3kwe

From Proteopedia

(Difference between revisions)

Current revision

Inactive truncation of the beta-carboxysomal gamma-Carbonic Anhydrase, CcmM, form 2

Structural highlights

3kwe is a 1 chain structure with sequence from Thermosynechococcus vestitus BP-1. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.1Å
Ligands:	, , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

CCMM_THEVB Functions as a scaffold protein for the assembly of beta-carboxysomes, initiates carboxysome assembly by coalescing RuBisCO (ribulose bisphosphate carboxylase, rbcL-rbcS) (Probable). Produced as a full-length and a shorter form; both forms are required for correct carboxysome assembly and growth (By similarity).[UniProtKB:Q03513]^[1] A carbonic anhydrase, catalyzes the reversible hydration of carbon dioxide. Essential to photosynthetic carbon dioxide fixation, supplies CO(2) to ribulose bisphosphate carboxylase (RuBisCO) in the carboxysome. Active when the disulfide bond (194-200) is oxidized, suggesting the interior of the carboxysome is oxidizing.^[2] Beta-carboxysome assembly initiates when soluble RuBisCO is condensed into a liquid matrix in a pre-carboxysome by the RbcS-like domains of probably both forms of CcmM (Probable). CcmN interacts with the N-terminus of full length CcmM, and then recruits the shell proteins (CcmK) via CcmN's encapsulation peptide. Shell formation requires both CcmK proteins and CcmO. CcmL caps the otherwise elongated carboxysome. Once fully encapsulated carboxysomes are formed, they migrate within the cell probably via interactions with the cytoskeleton (By similarity).[UniProtKB:Q03513]^[3]

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

Cyanobacterial RuBisCO is sequestered in large, icosahedral, protein-bounded microcompartments called carboxysomes. Bicarbonate is pumped into the cytosol, diffuses into the carboxysome through small pores in its shell, and is then converted to CO(2) by carbonic anhydrase (CA) prior to fixation. Paradoxically, many beta-cyanobacteria, including Thermosynechococcus elongatus BP-1, lack the conventional carboxysomal beta-CA, ccaA. The N-terminal domain of the carboxysomal protein CcmM is homologous to gamma-CA from Methanosarcina thermophila (Cam) but recombinant CcmM derived from ccaA-containing cyanobacteria show no CA activity. We demonstrate here that either full length CcmM from T. elongatus, or a construct truncated after 209 residues (CcmM209), is active as a CA-the first catalytically active bacterial gamma-CA reported. The 2.0 A structure of CcmM209 reveals a trimeric, left-handed beta-helix structure that closely resembles Cam, except that residues 198-207 form a third alpha-helix stabilized by an essential Cys194-Cys200 disulfide bond. Deleting residues 194-209 (CcmM193) results in an inactive protein whose 1.1 A structure shows disordering of the N- and C-termini, and reorganization of the trimeric interface and active site. Under reducing conditions, CcmM209 is similarly partially disordered and inactive as a CA. CcmM protein in fresh E. coli cell extracts is inactive, implying that the cellular reducing machinery can reduce and inactivate CcmM, while diamide, a thiol oxidizing agent, activates the enzyme. Thus, like membrane-bound eukaryotic cellular compartments, the beta-carboxysome appears to be able to maintain an oxidizing interior by precluding the entry of thioredoxin and other endogenous reducing agents.

Structural basis of the oxidative activation of the carboxysomal gamma-carbonic anhydrase, CcmM.,Pena KL, Castel SE, de Araujo C, Espie GS, Kimber MS Proc Natl Acad Sci U S A. 2010 Feb 9;107(6):2455-60. Epub 2010 Jan 25. PMID:20133749^[4]

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

References

↑ Ryan P, Forrester TJB, Wroblewski C, Kenney TMG, Kitova EN, Klassen JS, Kimber MS. The small RbcS-like domains of the beta-carboxysome structural protein, CcmM, bind RubisCO at a site distinct from that binding the RbcS subunit. J Biol Chem. 2018 Dec 27. pii: RA118.006330. doi: 10.1074/jbc.RA118.006330. PMID:30591587 doi:http://dx.doi.org/10.1074/jbc.RA118.006330
↑ Pena KL, Castel SE, de Araujo C, Espie GS, Kimber MS. Structural basis of the oxidative activation of the carboxysomal gamma-carbonic anhydrase, CcmM. Proc Natl Acad Sci U S A. 2010 Feb 9;107(6):2455-60. Epub 2010 Jan 25. PMID:20133749
↑ Ryan P, Forrester TJB, Wroblewski C, Kenney TMG, Kitova EN, Klassen JS, Kimber MS. The small RbcS-like domains of the beta-carboxysome structural protein, CcmM, bind RubisCO at a site distinct from that binding the RbcS subunit. J Biol Chem. 2018 Dec 27. pii: RA118.006330. doi: 10.1074/jbc.RA118.006330. PMID:30591587 doi:http://dx.doi.org/10.1074/jbc.RA118.006330
↑ Pena KL, Castel SE, de Araujo C, Espie GS, Kimber MS. Structural basis of the oxidative activation of the carboxysomal gamma-carbonic anhydrase, CcmM. Proc Natl Acad Sci U S A. 2010 Feb 9;107(6):2455-60. Epub 2010 Jan 25. PMID:20133749

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

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

Categories: Large Structures | Thermosynechococcus vestitus BP-1 | Castel SE | Kimber MS | Pena KL

@@ Line 1: / Line 1: @@
 ==Inactive truncation of the beta-carboxysomal gamma-Carbonic Anhydrase, CcmM, form 2==
-<StructureSection load='3kwe' size='340' side='right' caption='[[3kwe]], [[Resolution|resolution]] 1.10&Aring;' scene=''>
+<StructureSection load='3kwe' size='340' side='right'caption='[[3kwe]], [[Resolution|resolution]] 1.10&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3kwe]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermosynechococcus_elongatus Thermosynechococcus elongatus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KWE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3KWE FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3kwe]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermosynechococcus_vestitus_BP-1 Thermosynechococcus vestitus BP-1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KWE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3KWE FirstGlance]. <br>
-</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=HEZ:HEXANE-1,6-DIOL'>HEZ</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><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]] 1.1&#8491;</td></tr>
-<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3kwc|3kwc]], [[3kwd|3kwd]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=HEZ:HEXANE-1,6-DIOL'>HEZ</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-<tr><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ccmM, tll0944 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=146786 Thermosynechococcus elongatus])</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=3kwe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kwe OCA], [https://pdbe.org/3kwe PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3kwe RCSB], [https://www.ebi.ac.uk/pdbsum/3kwe PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3kwe ProSAT]</span></td></tr>
-<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Carbonate_dehydratase Carbonate dehydratase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.1 4.2.1.1] </span></td></tr>
+</table>
-<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3kwe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kwe OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3kwe RCSB], [http://www.ebi.ac.uk/pdbsum/3kwe PDBsum]</span></td></tr>
+== Function ==
-<table>
+[https://www.uniprot.org/uniprot/CCMM_THEVB CCMM_THEVB] Functions as a scaffold protein for the assembly of beta-carboxysomes, initiates carboxysome assembly by coalescing RuBisCO (ribulose bisphosphate carboxylase, rbcL-rbcS) (Probable). Produced as a full-length and a shorter form; both forms are required for correct carboxysome assembly and growth (By similarity).[UniProtKB:Q03513]<ref>PMID:30591587</ref>   A carbonic anhydrase, catalyzes the reversible hydration of carbon dioxide. Essential to photosynthetic carbon dioxide fixation, supplies CO(2) to ribulose bisphosphate carboxylase (RuBisCO) in the carboxysome. Active when the disulfide bond (194-200) is oxidized, suggesting the interior of the carboxysome is oxidizing.<ref>PMID:20133749</ref>   Beta-carboxysome assembly initiates when soluble RuBisCO is condensed into a liquid matrix in a pre-carboxysome by the RbcS-like domains of probably both forms of CcmM (Probable). CcmN interacts with the N-terminus of full length CcmM, and then recruits the shell proteins (CcmK) via CcmN's encapsulation peptide. Shell formation requires both CcmK proteins and CcmO. CcmL caps the otherwise elongated carboxysome. Once fully encapsulated carboxysomes are formed, they migrate within the cell probably via interactions with the cytoskeleton (By similarity).[UniProtKB:Q03513]<ref>PMID:30591587</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/kw/3kwe_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kw/3kwe_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
-</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/chain_selection.php?pdb_ID=2ata 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=3kwe ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 27: / Line 28: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 3kwe" style="background-color:#fffaf0;"></div>
 ==See Also==
-*[[Carbonic anhydrase|Carbonic anhydrase]]
+*[[Carbonic anhydrase 3D structures|Carbonic anhydrase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Carbonate dehydratase]]
+[[Category: Large Structures]]
-[[Category: Thermosynechococcus elongatus]]
+[[Category: Thermosynechococcus vestitus BP-1]]
-[[Category: Castel, S E.]]
+[[Category: Castel SE]]
-[[Category: Kimber, M S.]]
+[[Category: Kimber MS]]
-[[Category: Pena, K L.]]
+[[Category: Pena KL]]
-[[Category: Carboxysome]]
-[[Category: Disulfide bond dependent activity]]
-[[Category: Gamma carbonic anhydrase]]
-[[Category: Left-handed beta helix]]
-[[Category: Lyase]]
-[[Category: Photosynthesis]]
-[[Category: Protein binding]]

3kwe

From Proteopedia

Current revision

Inactive truncation of the beta-carboxysomal gamma-Carbonic Anhydrase, CcmM, form 2

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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