2d4l: Difference between revisions
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< | ==Crystal structure of truncated in C-terminal M-PMV dUTPase== | ||
<StructureSection load='2d4l' size='340' side='right'caption='[[2d4l]], [[Resolution|resolution]] 1.70Å' scene=''> | |||
== Structural highlights == | |||
or the | <table><tr><td colspan='2'>[[2d4l]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Mason-Pfizer_monkey_virus Mason-Pfizer monkey virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D4L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2D4L 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]] 1.7Å</td></tr> | |||
- | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene></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=2d4l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d4l OCA], [https://pdbe.org/2d4l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2d4l RCSB], [https://www.ebi.ac.uk/pdbsum/2d4l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2d4l ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/PRO_MPMV PRO_MPMV] Matrix protein. Nucleocapsid protein p14: Nucleocapsid protein. Capsid protein. The aspartyl protease mediates proteolytic cleavages of Gag and Gag-Pol polyproteins during or shortly after the release of the virion from the plasma membrane. Cleavages take place as an ordered, step-wise cascade to yield mature proteins. This process is called maturation. Displays maximal activity during the budding process just prior to particle release from the cell.[PROSITE-ProRule:PRU00275]<ref>PMID:9636364</ref> The aspartyl protease mediates proteolytic cleavages of Gag and Gag-Pol polyproteins during or shortly after the release of the virion from the plasma membrane. Cleavages take place as an ordered, step-wise cascade to yield mature proteins. This process is called maturation. Displays maximal activity during the budding process just prior to particle release from the cell.[PROSITE-ProRule:PRU00275]<ref>PMID:9636364</ref> Enhances the activity of the reverse transcriptase. May be part of the mature RT.<ref>PMID:22171253</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/d4/2d4l_consurf.spt"</scriptWhenChecked> | |||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=2d4l ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
The homotrimeric fusion protein nucleocapsid (NC)-dUTPase combines domains that participate in RNA/DNA folding, reverse transcription, and DNA repair in Mason-Pfizer monkey betaretrovirus infected cells. The structural organization of the fusion protein remained obscured by the N- and C-terminal flexible segments of dUTPase and the linker region connecting the two domains that are invisible in electron density maps. Small-angle X-ray scattering reveals that upon oligonucleotide binding the NC domains adopt the trimeric symmetry of dUTPase. High-resolution X-ray structures together with molecular modeling indicate that fusion with NC domains dramatically alters the conformation of the flexible C-terminus by perturbing the orientation of a critical beta-strand. Consequently, the C-terminal segment is capable of double backing upon the active site of its own monomer and stabilized by non-covalent interactions formed with the N-terminal segment. This co-folding of the dUTPase terminal segments, not observable in other homologous enzymes, is due to the presence of the fused NC domain. Structural and genomic advantages of fusing the NC domain to a shortened dUTPase in betaretroviruses and the possible physiological consequences are envisaged. | |||
Flexible segments modulate co-folding of dUTPase and nucleocapsid proteins.,Nemeth-Pongracz V, Barabas O, Fuxreiter M, Simon I, Pichova I, Rumlova M, Zabranska H, Svergun D, Petoukhov M, Harmat V, Klement E, Hunyadi-Gulyas E, Medzihradszky KF, Konya E, Vertessy BG Nucleic Acids Res. 2007;35(2):495-505. Epub 2006 Dec 14. PMID:17169987<ref>PMID:17169987</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 2d4l" style="background-color:#fffaf0;"></div> | |||
== | ==See Also== | ||
*[[DUTPase 3D structures|DUTPase 3D structures]] | |||
[[Category: Mason- | == References == | ||
<references/> | |||
__TOC__ | |||
[[Category: Barabas | </StructureSection> | ||
[[Category: Nemeth | [[Category: Large Structures]] | ||
[[Category: Vertessy | [[Category: Mason-Pfizer monkey virus]] | ||
[[Category: Barabas O]] | |||
[[Category: Nemeth V]] | |||
[[Category: Vertessy GB]] | |||
Latest revision as of 10:50, 23 October 2024
Crystal structure of truncated in C-terminal M-PMV dUTPaseCrystal structure of truncated in C-terminal M-PMV dUTPase
Structural highlights
FunctionPRO_MPMV Matrix protein. Nucleocapsid protein p14: Nucleocapsid protein. Capsid protein. The aspartyl protease mediates proteolytic cleavages of Gag and Gag-Pol polyproteins during or shortly after the release of the virion from the plasma membrane. Cleavages take place as an ordered, step-wise cascade to yield mature proteins. This process is called maturation. Displays maximal activity during the budding process just prior to particle release from the cell.[PROSITE-ProRule:PRU00275][1] The aspartyl protease mediates proteolytic cleavages of Gag and Gag-Pol polyproteins during or shortly after the release of the virion from the plasma membrane. Cleavages take place as an ordered, step-wise cascade to yield mature proteins. This process is called maturation. Displays maximal activity during the budding process just prior to particle release from the cell.[PROSITE-ProRule:PRU00275][2] Enhances the activity of the reverse transcriptase. May be part of the mature RT.[3] 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 homotrimeric fusion protein nucleocapsid (NC)-dUTPase combines domains that participate in RNA/DNA folding, reverse transcription, and DNA repair in Mason-Pfizer monkey betaretrovirus infected cells. The structural organization of the fusion protein remained obscured by the N- and C-terminal flexible segments of dUTPase and the linker region connecting the two domains that are invisible in electron density maps. Small-angle X-ray scattering reveals that upon oligonucleotide binding the NC domains adopt the trimeric symmetry of dUTPase. High-resolution X-ray structures together with molecular modeling indicate that fusion with NC domains dramatically alters the conformation of the flexible C-terminus by perturbing the orientation of a critical beta-strand. Consequently, the C-terminal segment is capable of double backing upon the active site of its own monomer and stabilized by non-covalent interactions formed with the N-terminal segment. This co-folding of the dUTPase terminal segments, not observable in other homologous enzymes, is due to the presence of the fused NC domain. Structural and genomic advantages of fusing the NC domain to a shortened dUTPase in betaretroviruses and the possible physiological consequences are envisaged. Flexible segments modulate co-folding of dUTPase and nucleocapsid proteins.,Nemeth-Pongracz V, Barabas O, Fuxreiter M, Simon I, Pichova I, Rumlova M, Zabranska H, Svergun D, Petoukhov M, Harmat V, Klement E, Hunyadi-Gulyas E, Medzihradszky KF, Konya E, Vertessy BG Nucleic Acids Res. 2007;35(2):495-505. Epub 2006 Dec 14. PMID:17169987[4] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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