5nv3: Difference between revisions

Latest revision as of 15:09, 22 November 2023

Structure of Rubisco from Rhodobacter sphaeroides in complex with CABPStructure of Rubisco from Rhodobacter sphaeroides in complex with CABP

5nv3, resolution 3.39Å

Structural highlights

5nv3 is a 16 chain structure with sequence from Cereibacter sphaeroides. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Electron Microscopy, Resolution 3.39Å
Ligands:
Experimental data:	Check
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RBL1_CERSP RuBisCO catalyzes two reactions: the carboxylation of D-ribulose 1,5-bisphosphate, the primary event in carbon dioxide fixation, as well as the oxidative fragmentation of the pentose substrate. Both reactions occur simultaneously and in competition at the same active site.[HAMAP-Rule:MF_01338]^[1]

Publication Abstract from PubMed

How AAA+ chaperones conformationally remodel specific target proteins in an ATP-dependent manner is not well understood. Here, we investigated the mechanism of the AAA+ protein Rubisco activase (Rca) in metabolic repair of the photosynthetic enzyme Rubisco, a complex of eight large (RbcL) and eight small (RbcS) subunits containing eight catalytic sites. Rubisco is prone to inhibition by tight-binding sugar phosphates, whose removal is catalyzed by Rca. We engineered a stable Rca hexamer ring and analyzed its functional interaction with Rubisco. Hydrogen/deuterium exchange and chemical crosslinking showed that Rca structurally destabilizes elements of the Rubisco active site with remarkable selectivity. Cryo-electron microscopy revealed that Rca docks onto Rubisco over one active site at a time, positioning the C-terminal strand of RbcL, which stabilizes the catalytic center, for access to the Rca hexamer pore. The pulling force of Rca is fine-tuned to avoid global destabilization and allow for precise enzyme repair.

Mechanism of Enzyme Repair by the AAA+ Chaperone Rubisco Activase.,Bhat JY, Milicic G, Thieulin-Pardo G, Bracher A, Maxwell A, Ciniawsky S, Mueller-Cajar O, Engen JR, Hartl FU, Wendler P, Hayer-Hartl M Mol Cell. 2017 Jul 20. pii: S1097-2765(17)30498-7. doi:, 10.1016/j.molcel.2017.07.004. PMID:28803776^[2]

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

References

↑ Horken KM, Tabita FR. Closely related form I ribulose bisphosphate carboxylase/oxygenase molecules that possess different CO2/O2 substrate specificities. Arch Biochem Biophys. 1999 Jan 15;361(2):183-94. PMID:9882445 doi:http://dx.doi.org/S0003-9861(98)90979-1
↑ Bhat JY, Milicic G, Thieulin-Pardo G, Bracher A, Maxwell A, Ciniawsky S, Mueller-Cajar O, Engen JR, Hartl FU, Wendler P, Hayer-Hartl M. Mechanism of Enzyme Repair by the AAA+ Chaperone Rubisco Activase. Mol Cell. 2017 Jul 20. pii: S1097-2765(17)30498-7. doi:, 10.1016/j.molcel.2017.07.004. PMID:28803776 doi:http://dx.doi.org/10.1016/j.molcel.2017.07.004

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OCA

[1] Horken KM, Tabita FR. Closely related form I ribulose bisphosphate carboxylase/oxygenase molecules that possess different CO2/O2 substrate specificities. Arch Biochem Biophys. 1999 Jan 15;361(2):183-94. PMID:9882445 doi:http://dx.doi.org/S0003-9861(98)90979-1

[2] Bhat JY, Milicic G, Thieulin-Pardo G, Bracher A, Maxwell A, Ciniawsky S, Mueller-Cajar O, Engen JR, Hartl FU, Wendler P, Hayer-Hartl M. Mechanism of Enzyme Repair by the AAA+ Chaperone Rubisco Activase. Mol Cell. 2017 Jul 20. pii: S1097-2765(17)30498-7. doi:, 10.1016/j.molcel.2017.07.004. PMID:28803776 doi:http://dx.doi.org/10.1016/j.molcel.2017.07.004

[1]

[2]

@@ Line 3: / Line 3: @@
 <SX load='5nv3' size='340' side='right' viewer='molstar' caption='[[5nv3]], [[Resolution|resolution]] 3.39&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5nv3]] is a 16 chain structure with sequence from [http://en.wikipedia.org/wiki/"rhodococcus_capsulatus"_molisch_1907 "rhodococcus capsulatus" molisch 1907]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NV3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5NV3 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5nv3]] is a 16 chain structure with sequence from [https://en.wikipedia.org/wiki/Cereibacter_sphaeroides Cereibacter sphaeroides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NV3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5NV3 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CAP:2-CARBOXYARABINITOL-1,5-DIPHOSPHATE'>CAP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 3.39&#8491;</td></tr>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CAP:2-CARBOXYARABINITOL-1,5-DIPHOSPHATE'>CAP</scene>, <scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">cbbL, cbbL1, rbcL ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1063 "Rhodococcus capsulatus" Molisch 1907]), cbbS, rbcS ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1063 "Rhodococcus capsulatus" Molisch 1907])</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=5nv3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5nv3 OCA], [https://pdbe.org/5nv3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5nv3 RCSB], [https://www.ebi.ac.uk/pdbsum/5nv3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5nv3 ProSAT]</span></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribulose-bisphosphate_carboxylase Ribulose-bisphosphate carboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.39 4.1.1.39] </span></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=5nv3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5nv3 OCA], [http://pdbe.org/5nv3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5nv3 RCSB], [http://www.ebi.ac.uk/pdbsum/5nv3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5nv3 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/RBL1_RHOSH RBL1_RHOSH]] RuBisCO catalyzes two reactions: the carboxylation of D-ribulose 1,5-bisphosphate, the primary event in carbon dioxide fixation, as well as the oxidative fragmentation of the pentose substrate. Both reactions occur simultaneously and in competition at the same active site.[HAMAP-Rule:MF_01338]<ref>PMID:9882445</ref>  [[http://www.uniprot.org/uniprot/RBS1_RHOSH RBS1_RHOSH]] RuBisCO catalyzes two reactions: the carboxylation of D-ribulose 1,5-bisphosphate, the primary event in carbon dioxide fixation, as well as the oxidative fragmentation of the pentose substrate. Both reactions occur simultaneously and in competition at the same active site.<ref>PMID:9882445</ref>
+[https://www.uniprot.org/uniprot/RBL1_CERSP RBL1_CERSP] RuBisCO catalyzes two reactions: the carboxylation of D-ribulose 1,5-bisphosphate, the primary event in carbon dioxide fixation, as well as the oxidative fragmentation of the pentose substrate. Both reactions occur simultaneously and in competition at the same active site.[HAMAP-Rule:MF_01338]<ref>PMID:9882445</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 28: / Line 26: @@
 __TOC__
 </SX>
-[[Category: Rhodococcus capsulatus molisch 1907]]
+[[Category: Cereibacter sphaeroides]]
 [[Category: Large Structures]]
-[[Category: Ribulose-bisphosphate carboxylase]]
+[[Category: Bracher A]]
-[[Category: Bracher, A]]
+[[Category: Ciniawsky S]]
-[[Category: Ciniawsky, S]]
+[[Category: Hartl FU]]
-[[Category: Hartl, F U]]
+[[Category: Hayer-Hartl M]]
-[[Category: Hayer-Hartl, M]]
+[[Category: Milicic G]]
-[[Category: Milicic, G]]
+[[Category: Wendler P]]
-[[Category: Wendler, P]]
-[[Category: Beta barrel]]
-[[Category: Lyase]]

5nv3: Difference between revisions

Latest revision as of 15:09, 22 November 2023

Structure of Rubisco from Rhodobacter sphaeroides in complex with CABPStructure of Rubisco from Rhodobacter sphaeroides in complex with CABP

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

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5nv3: Difference between revisions

Latest revision as of 15:09, 22 November 2023

Structure of Rubisco from Rhodobacter sphaeroides in complex with CABPStructure of Rubisco from Rhodobacter sphaeroides in complex with CABP

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

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