1v8o: Difference between revisions
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New page: left|200px<br /><applet load="1v8o" size="450" color="white" frame="true" align="right" spinBox="true" caption="1v8o, resolution 2.80Å" /> '''Crystal Structure of... |
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== | ==Crystal Structure of PAE2754 from Pyrobaculum aerophilum== | ||
Genome sequencing projects have focused attention on the problem of | <StructureSection load='1v8o' size='340' side='right'caption='[[1v8o]], [[Resolution|resolution]] 2.80Å' scene=''> | ||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[1v8o]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrobaculum_aerophilum Pyrobaculum aerophilum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1V8O OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1V8O 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]] 2.8Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</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=1v8o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1v8o OCA], [https://pdbe.org/1v8o PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1v8o RCSB], [https://www.ebi.ac.uk/pdbsum/1v8o PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1v8o ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/VAPC9_PYRAE VAPC9_PYRAE] Toxic component of a toxin-antitoxin (TA) module (By similarity). Has ribonuclease activity. Has a slow ssDNA exonuclease activity.<ref>PMID:22539524</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/v8/1v8o_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=1v8o ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Genome sequencing projects have focused attention on the problem of discovering the functions of protein domains that are widely distributed throughout living species but which are, as yet, largely uncharacterized. One such example is the PIN domain, found in eukaryotes, bacteria, and Archaea, and with suggested roles in signaling, RNase editing, and/or nucleotide binding. The first reported crystal structure of a PIN domain (open reading frame PAE2754, derived from the crenarchaeon, Pyrobaculum aerophilum) has been determined to 2.5 A resolution and is presented here. Mapping conserved residues from a multiple sequence alignment onto the structure identifies a putative active site. The discovery of distant structural homology with several exonucleases, including T4 phage RNase H and flap endonuclease (FEN1), further suggests a likely function for PIN domains as Mg2+-dependent exonucleases, a hypothesis that we have confirmed in vitro. The tetrameric structure of PAE2754, with the active sites inside a tunnel, suggests a mechanism for selective cleavage of single-stranded overhangs or flap structures. These results indicate likely DNA or RNA editing roles for prokaryotic PIN domains, which are strikingly numerous in thermophiles, and in organisms such as Mycobacterium tuberculosis. They also support previous hypotheses that eukaryotic PIN domains participate in RNAi and nonsense-mediated RNA degradation. | |||
Distant structural homology leads to the functional characterization of an archaeal PIN domain as an exonuclease.,Arcus VL, Backbro K, Roos A, Daniel EL, Baker EN J Biol Chem. 2004 Apr 16;279(16):16471-8. Epub 2004 Jan 20. PMID:14734548<ref>PMID:14734548</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 1v8o" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Pyrobaculum aerophilum]] | [[Category: Pyrobaculum aerophilum]] | ||
[[Category: Arcus VL]] | |||
[[Category: Arcus | [[Category: Backbro K]] | ||
[[Category: Backbro | [[Category: Baker EN]] | ||
[[Category: Baker | [[Category: Daniel EL]] | ||
[[Category: Daniel | [[Category: Roos A]] | ||
[[Category: Roos | |||
Latest revision as of 07:57, 17 October 2024
Crystal Structure of PAE2754 from Pyrobaculum aerophilumCrystal Structure of PAE2754 from Pyrobaculum aerophilum
Structural highlights
FunctionVAPC9_PYRAE Toxic component of a toxin-antitoxin (TA) module (By similarity). Has ribonuclease activity. Has a slow ssDNA exonuclease activity.[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 PubMedGenome sequencing projects have focused attention on the problem of discovering the functions of protein domains that are widely distributed throughout living species but which are, as yet, largely uncharacterized. One such example is the PIN domain, found in eukaryotes, bacteria, and Archaea, and with suggested roles in signaling, RNase editing, and/or nucleotide binding. The first reported crystal structure of a PIN domain (open reading frame PAE2754, derived from the crenarchaeon, Pyrobaculum aerophilum) has been determined to 2.5 A resolution and is presented here. Mapping conserved residues from a multiple sequence alignment onto the structure identifies a putative active site. The discovery of distant structural homology with several exonucleases, including T4 phage RNase H and flap endonuclease (FEN1), further suggests a likely function for PIN domains as Mg2+-dependent exonucleases, a hypothesis that we have confirmed in vitro. The tetrameric structure of PAE2754, with the active sites inside a tunnel, suggests a mechanism for selective cleavage of single-stranded overhangs or flap structures. These results indicate likely DNA or RNA editing roles for prokaryotic PIN domains, which are strikingly numerous in thermophiles, and in organisms such as Mycobacterium tuberculosis. They also support previous hypotheses that eukaryotic PIN domains participate in RNAi and nonsense-mediated RNA degradation. Distant structural homology leads to the functional characterization of an archaeal PIN domain as an exonuclease.,Arcus VL, Backbro K, Roos A, Daniel EL, Baker EN J Biol Chem. 2004 Apr 16;279(16):16471-8. Epub 2004 Jan 20. PMID:14734548[2] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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