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.

2kwv

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Current revision

Solution Structure of UBM1 of murine Polymerase iota in Complex with Ubiquitin

Structural highlights

2kwv is a 2 chain structure with sequence from Homo sapiens and Mus musculus. 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

POLI_MOUSE Error-prone DNA polymerase specifically involved in DNA repair. Plays an important role in translesion synthesis, where the normal high-fidelity DNA polymerases cannot proceed and DNA synthesis stalls. Favors Hoogsteen base-pairing in the active site. Inserts the correct base with high-fidelity opposite an adenosine template. Exhibits low fidelity and efficiency opposite a thymidine template, where it will preferentially insert guanosine. May play a role in hypermutation of immunogobulin genes. Forms a Schiff base with 5'-deoxyribose phosphate at abasic sites, but may not have lyase activity (By similarity).^[1]

Evolutionary Conservation

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

Publication Abstract from PubMed

Ubiquitin-binding domains (UBDs) provide specificity to the ubiquitin system, which is also involved in translesion synthesis (TLS) in eukaryotic cells. Upon DNA damage, the UBDs (UBM domains) of polymerase iota (Pol iota) interact with ubiquitinated proliferating cell nuclear antigen to regulate the interchange between processive DNA polymerases and TLS. We report a biophysical analysis and solution structures of the two conserved UBM domains located in the C-terminal tail of murine Pol iota in complex with ubiquitin. The 35-amino acid core folds into a helix-turn-helix motif, which belongs to a novel domain fold. Similar to other UBDs, UBMs bind to ubiquitin on the hydrophobic surface delineated by Leu-8, Ile-44, and Val-70, however, slightly shifted toward the C terminus. In addition, UBMs also use electrostatic interactions to stabilize binding. NMR and fluorescence spectroscopy measurements revealed that UBMs bind monoubiquitin, and Lys-63- but not Lys-48-linked chains. Importantly, these biophysical data are supported by functional studies. Indeed, yeast cells expressing ubiquitin mutants specifically defective for UBM binding are viable but sensitive to DNA damaging conditions that require TLS for repair.

Structural Analysis of the Conserved Ubiquitin-binding Motifs (UBMs) of the Translesion Polymerase iota in Complex with Ubiquitin.,Burschowsky D, Rudolf F, Rabut G, Herrmann T, Matthias P, Wider G J Biol Chem. 2011 Jan 14;286(2):1364-73. Epub 2010 Oct 6. PMID:20929865^[2]

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

References

↑ Wang M, Devereux TR, Vikis HG, McCulloch SD, Holliday W, Anna C, Wang Y, Bebenek K, Kunkel TA, Guan K, You M. Pol iota is a candidate for the mouse pulmonary adenoma resistance 2 locus, a major modifier of chemically induced lung neoplasia. Cancer Res. 2004 Mar 15;64(6):1924-31. PMID:15026325
↑ Burschowsky D, Rudolf F, Rabut G, Herrmann T, Matthias P, Wider G. Structural Analysis of the Conserved Ubiquitin-binding Motifs (UBMs) of the Translesion Polymerase iota in Complex with Ubiquitin. J Biol Chem. 2011 Jan 14;286(2):1364-73. Epub 2010 Oct 6. PMID:20929865 doi:10.1074/jbc.M110.135038

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

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

@@ Line 1: / Line 1: @@
 ==Solution Structure of UBM1 of murine Polymerase iota in Complex with Ubiquitin==
-<StructureSection load='2kwv' size='340' side='right'caption='[[2kwv]], [[NMR_Ensembles_of_Models | 20 NMR models]]' scene=''>
+<StructureSection load='2kwv' size='340' side='right'caption='[[2kwv]]' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2kwv]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human] and [https://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KWV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2KWV FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2kwv]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KWV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2KWV FirstGlance]. <br>
-</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2kwu|2kwu]]</div></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='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Poli, Rad30b ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 LK3 transgenic mice]), RPS27A, UBA80, UBCEP1, UBA52, UBCEP2, UBB, UBC ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=2kwv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2kwv OCA], [https://pdbe.org/2kwv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2kwv RCSB], [https://www.ebi.ac.uk/pdbsum/2kwv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2kwv ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/POLI_MOUSE POLI_MOUSE]] Error-prone DNA polymerase specifically involved in DNA repair. Plays an important role in translesion synthesis, where the normal high-fidelity DNA polymerases cannot proceed and DNA synthesis stalls. Favors Hoogsteen base-pairing in the active site. Inserts the correct base with high-fidelity opposite an adenosine template. Exhibits low fidelity and efficiency opposite a thymidine template, where it will preferentially insert guanosine. May play a role in hypermutation of immunogobulin genes. Forms a Schiff base with 5'-deoxyribose phosphate at abasic sites, but may not have lyase activity (By similarity).<ref>PMID:15026325</ref>
+[https://www.uniprot.org/uniprot/POLI_MOUSE POLI_MOUSE] Error-prone DNA polymerase specifically involved in DNA repair. Plays an important role in translesion synthesis, where the normal high-fidelity DNA polymerases cannot proceed and DNA synthesis stalls. Favors Hoogsteen base-pairing in the active site. Inserts the correct base with high-fidelity opposite an adenosine template. Exhibits low fidelity and efficiency opposite a thymidine template, where it will preferentially insert guanosine. May play a role in hypermutation of immunogobulin genes. Forms a Schiff base with 5'-deoxyribose phosphate at abasic sites, but may not have lyase activity (By similarity).<ref>PMID:15026325</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 31: / Line 30: @@
 ==See Also==
+*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
 *[[3D structures of ubiquitin|3D structures of ubiquitin]]
 == References ==
@@ Line 36: / Line 36: @@
 __TOC__
 </StructureSection>
-[[Category: Human]]
+[[Category: Homo sapiens]]
 [[Category: Large Structures]]
-[[Category: Lk3 transgenic mice]]
+[[Category: Mus musculus]]
-[[Category: Burschowsky, D]]
+[[Category: Burschowsky D]]
-[[Category: Herrmann, T]]
+[[Category: Herrmann T]]
-[[Category: Peter, M]]
+[[Category: Peter M]]
-[[Category: Rabut, G]]
+[[Category: Rabut G]]
-[[Category: Rudolf, F]]
+[[Category: Rudolf F]]
-[[Category: Wider, G]]
+[[Category: Wider G]]
-[[Category: Polymerase iota]]
-[[Category: Protein binding-signaling protein complex]]
-[[Category: Tl]]
-[[Category: Ubiquitin]]
-[[Category: Ubiquitin-binding motif]]
-[[Category: Ubm]]

2kwv

From Proteopedia

Current revision

Solution Structure of UBM1 of murine Polymerase iota in Complex with Ubiquitin

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox