2l3u: Difference between revisions

From Proteopedia
Jump to navigationJump to search
← Older edit
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,328,572 edits
No edit summary
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,328,572 edits
No edit summary
 
Line 1: Line 1:


==Solution Structure of Domain IV from the YbbR family protein of Desulfitobacterium hafniense: Northeast Structural Genomics Consortium target DhR29A==
==Solution Structure of Domain IV from the YbbR family protein of Desulfitobacterium hafniense: Northeast Structural Genomics Consortium target DhR29A==
<StructureSection load='2l3u' size='340' side='right'caption='[[2l3u]], [[NMR_Ensembles_of_Models | 10 NMR models]]' scene=''>
<StructureSection load='2l3u' size='340' side='right'caption='[[2l3u]]' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[2l3u]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Deshd Deshd]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2kps 2kps]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2L3U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2L3U FirstGlance]. <br>
<table><tr><td colspan='2'>[[2l3u]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Desulfitobacterium_hafniense_DCB-2 Desulfitobacterium hafniense DCB-2]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2kps 2kps]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2L3U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2L3U FirstGlance]. <br>
</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Dhaf_0833 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=272564 DESHD])</td></tr>
</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=2l3u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2l3u OCA], [https://pdbe.org/2l3u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2l3u RCSB], [https://www.ebi.ac.uk/pdbsum/2l3u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2l3u ProSAT]</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=2l3u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2l3u OCA], [https://pdbe.org/2l3u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2l3u RCSB], [https://www.ebi.ac.uk/pdbsum/2l3u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2l3u ProSAT]</span></td></tr>
</table>
</table>
== Function ==
[https://www.uniprot.org/uniprot/B8FX10_DESHD B8FX10_DESHD]
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
Line 17: Line 19:
</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=2l3u ConSurf].
</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=2l3u ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
YbbR domains are widespread throughout Eubacteria and are expressed as monomeric units, linked in tandem repeats or cotranslated with other domains. Although the precise role of these domains remains undefined, the location of the multiple YbbR domain-encoding ybbR gene in the Bacillus subtilis glmM operon and its previous identification as a substrate for a surfactin-type phosphopantetheinyl transferase suggests a role in cell growth, division, and virulence. To further characterize the YbbR domains, structures of two of the four domains (I and IV) from the YbbR-like protein of Desulfitobacterium hafniense Y51 were solved by solution nuclear magnetic resonance and X-ray crystallography. The structures show the domains to have nearly identical topologies despite a low amino acid identity (23%). The topology is dominated by beta-strands, roughly following a "figure 8" pattern with some strands coiling around the domain perimeter and others crossing the center. A similar topology is found in the C-terminal domain of two stress-responsive bacterial ribosomal proteins, TL5 and L25. Based on these models, a structurally guided amino acid alignment identifies features of the YbbR domains that are not evident from naive amino acid sequence alignments. A structurally conserved cis-proline (cis-Pro) residue was identified in both domains, though the local structure in the immediate vicinities surrounding this residue differed between the two models. The conservation and location of this cis-Pro, plus anchoring Val residues, suggest this motif may be significant to protein function.
Structures of domains I and IV from YbbR are representative of a widely distributed protein family.,Barb AW, Cort JR, Seetharaman J, Lew S, Lee HW, Acton T, Xiao R, Kennedy MA, Tong L, Montelione GT, Prestegard JH Protein Sci. 2011 Feb;20(2):396-405. doi: 10.1002/pro.571. Epub 2011 Jan, 18. PMID:21154411<ref>PMID:21154411</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 2l3u" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Deshd]]
[[Category: Desulfitobacterium hafniense DCB-2]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Acton, T B]]
[[Category: Acton TB]]
[[Category: Barb, A W]]
[[Category: Barb AW]]
[[Category: Belote, R L]]
[[Category: Belote RL]]
[[Category: Ciccosanti, C]]
[[Category: Ciccosanti C]]
[[Category: Everett, J K]]
[[Category: Everett JK]]
[[Category: Hamilton, K]]
[[Category: Hamilton K]]
[[Category: Lee, H]]
[[Category: Lee H]]
[[Category: Montelione, G T]]
[[Category: Montelione GT]]
[[Category: Structural genomic]]
[[Category: Prestegard JH]]
[[Category: Prestegard, J H]]
[[Category: Xiao R]]
[[Category: Xiao, R]]
[[Category: Beta strand]]
[[Category: Figure 8]]
[[Category: Figure eight]]
[[Category: Nesg]]
[[Category: PSI, Protein structure initiative]]
[[Category: Psi-biology]]
[[Category: Unknown function]]
Retrieved from "https://proteopedia.org/2l3u"