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New page: left|200px<br /><applet load="1sf0" size="450" color="white" frame="true" align="right" spinBox="true" caption="1sf0" /> '''BACKBONE SOLUTION STRUCTURE OF MIXED ALPHA/B...
 
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[[Image:1sf0.gif|left|200px]]<br /><applet load="1sf0" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1sf0" />
'''BACKBONE SOLUTION STRUCTURE OF MIXED ALPHA/BETA PROTEIN PF1061'''<br />


==Overview==
==BACKBONE SOLUTION STRUCTURE OF MIXED ALPHA/BETA PROTEIN PF1061==
Structural genomics (or proteomics) activities are critically dependent on, the availability of high-throughput structure determination methodology., Development of such methodology has been a particular challenge for NMR, based structure determination because of the demands for isotopic labeling, of proteins and the requirements for very long data acquisition times. We, present here a methodology that gains efficiency from a focus on, determination of backbone structures of proteins as opposed to full, structures with all sidechains in place. This focus is appropriate given, the presumption that many protein structures in the future will be built, using computational methods that start from representative fold family, structures and replace as many as 70% of the sidechains in the course of, structure determination. The methodology we present is based primarily on, residual dipolar couplings (RDCs), readily accessible NMR observables that, constrain the orientation of backbone fragments irrespective of separation, in space. A new software tool is described for the assembly of backbone, fragments under RDC constraints and an application to a structural, genomics target is presented. The target is an 8.7 kDa protein from, Pyrococcus furiosus, PF1061, that was previously not well annotated, and, had a nearest structurally characterized neighbor with only 33% sequence, identity. The structure produced shows structural similarity to this, sequence homologue, but also shows similarity to other proteins, which, suggests a functional role in sulfur transfer. Given the backbone, structure and a possible functional link this should be an ideal target, for development of modeling methods.
<StructureSection load='1sf0' size='340' side='right'caption='[[1sf0]]' scene=''>
 
== Structural highlights ==
==About this Structure==
<table><tr><td colspan='2'>[[1sf0]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_furiosus_DSM_3638 Pyrococcus furiosus DSM 3638]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SF0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1SF0 FirstGlance]. <br>
1SF0 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Pyrococcus_furiosus_dsm_3638 Pyrococcus furiosus dsm 3638]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1SF0 OCA].  
</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=1sf0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1sf0 OCA], [https://pdbe.org/1sf0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1sf0 RCSB], [https://www.ebi.ac.uk/pdbsum/1sf0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1sf0 ProSAT], [https://www.topsan.org/Proteins/SECSG/1sf0 TOPSAN]</span></td></tr>
==Reference==
</table>
Backbone solution structures of proteins using residual dipolar couplings: application to a novel structural genomics target., Valafar H, Mayer KL, Bougault CM, LeBlond PD, Jenney FE Jr, Brereton PS, Adams MW, Prestegard JH, J Struct Funct Genomics. 2004;5(4):241-54. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15704012 15704012]
== Function ==
[[Category: Pyrococcus furiosus dsm 3638]]
[https://www.uniprot.org/uniprot/SAMP2_PYRFU SAMP2_PYRFU] Functions as a protein modifier covalently attached to lysine residues of substrate proteins, as well as a sulfur carrier in tRNA thiolation. The protein modification process is termed sampylation and involves the formation of an isopeptide bond between the SAMP2 C-terminal glycine carboxylate and the epsilon-amino group of lysine residues on target proteins. Is able to form polymeric chains with itself likely at Lys-55, similar to ubiquitin and other ubiquitin-like proteins. May serve as a proteolytic signal in the cell to target proteins for degradation by proteasomes.[UniProtKB:D4GZE7]<ref>PMID:15704012</ref>
[[Category: Single protein]]
== Evolutionary Conservation ==
[[Category: Mayer, K.L.]]
[[Image:Consurf_key_small.gif|200px|right]]
[[Category: Prestegard, J.H.]]
Check<jmol>
[[Category: SECSG, Southeast.Collaboratory.for.Structural.Genomics.]]
  <jmolCheckbox>
[[Category: Valafar, H.]]
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/sf/1sf0_consurf.spt"</scriptWhenChecked>
[[Category: nmr]]
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
[[Category: protein structure initiative]]
    <text>to colour the structure by Evolutionary Conservation</text>
[[Category: psi]]
  </jmolCheckbox>
[[Category: residual dipolar couplings]]
</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=1sf0 ConSurf].
[[Category: secsg]]
<div style="clear:both"></div>
[[Category: southeast collaboratory for structural genomics]]
== References ==
[[Category: structural genomics]]
<references/>
 
__TOC__
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sun Nov 25 00:22:36 2007''
</StructureSection>
[[Category: Large Structures]]
[[Category: Pyrococcus furiosus DSM 3638]]
[[Category: Mayer KL]]
[[Category: Prestegard JH]]
[[Category: Valafar H]]
Retrieved from "https://proteopedia.org/1sf0"