2fdo: Difference between revisions
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< | ==Crystal Structure of the Conserved Protein of Unknown Function AF2331 from Archaeoglobus fulgidus DSM 4304 Reveals a New Type of Alpha/Beta Fold== | ||
<StructureSection load='2fdo' size='340' side='right'caption='[[2fdo]], [[Resolution|resolution]] 2.40Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[2fdo]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Archaeoglobus_fulgidus_DSM_4304 Archaeoglobus fulgidus DSM 4304]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FDO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2FDO 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]] 2.4Å</td></tr> | |||
- | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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=2fdo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fdo OCA], [https://pdbe.org/2fdo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2fdo RCSB], [https://www.ebi.ac.uk/pdbsum/2fdo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2fdo ProSAT], [https://www.topsan.org/Proteins/MCSG/2fdo TOPSAN]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/Y2331_ARCFU Y2331_ARCFU] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
The structure of AF2331, a 11-kDa orphan protein of unknown function from Archaeoglobus fulgidus, was solved by Se-Met MAD to 2.4 A resolution. The structure consists of an alpha + beta fold formed by an unusual homodimer, where the two core beta-sheets are interdigitated, containing strands alternating from both subunits. The decrease in solvent-accessible surface area upon dimerization is unusually large (3960 A(2)) for a protein of its size. The percentage of the total surface area buried in the interface (41.1%) is one of the largest observed in a nonredundant set of homodimers in the PDB and is above the mean for nearly all other types of homo-oligomers. AF2331 has no sequence homologs, and no structure similar to AF2331 could be found in the PDB using the CE, TM-align, DALI, or SSM packages. The protein has been identified in Pfam 23.0 as the archetype of a new superfamily and is topologically dissimilar to all other proteins with the "3-Layer (BBA) Sandwich" fold in CATH. Therefore, we propose that AF2331 forms a novel alpha + beta fold. AF2331 contains multiple negatively charged surface clusters and is located on the same operon as the basic protein AF2330. We hypothesize that AF2331 and AF2330 may form a charge-stabilized complex in vivo, though the role of the negatively charged surface clusters is not clear. | |||
The crystal structure of the AF2331 protein from Archaeoglobus fulgidus DSM 4304 forms an unusual interdigitated dimer with a new type of alpha + beta fold.,Wang S, Kirillova O, Chruszcz M, Gront D, Zimmerman MD, Cymborowski MT, Shumilin IA, Skarina T, Gorodichtchenskaia E, Savchenko A, Edwards AM, Minor W Protein Sci. 2009 Nov;18(11):2410-9. PMID:19768810<ref>PMID:19768810</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 2fdo" style="background-color:#fffaf0;"></div> | |||
[[Category: Archaeoglobus fulgidus]] | == References == | ||
[[Category: | <references/> | ||
[[Category: Chruszcz | __TOC__ | ||
[[Category: Cymborowski | </StructureSection> | ||
[[Category: Edwards | [[Category: Archaeoglobus fulgidus DSM 4304]] | ||
[[Category: Gorodichtchenskaia | [[Category: Large Structures]] | ||
[[Category: | [[Category: Chruszcz M]] | ||
[[Category: | [[Category: Cymborowski MT]] | ||
[[Category: Minor | [[Category: Edwards AM]] | ||
[[Category: Savchenko | [[Category: Gorodichtchenskaia E]] | ||
[[Category: Skarina | [[Category: Joachimiak A]] | ||
[[Category: Wang | [[Category: Kirillova O]] | ||
[[Category: Minor W]] | |||
[[Category: Savchenko A]] | |||
[[Category: Skarina T]] | |||
[[Category: Wang S]] | |||
Latest revision as of 15:44, 17 January 2024
Crystal Structure of the Conserved Protein of Unknown Function AF2331 from Archaeoglobus fulgidus DSM 4304 Reveals a New Type of Alpha/Beta FoldCrystal Structure of the Conserved Protein of Unknown Function AF2331 from Archaeoglobus fulgidus DSM 4304 Reveals a New Type of Alpha/Beta Fold
Structural highlights
FunctionPublication Abstract from PubMedThe structure of AF2331, a 11-kDa orphan protein of unknown function from Archaeoglobus fulgidus, was solved by Se-Met MAD to 2.4 A resolution. The structure consists of an alpha + beta fold formed by an unusual homodimer, where the two core beta-sheets are interdigitated, containing strands alternating from both subunits. The decrease in solvent-accessible surface area upon dimerization is unusually large (3960 A(2)) for a protein of its size. The percentage of the total surface area buried in the interface (41.1%) is one of the largest observed in a nonredundant set of homodimers in the PDB and is above the mean for nearly all other types of homo-oligomers. AF2331 has no sequence homologs, and no structure similar to AF2331 could be found in the PDB using the CE, TM-align, DALI, or SSM packages. The protein has been identified in Pfam 23.0 as the archetype of a new superfamily and is topologically dissimilar to all other proteins with the "3-Layer (BBA) Sandwich" fold in CATH. Therefore, we propose that AF2331 forms a novel alpha + beta fold. AF2331 contains multiple negatively charged surface clusters and is located on the same operon as the basic protein AF2330. We hypothesize that AF2331 and AF2330 may form a charge-stabilized complex in vivo, though the role of the negatively charged surface clusters is not clear. The crystal structure of the AF2331 protein from Archaeoglobus fulgidus DSM 4304 forms an unusual interdigitated dimer with a new type of alpha + beta fold.,Wang S, Kirillova O, Chruszcz M, Gront D, Zimmerman MD, Cymborowski MT, Shumilin IA, Skarina T, Gorodichtchenskaia E, Savchenko A, Edwards AM, Minor W Protein Sci. 2009 Nov;18(11):2410-9. PMID:19768810[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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