2ook

From Proteopedia

(Difference between revisions)

Revision as of 13:01, 9 June 2021

Crystal structure of a protein with unknown function (YP_749275.1) from Shewanella Frigidimarina NCIMB 400 at 1.80 A resolution

Structural highlights

2ook is a 2 chain structure with sequence from Shefn. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
NonStd Res:
Gene:	YP_749275.1, Sfri_0576 (SHEFN)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT, TOPSAN

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 PubMed

The crystal structures of the proteins encoded by the YP_749275.1 and YP_001095227.1 genes from Shewanella frigidimarina and S. loihica, respectively, have been determined at 1.8 and 2.25 A resolution, respectively. These proteins are members of a novel family of bacterial proteins that adopt the alpha/beta SpoIIAA-like fold found in STAS and CRAL-TRIO domains. Despite sharing 54% sequence identity, these two proteins adopt distinct conformations arising from different dispositions of their alpha2 and alpha3 helices. In the `open' conformation (YP_001095227.1), these helices are 15 A apart, leading to the creation of a deep nonpolar cavity. In the `closed' structure (YP_749275.1), the helices partially unfold and rearrange, occluding the cavity and decreasing the solvent-exposed hydrophobic surface. These two complementary structures are reminiscent of the conformational switch in CRAL-TRIO carriers of hydrophobic compounds. It is suggested that both proteins may associate with the lipid bilayer in their `open' monomeric state by inserting their amphiphilic helices, alpha2 and alpha3, into the lipid bilayer. These bacterial proteins may function as carriers of nonpolar substances or as interfacially activated enzymes.

Open and closed conformations of two SpoIIAA-like proteins (YP_749275.1 and YP_001095227.1) provide insights into membrane association and ligand binding.,Kumar A, Lomize A, Jin KK, Carlton D, Miller MD, Jaroszewski L, Abdubek P, Astakhova T, Axelrod HL, Chiu HJ, Clayton T, Das D, Deller MC, Duan L, Feuerhelm J, Grant JC, Grzechnik A, Han GW, Klock HE, Knuth MW, Kozbial P, Krishna SS, Marciano D, McMullan D, Morse AT, Nigoghossian E, Okach L, Reyes R, Rife CL, Sefcovic N, Tien HJ, Trame CB, van den Bedem H, Weekes D, Xu Q, Hodgson KO, Wooley J, Elsliger MA, Deacon AM, Godzik A, Lesley SA, Wilson IA Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010 Oct 1;66(Pt, 10):1245-53. Epub 2009 Dec 8. PMID:20944218^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Kumar A, Lomize A, Jin KK, Carlton D, Miller MD, Jaroszewski L, Abdubek P, Astakhova T, Axelrod HL, Chiu HJ, Clayton T, Das D, Deller MC, Duan L, Feuerhelm J, Grant JC, Grzechnik A, Han GW, Klock HE, Knuth MW, Kozbial P, Krishna SS, Marciano D, McMullan D, Morse AT, Nigoghossian E, Okach L, Reyes R, Rife CL, Sefcovic N, Tien HJ, Trame CB, van den Bedem H, Weekes D, Xu Q, Hodgson KO, Wooley J, Elsliger MA, Deacon AM, Godzik A, Lesley SA, Wilson IA. Open and closed conformations of two SpoIIAA-like proteins (YP_749275.1 and YP_001095227.1) provide insights into membrane association and ligand binding. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010 Oct 1;66(Pt, 10):1245-53. Epub 2009 Dec 8. PMID:20944218 doi:10.1107/S1744309109042481

1 Structural highlights
2 Evolutionary Conservation
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2ook"

@@ Line 1: / Line 1: @@
 ==Crystal structure of a protein with unknown function (YP_749275.1) from Shewanella Frigidimarina NCIMB 400 at 1.80 A resolution==
-<StructureSection load='2ook' size='340' side='right' caption='[[2ook]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
+<StructureSection load='2ook' size='340' side='right'caption='[[2ook]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2ook]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Shefn Shefn]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OOK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2OOK FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2ook]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Shefn Shefn]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OOK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2OOK FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>
 <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">YP_749275.1, Sfri_0576 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=318167 SHEFN])</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">YP_749275.1, Sfri_0576 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=318167 SHEFN])</td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ook FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ook OCA], [http://pdbe.org/2ook PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2ook RCSB], [http://www.ebi.ac.uk/pdbsum/2ook PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2ook ProSAT], [http://www.topsan.org/Proteins/JCSG/2ook TOPSAN]</span></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=2ook FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ook OCA], [https://pdbe.org/2ook PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ook RCSB], [https://www.ebi.ac.uk/pdbsum/2ook PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ook ProSAT], [https://www.topsan.org/Proteins/JCSG/2ook TOPSAN]</span></td></tr>
 </table>
 == Evolutionary Conservation ==
@@ Line 13: / Line 13: @@
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/oo/2ook_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/oo/2ook_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 32: / Line 32: @@
 __TOC__
 </StructureSection>
+[[Category: Large Structures]]
 [[Category: Shefn]]
 [[Category: Structural genomic]]

2ook

From Proteopedia

Revision as of 13:01, 9 June 2021

Crystal structure of a protein with unknown function (YP_749275.1) from Shewanella Frigidimarina NCIMB 400 at 1.80 A resolution

Structural highlights

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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