3axk: Difference between revisions

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<StructureSection load='3axk' size='340' side='right'caption='[[3axk]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
<StructureSection load='3axk' size='340' side='right'caption='[[3axk]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3axk]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Oryza_sativa_japonica_group Oryza sativa japonica group]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3AXK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3AXK FirstGlance]. <br>
<table><tr><td colspan='2'>[[3axk]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Oryza_sativa_Japonica_Group Oryza sativa Japonica Group]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3AXK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3AXK FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</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]] 1.9&#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>, <scene name='pdbligand=NME:METHYLAMINE'>NME</scene></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</scene>, <scene name='pdbligand=NME:METHYLAMINE'>NME</scene></td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1wdd|1wdd]], [[3axm|3axm]]</div></td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Ribulose-bisphosphate_carboxylase Ribulose-bisphosphate carboxylase], with EC number [https://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'>[https://proteopedia.org/fgij/fg.htm?mol=3axk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3axk OCA], [https://pdbe.org/3axk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3axk RCSB], [https://www.ebi.ac.uk/pdbsum/3axk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3axk 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=3axk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3axk OCA], [https://pdbe.org/3axk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3axk RCSB], [https://www.ebi.ac.uk/pdbsum/3axk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3axk ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[https://www.uniprot.org/uniprot/RBL_ORYSJ RBL_ORYSJ]] 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 in the photorespiration process. Both reactions occur simultaneously and in competition at the same active site. [[https://www.uniprot.org/uniprot/RBS1_ORYSJ RBS1_ORYSJ]] 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 (By similarity).
[https://www.uniprot.org/uniprot/RBL_ORYSJ RBL_ORYSJ] 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 in the photorespiration process. Both reactions occur simultaneously and in competition at the same active site.
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The key enzyme of plant photosynthesis, d-ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco), must be activated to become catalytically competent via the carbamylation of Lys201 of the large subunit and subsequent stabilization by Mg(2+) coordination. Many biochemical studies have reported that reduced nicotinamide adenine dinucleotide phosphate (NADPH) and 6-phosphogluconate (6PG) function as positive effectors to promote activation. However, the structural mechanism remains unknown. Here, we have determined the crystal structures of activated rice Rubisco in complex with NADPH, 6PG, or 2-carboxy-d-arabinitol 1,5-bisphosphate (2CABP). The structures of the NADPH and 6PG complexes adopt open-state conformations, in which loop 6 at the catalytic site and some other loops are disordered. The structure of the 2CABP complex is in a closed state, similar to the previous 2CABP-bound activated structures from other sources. The catalytic sites of the NADPH and 6PG complexes are fully activated, despite the fact that bicarbonate (NaHCO(3)) was not added into the crystallization solution. In the catalytic site, NADPH does not interact with Mg(2+) directly but interacts with Mg(2+)-coordinated water molecules, while 6PG interacts with Mg(2+) directly. These observations suggest that the two effectors promote Rubisco activation by stabilizing the complex of Mg(2+) and the carbamylated Lys201 with unique interactions and preventing its dissociation. The structure also reveals that the relaxed complex of the effectors (NADPH or 6PG), distinct from the tight-binding mode of 2CABP, would allow rapid exchange of the effectors in the catalytic sites by substrate d-ribulose 1,5-bisphosphate for catalysis in physiological conditions.
 
Crystal Structure of Rice Rubisco and Implications for Activation Induced by Positive Effectors NADPH and 6-Phosphogluconate.,Matsumura H, Mizohata E, Ishida H, Kogami A, Ueno T, Makino A, Inoue T, Yokota A, Mae T, Kai Y J Mol Biol. 2012 May 17. PMID:22609438<ref>PMID:22609438</ref>
 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 3axk" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[RuBisCO 3D structures|RuBisCO 3D structures]]
*[[RuBisCO 3D structures|RuBisCO 3D structures]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Oryza sativa japonica group]]
[[Category: Oryza sativa Japonica Group]]
[[Category: Ribulose-bisphosphate carboxylase]]
[[Category: Inoue T]]
[[Category: Inoue, T]]
[[Category: Ishida H]]
[[Category: Ishida, H]]
[[Category: Kai Y]]
[[Category: Kai, Y]]
[[Category: Kogami A]]
[[Category: Kogami, A]]
[[Category: Mae T]]
[[Category: Mae, T]]
[[Category: Makino A]]
[[Category: Makino, A]]
[[Category: Matsumura H]]
[[Category: Matsumura, H]]
[[Category: Mizohata E]]
[[Category: Mizohata, E]]
[[Category: Ueno T]]
[[Category: Ueno, T]]
[[Category: Yokota A]]
[[Category: Yokota, A]]
[[Category: Alpha/beta barrel]]
[[Category: Lyase]]
[[Category: Photosynthetic carbon reduction]]

Latest revision as of 12:57, 14 February 2024

Structure of rice Rubisco in complex with NADP(H)Structure of rice Rubisco in complex with NADP(H)

Structural highlights

3axk is a 4 chain structure with sequence from Oryza sativa Japonica Group. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.9Å
Ligands:, , , ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RBL_ORYSJ 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 in the photorespiration process. Both reactions occur simultaneously and in competition at the same active site.

See Also

3axk, resolution 1.90Å

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