3h8y

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of carboxysome small shell protein CsoS1C from Halothiobacillus neapolitanus

Structural highlights

3h8y is a 1 chain structure with sequence from Halothiobacillus neapolitanus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.51Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

CSOSC_HALNC One of shell proteins of the carboxysome, a polyhedral inclusion where RuBisCO (ribulose bisphosphate carboxylase, ccbL-ccbS) is sequestered. Assembles into hexamers which make sheets that form the facets of the polyhedral carboxysome (Probable). The shell probably limits the diffusion of CO(2) into and out of the carboxysome (Probable). There are estimated to be 2970 CsoS1A/CsoS1C proteins per carboxysome (the proteins differ by only 1 residue) (Ref.4).^[1] ^[2] ^[3] Unlike beta-carboxysomes, alpha-carboxysomes (Cb) can form without cargo protein. CsoS2 is essential for Cb formation and is also capable of targeting foreign proteins to the Cb. The Cb shell assembles with the aid of CsoS2; CsoS1A, CsoS1B and CsoS1C form the majority of the shell while CsoS4A and CsoS4B form vertices. CsoS1D forms pseudohexamers that probably control metabolite flux into and out of the shell.^[4]

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

Lattice-translocation or crystal order-disorder phenomena occur when some layers or groups of molecules in a crystal are randomly displaced relative to other groups of molecules by a discrete set of vectors. In previous work, the effects of lattice translocation on diffraction intensities have been corrected by considering that the observed intensities are the product of the intensities from an ideal crystal (lacking disorder) multiplied by the squared magnitude of the Fourier transform of the set of translocation vectors. Here, the structure determination is presented of carboxysome protein CsoS1C from Halothiobacillius neapolitanus in a crystal exhibiting a lattice translocation with unique features. The diffraction data are fully accounted for by a crystal unit cell composed of two layers of cyclic protein hexamers. The first layer is fully ordered (i.e. has one fixed position), while the second layer randomly takes one of three alternative positions whose displacements are related to each other by threefold symmetry. Remarkably, the highest symmetry present in the crystal is P3, yet the intensity data (and the Patterson map) obey 6/m instead of \overline 3 symmetry; the intensities exceed the symmetry expected from combining the crystal space group with an inversion center. The origin of this rare phenomenon, known as symmetry enhancement, is discussed and shown to be possible even for a perfectly ordered crystal. The lattice-translocation treatment described here may be useful in analyzing other cases of disorder in which layers or groups of molecules are shifted in multiple symmetry-related directions.

Analysis of lattice-translocation disorder in the layered hexagonal structure of carboxysome shell protein CsoS1C.,Tsai Y, Sawaya MR, Yeates TO Acta Crystallogr D Biol Crystallogr. 2009 Sep;65(Pt 9):980-8. Epub 2009, Aug 14. PMID:19690376^[5]

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

References

↑ Bonacci W, Teng PK, Afonso B, Niederholtmeyer H, Grob P, Silver PA, Savage DF. Modularity of a carbon-fixing protein organelle. Proc Natl Acad Sci U S A. 2012 Jan 10;109(2):478-83. doi:, 10.1073/pnas.1108557109. Epub 2011 Dec 19. PMID:22184212 doi:http://dx.doi.org/10.1073/pnas.1108557109
↑ Dou Z, Heinhorst S, Williams EB, Murin CD, Shively JM, Cannon GC. CO2 fixation kinetics of Halothiobacillus neapolitanus mutant carboxysomes lacking carbonic anhydrase suggest the shell acts as a diffusional barrier for CO2. J Biol Chem. 2008 Apr 18;283(16):10377-84. PMID:18258595 doi:10.1074/jbc.M709285200
↑ Tsai Y, Sawaya MR, Yeates TO. Analysis of lattice-translocation disorder in the layered hexagonal structure of carboxysome shell protein CsoS1C. Acta Crystallogr D Biol Crystallogr. 2009 Sep;65(Pt 9):980-8. Epub 2009, Aug 14. PMID:19690376 doi:10.1107/S0907444909025153
↑ Li T, Jiang Q, Huang J, Aitchison CM, Huang F, Yang M, Dykes GF, He HL, Wang Q, Sprick RS, Cooper AI, Liu LN. Reprogramming bacterial protein organelles as a nanoreactor for hydrogen production. Nat Commun. 2020 Oct 28;11(1):5448. doi: 10.1038/s41467-020-19280-0. PMID:33116131 doi:http://dx.doi.org/10.1038/s41467-020-19280-0
↑ Tsai Y, Sawaya MR, Yeates TO. Analysis of lattice-translocation disorder in the layered hexagonal structure of carboxysome shell protein CsoS1C. Acta Crystallogr D Biol Crystallogr. 2009 Sep;65(Pt 9):980-8. Epub 2009, Aug 14. PMID:19690376 doi:10.1107/S0907444909025153

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/3h8y"

Categories: Halothiobacillus neapolitanus | Large Structures | Sawaya MR | Tsai Y | Yeates TO

@@ Line 3: / Line 3: @@
 <StructureSection load='3h8y' size='340' side='right'caption='[[3h8y]], [[Resolution|resolution]] 2.51&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3h8y]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"thiobacillus_x"_parker_and_prisk_1953 "thiobacillus x" parker and prisk 1953]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3H8Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3H8Y FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3h8y]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Halothiobacillus_neapolitanus Halothiobacillus neapolitanus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3H8Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3H8Y FirstGlance]. <br>
-</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">csoS1C ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=927 "Thiobacillus X" Parker and Prisk 1953])</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]] 2.51&#8491;</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=3h8y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3h8y OCA], [https://pdbe.org/3h8y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3h8y RCSB], [https://www.ebi.ac.uk/pdbsum/3h8y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3h8y ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/CSOC_HALNC CSOC_HALNC]] Involved in the formation of the carboxysome, a polyhedral inclusion where RuBisCO is sequestered.
+[https://www.uniprot.org/uniprot/CSOSC_HALNC CSOSC_HALNC] One of shell proteins of the carboxysome, a polyhedral inclusion where RuBisCO (ribulose bisphosphate carboxylase, ccbL-ccbS) is sequestered. Assembles into hexamers which make sheets that form the facets of the polyhedral carboxysome (Probable). The shell probably limits the diffusion of CO(2) into and out of the carboxysome (Probable). There are estimated to be 2970 CsoS1A/CsoS1C proteins per carboxysome (the proteins differ by only 1 residue) (Ref.4).<ref>PMID:22184212</ref> <ref>PMID:18258595</ref> <ref>PMID:19690376</ref>   Unlike beta-carboxysomes, alpha-carboxysomes (Cb) can form without cargo protein. CsoS2 is essential for Cb formation and is also capable of targeting foreign proteins to the Cb. The Cb shell assembles with the aid of CsoS2; CsoS1A, CsoS1B and CsoS1C form the majority of the shell while CsoS4A and CsoS4B form vertices. CsoS1D forms pseudohexamers that probably control metabolite flux into and out of the shell.<ref>PMID:33116131</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 32: / Line 32: @@
 __TOC__
 </StructureSection>
-[[Category: Thiobacillus x parker and prisk 1953]]
+[[Category: Halothiobacillus neapolitanus]]
 [[Category: Large Structures]]
-[[Category: Sawaya, M R]]
+[[Category: Sawaya MR]]
-[[Category: Tsai, Y]]
+[[Category: Tsai Y]]
-[[Category: Yeates, T O]]
+[[Category: Yeates TO]]
-[[Category: Bacterial microcompartment domain]]
-[[Category: Structural protein]]

3h8y

From Proteopedia

Current revision

Crystal structure of carboxysome small shell protein CsoS1C from Halothiobacillus neapolitanus

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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