This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

3f56

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Current revision

The structure of a previously undetected carboxysome shell protein: CsoS1D from Prochlorococcus marinus MED4

Structural highlights

3f56 is a 6 chain structure with sequence from Prochlorococcus marinus subsp. pastoris str. CCMP1986. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.303Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

CSOSD_PROMP Part of the carboxysome shell, a polyhedral inclusion where RuBisCO (ribulose bisphosphate carboxylase, cbbL-cbbS) is sequestered (Probable) (PubMed:22155772). It may control transport of RuBisCO reactants in and out of the carboxysome (Probable). There are estimated to be 6 CsoS1D hexamers per carboxysome (PubMed:22155772).^[1] ^[2]

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

Bacterial microcompartments (BMCs) are polyhedral bodies, composed entirely of proteins, that function as organelles in bacteria; they promote subcellular processes by encapsulating and co-localizing targeted enzymes with their substrates. The best-characterized BMC is the carboxysome, a central part of the carbon-concentrating mechanism that greatly enhances carbon fixation in cyanobacteria and some chemoautotrophs. Here we report the first structural insights into the carboxysome of Prochlorococcus, the numerically dominant cyanobacterium in the world's oligotrophic oceans. Bioinformatic methods, substantiated by analysis of gene expression data, were used to identify a new carboxysome shell component, CsoS1D, in the genome of Prochlorococcus strain MED4; orthologs were subsequently found in all cyanobacteria. Two independent crystal structures of Prochlorococcus MED4 CsoS1D reveal three features not seen in any BMC-domain protein structure solved to date. First, CsoS1D is composed of a fused pair of BMC domains. Second, this double-domain protein trimerizes to form a novel pseudohexameric building block for incorporation into the carboxysome shell, and the trimers further dimerize, forming a two-tiered shell building block. Third, and most strikingly, the large pore formed at the 3-fold axis of symmetry appears to be gated. Each dimer of trimers contains one trimer with an open pore and one whose pore is obstructed due to side-chain conformations of two residues that are invariant among all CsoS1D orthologs. This is the first evidence of the potential for gated transport across the carboxysome shell and reveals a new type of building block for BMC shells.

Identification and structural analysis of a novel carboxysome shell protein with implications for metabolite transport.,Klein MG, Zwart P, Bagby SC, Cai F, Chisholm SW, Heinhorst S, Cannon GC, Kerfeld CA J Mol Biol. 2009 Sep 18;392(2):319-33. Epub 2009 Mar 27. PMID:19328811^[3]

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

References

↑ Roberts EW, Cai F, Kerfeld CA, Cannon GC, Heinhorst S. Isolation and characterization of the Prochlorococcus carboxysome reveal the presence of the novel shell protein CsoS1D. J Bacteriol. 2012 Feb;194(4):787-95. PMID:22155772 doi:10.1128/JB.06444-11
↑ Klein MG, Zwart P, Bagby SC, Cai F, Chisholm SW, Heinhorst S, Cannon GC, Kerfeld CA. Identification and structural analysis of a novel carboxysome shell protein with implications for metabolite transport. J Mol Biol. 2009 Sep 18;392(2):319-33. Epub 2009 Mar 27. PMID:19328811 doi:10.1016/j.jmb.2009.03.056
↑ Klein MG, Zwart P, Bagby SC, Cai F, Chisholm SW, Heinhorst S, Cannon GC, Kerfeld CA. Identification and structural analysis of a novel carboxysome shell protein with implications for metabolite transport. J Mol Biol. 2009 Sep 18;392(2):319-33. Epub 2009 Mar 27. PMID:19328811 doi:10.1016/j.jmb.2009.03.056

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3f56"

Categories: Large Structures | Prochlorococcus marinus subsp. pastoris str. CCMP1986 | Kerfeld CA | Klein MG | Zwart P

@@ Line 1: / Line 1: @@
 ==The structure of a previously undetected carboxysome shell protein: CsoS1D from Prochlorococcus marinus MED4==
-<StructureSection load='3f56' size='340' side='right' caption='[[3f56]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
+<StructureSection load='3f56' size='340' side='right'caption='[[3f56]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3f56]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Promp Promp]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3F56 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3F56 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3f56]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Prochlorococcus_marinus_subsp._pastoris_str._CCMP1986 Prochlorococcus marinus subsp. pastoris str. CCMP1986]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3F56 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3F56 FirstGlance]. <br>
-</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>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.303&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PMM0547 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=59919 PROMP])</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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3f56 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3f56 OCA], [http://pdbe.org/3f56 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3f56 RCSB], [http://www.ebi.ac.uk/pdbsum/3f56 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3f56 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=3f56 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3f56 OCA], [https://pdbe.org/3f56 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3f56 RCSB], [https://www.ebi.ac.uk/pdbsum/3f56 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3f56 ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/CSOSD_PROMP CSOSD_PROMP] Part of the carboxysome shell, a polyhedral inclusion where RuBisCO (ribulose bisphosphate carboxylase, cbbL-cbbS) is sequestered (Probable) (PubMed:22155772). It may control transport of RuBisCO reactants in and out of the carboxysome (Probable). There are estimated to be 6 CsoS1D hexamers per carboxysome (PubMed:22155772).<ref>PMID:22155772</ref> <ref>PMID:19328811</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/f5/3f56_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/f5/3f56_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 31: / Line 33: @@
 __TOC__
 </StructureSection>
-[[Category: Promp]]
+[[Category: Large Structures]]
-[[Category: Kerfeld, C A]]
+[[Category: Prochlorococcus marinus subsp. pastoris str. CCMP1986]]
-[[Category: Klein, M G]]
+[[Category: Kerfeld CA]]
-[[Category: Zwart, P]]
+[[Category: Klein MG]]
-[[Category: Carboxysome]]
+[[Category: Zwart P]]
-[[Category: Hexamer]]
-[[Category: Structural protein]]

3f56

From Proteopedia

Current revision

The structure of a previously undetected carboxysome shell protein: CsoS1D from Prochlorococcus marinus MED4

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox