1sf0: Difference between revisions

From Proteopedia
Jump to navigation Jump to search
← Older edit
No edit summary
No edit summary
 
(12 intermediate revisions by the same user not shown)
Line 1: Line 1:
[[Image:1sf0.gif|left|200px]]


{{Structure
==BACKBONE SOLUTION STRUCTURE OF MIXED ALPHA/BETA PROTEIN PF1061==
|PDB= 1sf0 |SIZE=350|CAPTION= <scene name='initialview01'>1sf0</scene>
<StructureSection load='1sf0' size='340' side='right'caption='[[1sf0]]' scene=''>
|SITE=  
== Structural highlights ==
|LIGAND=  
<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>
|ACTIVITY=  
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
|GENE= PF1061 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=186497 Pyrococcus furiosus DSM 3638])
<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>
|DOMAIN=<span class='plainlinks'>[http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=PRK08364 PRK08364]</span>
</table>
|RELATEDENTRY=
== Function ==
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1sf0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1sf0 OCA], [http://www.ebi.ac.uk/pdbsum/1sf0 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1sf0 RCSB]</span>
[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>
}}
== Evolutionary Conservation ==
 
[[Image:Consurf_key_small.gif|200px|right]]
'''BACKBONE SOLUTION STRUCTURE OF MIXED ALPHA/BETA PROTEIN PF1061'''
Check<jmol>
 
  <jmolCheckbox>
 
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/sf/1sf0_consurf.spt"</scriptWhenChecked>
==Overview==
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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.
    <text>to colour the structure by Evolutionary Conservation</text>
 
  </jmolCheckbox>
==About this Structure==
</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].
1SF0 is a [[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://oca.weizmann.ac.il/oca-bin/ocashort?id=1SF0 OCA].  
<div style="clear:both"></div>
 
== References ==
==Reference==
<references/>
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://www.ncbi.nlm.nih.gov/pubmed/15704012 15704012]
__TOC__
[[Category: Pyrococcus furiosus dsm 3638]]
</StructureSection>
[[Category: Single protein]]
[[Category: Large Structures]]
[[Category: Mayer, K L.]]
[[Category: Pyrococcus furiosus DSM 3638]]
[[Category: Prestegard, J H.]]
[[Category: Mayer KL]]
[[Category: SECSG, Southeast Collaboratory for Structural Genomics.]]
[[Category: Prestegard JH]]
[[Category: Valafar, H.]]
[[Category: Valafar H]]
[[Category: nmr]]
[[Category: protein structure initiative]]
[[Category: psi]]
[[Category: residual dipolar coupling]]
[[Category: secsg]]
[[Category: southeast collaboratory for structural genomic]]
[[Category: structural genomic]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 23:41:12 2008''

Latest revision as of 09:34, 1 May 2024

BACKBONE SOLUTION STRUCTURE OF MIXED ALPHA/BETA PROTEIN PF1061BACKBONE SOLUTION STRUCTURE OF MIXED ALPHA/BETA PROTEIN PF1061

Structural highlights

1sf0 is a 1 chain structure with sequence from Pyrococcus furiosus DSM 3638. 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, TOPSAN

Function

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][1]

Evolutionary Conservation

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

References

  1. ↑ Valafar H, Mayer KL, Bougault CM, LeBlond PD, Jenney FE Jr, Brereton PS, Adams MW, Prestegard JH. Backbone solution structures of proteins using residual dipolar couplings: application to a novel structural genomics target. J Struct Funct Genomics. 2004;5(4):241-54. PMID:15704012 doi:10.1007/s10969-005-4899-5
Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA
Retrieved from "https://proteopedia.openfox.io/wiki/index.php?title=1sf0&oldid=4135154"