This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

2le2

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Current revision

Novel dimeric structure of phage phi29-encoded protein p56: Insights into Uracil-DNA glycosylase inhibition

Structural highlights

2le2 is a 2 chain structure with sequence from Bacillus virus phi29. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Solution NMR
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

P56_BPPH2 Inhibits the host uracil-DNA glycosylase (UDG), an enzyme which removes uracil residues from DNA by the base excision repair. Interacts with host uracil-DNA glycosylase and prevents the latter from binding to DNA. Since the viral DNA polymerase efficiently incorporates dUMP into DNA, the virus needs to prevent the deleterious effect caused by host UDG when it eliminates uracil residues present in the viral genome.^[1] ^[2] ^[3]

Publication Abstract from PubMed

Protein p56 encoded by the Bacillus subtilis phage 29 inhibits the host uracil-DNA glycosylase (UDG) activity. To get insights into the structural basis for this inhibition, the NMR solution structure of p56 has been determined. The inhibitor defines a novel dimeric fold, stabilized by a combination of polar and extensive hydrophobic interactions. Each polypeptide chain contains three stretches of anti-parallel beta-sheets and a helical region linked by three short loops. In addition, microcalorimetry titration experiments showed that it forms a tight 2:1 complex with UDG, strongly suggesting that the dimer represents the functional form of the inhibitor. This was further confirmed by the functional analysis of p56 mutants unable to assemble into dimers. We have also shown that the highly anionic region of the inhibitor plays a significant role in the inhibition of UDG. Thus, based on these findings and taking into account previous results that revealed similarities between the association mode of p56 and the phage PBS-1/PBS-2-encoded inhibitor Ugi with UDG, we propose that protein p56 might inhibit the enzyme by mimicking its DNA substrate.

Novel dimeric structure of phage {phi}29-encoded protein p56: insights into uracil-DNA glycosylase inhibition.,Asensio JL, Perez-Lago L, Lazaro JM, Gonzalez C, Serrano-Heras G, Salas M Nucleic Acids Res. 2011 Sep 2. PMID:21890898^[4]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Serrano-Heras G, Ruiz-Masó JA, del Solar G, Espinosa M, Bravo A, Salas M. Protein p56 from the Bacillus subtilis phage phi29 inhibits DNA-binding ability of uracil-DNA glycosylase. Nucleic Acids Res. 2007;35(16):5393-401. PMID:17698500 doi:10.1093/nar/gkm584
↑ Serrano-Heras G, Bravo A, Salas M. Phage phi29 protein p56 prevents viral DNA replication impairment caused by uracil excision activity of uracil-DNA glycosylase. Proc Natl Acad Sci U S A. 2008 Dec 9;105(49):19044-9. PMID:18845683 doi:10.1073/pnas.0808797105
↑ Pérez-Lago L, Serrano-Heras G, Baños B, Lázaro JM, Alcorlo M, Villar L, Salas M. Characterization of Bacillus subtilis uracil-DNA glycosylase and its inhibition by phage φ29 protein p56. Mol Microbiol. 2011 Jun;80(6):1657-66. PMID:21542855 doi:10.1111/j.1365-2958.2011.07675.x
↑ Asensio JL, Perez-Lago L, Lazaro JM, Gonzalez C, Serrano-Heras G, Salas M. Novel dimeric structure of phage {phi}29-encoded protein p56: insights into uracil-DNA glycosylase inhibition. Nucleic Acids Res. 2011 Sep 2. PMID:21890898 doi:10.1093/nar/gkr667

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2le2"

@@ Line 4: / Line 4: @@
 == Structural highlights ==
 <table><tr><td colspan='2'>[[2le2]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_virus_phi29 Bacillus virus phi29]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LE2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2LE2 FirstGlance]. <br>
-</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=2le2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2le2 OCA], [https://pdbe.org/2le2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2le2 RCSB], [https://www.ebi.ac.uk/pdbsum/2le2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2le2 ProSAT]</span></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</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=2le2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2le2 OCA], [https://pdbe.org/2le2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2le2 RCSB], [https://www.ebi.ac.uk/pdbsum/2le2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2le2 ProSAT]</span></td></tr>
 </table>
 == Function ==

2le2

From Proteopedia

Current revision

Novel dimeric structure of phage phi29-encoded protein p56: Insights into Uracil-DNA glycosylase inhibition

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox