2vkc: Difference between revisions
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< | ==Solution structure of the B3BP Smr domain== | ||
<StructureSection load='2vkc' size='340' side='right'caption='[[2vkc]], [[NMR_Ensembles_of_Models | 28 NMR models]]' scene=''> | |||
You may | == Structural highlights == | ||
<table><tr><td colspan='2'>[[2vkc]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VKC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VKC 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;'>[[2d9i|2d9i]]</div></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=2vkc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vkc OCA], [https://pdbe.org/2vkc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2vkc RCSB], [https://www.ebi.ac.uk/pdbsum/2vkc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2vkc ProSAT]</span></td></tr> | ||
</table> | |||
== Function == | |||
[[https://www.uniprot.org/uniprot/N4BP2_HUMAN N4BP2_HUMAN]] Has 5'-polynucleotide kinase and nicking endonuclease activity. May play a role in DNA repair or recombination.<ref>PMID:12730195</ref> | |||
== 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/vk/2vkc_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=2vkc ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
The MutS1 protein recognizes unpaired bases and initiates mismatch repair, which are essential for high-fidelity DNA replication. The homologous MutS2 protein does not contribute to mismatch repair, but suppresses homologous recombination. MutS2 lacks the damage-recognition domain of MutS1, but contains an additional C-terminal extension: the small MutS-related (Smr) domain. This domain, which is present in both prokaryotes and eukaryotes, has previously been reported to bind to DNA and to possess nicking endonuclease activity. We determine here the solution structure of the functionally active Smr domain of the Bcl3-binding protein (also known as Nedd4-binding protein 2), a protein with unknown function that lacks other domains present in MutS proteins. The Smr domain adopts a two-layer alpha-beta sandwich fold, which has a structural similarity to the C-terminal domain of IF3, the R3H domain, and the N-terminal domain of DNase I. The most conserved residues are located in three loops that form a contiguous, exposed, and positively charged surface with distinct sequence identity for prokaryotic and eukaryotic Smr domains. NMR titration experiments and DNA binding studies using Bcl3-binding protein-Smr domain mutants suggested that these most conserved loop regions participate in DNA binding to single-stranded/double-stranded DNA junctions. Based on the observed DNA-binding-induced multimerization, the structural similarity with both subdomains of DNase I, and the experimentally identified DNA-binding surface, we propose a model for DNA recognition by the Smr domain. | |||
Solution Structure and Characterization of the DNA-Binding Activity of the B3BP-Smr Domain.,Diercks T, Ab E, Daniels MA, de Jong RN, Besseling R, Kaptein R, Folkers GE J Mol Biol. 2008 Sep 12. PMID:18804481<ref>PMID:18804481</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 2vkc" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
== | [[Category: Human]] | ||
[[Category: Large Structures]] | |||
[[Category: Ab, E]] | |||
== | [[Category: Besseling, R]] | ||
< | [[Category: Daniels, M A]] | ||
[[Category: | [[Category: Diercks, T]] | ||
[[Category: Ab, E | [[Category: Folkers, G E]] | ||
[[Category: Besseling, R | [[Category: Kaptein, R]] | ||
[[Category: Daniels, M A | [[Category: DeJong, R N]] | ||
[[Category: | |||
[[Category: | |||
[[Category: | |||
[[Category: | |||
[[Category: Alternative splicing]] | [[Category: Alternative splicing]] | ||
[[Category: Atp-binding]] | [[Category: Atp-binding]] | ||
| Line 46: | Line 55: | ||
[[Category: Smr]] | [[Category: Smr]] | ||
[[Category: Ubl conjugation]] | [[Category: Ubl conjugation]] | ||
Latest revision as of 14:38, 30 March 2022
Solution structure of the B3BP Smr domainSolution structure of the B3BP Smr domain
Structural highlights
Function[N4BP2_HUMAN] Has 5'-polynucleotide kinase and nicking endonuclease activity. May play a role in DNA repair or recombination.[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 PubMedThe MutS1 protein recognizes unpaired bases and initiates mismatch repair, which are essential for high-fidelity DNA replication. The homologous MutS2 protein does not contribute to mismatch repair, but suppresses homologous recombination. MutS2 lacks the damage-recognition domain of MutS1, but contains an additional C-terminal extension: the small MutS-related (Smr) domain. This domain, which is present in both prokaryotes and eukaryotes, has previously been reported to bind to DNA and to possess nicking endonuclease activity. We determine here the solution structure of the functionally active Smr domain of the Bcl3-binding protein (also known as Nedd4-binding protein 2), a protein with unknown function that lacks other domains present in MutS proteins. The Smr domain adopts a two-layer alpha-beta sandwich fold, which has a structural similarity to the C-terminal domain of IF3, the R3H domain, and the N-terminal domain of DNase I. The most conserved residues are located in three loops that form a contiguous, exposed, and positively charged surface with distinct sequence identity for prokaryotic and eukaryotic Smr domains. NMR titration experiments and DNA binding studies using Bcl3-binding protein-Smr domain mutants suggested that these most conserved loop regions participate in DNA binding to single-stranded/double-stranded DNA junctions. Based on the observed DNA-binding-induced multimerization, the structural similarity with both subdomains of DNase I, and the experimentally identified DNA-binding surface, we propose a model for DNA recognition by the Smr domain. Solution Structure and Characterization of the DNA-Binding Activity of the B3BP-Smr Domain.,Diercks T, Ab E, Daniels MA, de Jong RN, Besseling R, Kaptein R, Folkers GE J Mol Biol. 2008 Sep 12. PMID:18804481[2] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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