycosylase|Uracil-DNA glycosylase]]
-==Reference==
+*[[Uracil-DNA glycosylase inhibitor|Uracil-DNA glycosylase inhibitor]]
-<ref group="xtra">PMID:010080896</ref><references group="xtra"/>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Bacillus phage pbs2]]
 [[Category: Escherichia coli k-12]]