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| | <StructureSection load='5n9z' size='340' side='right'caption='[[5n9z]], [[Resolution|resolution]] 1.90Å' scene=''> | | <StructureSection load='5n9z' size='340' side='right'caption='[[5n9z]], [[Resolution|resolution]] 1.90Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5n9z]] is a 16 chain structure with sequence from [http://en.wikipedia.org/wiki/Thalassiosira_hyalina Thalassiosira hyalina]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5N9Z OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5N9Z FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5n9z]] is a 16 chain structure with sequence from [https://en.wikipedia.org/wiki/Thalassiosira_hyalina Thalassiosira hyalina]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5N9Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5N9Z 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=EDO:1,2-ETHANEDIOL'>EDO</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">X-ray diffraction, [[Resolution|Resolution]] 1.899Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=8RE:'>8RE</scene>, <scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene>, <scene name='pdbligand=HLU:BETA-HYDROXYLEUCINE'>HLU</scene>, <scene name='pdbligand=HYP:4-HYDROXYPROLINE'>HYP</scene>, <scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene>, <scene name='pdbligand=LYO:4-HYDROXY-LYSINE'>LYO</scene>, <scene name='pdbligand=M3L:N-TRIMETHYLLYSINE'>M3L</scene></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=8RE:3,4-dihydroxylysine'>8RE</scene>, <scene name='pdbligand=CAP:2-CARBOXYARABINITOL-1,5-DIPHOSPHATE'>CAP</scene>, <scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=HLU:BETA-HYDROXYLEUCINE'>HLU</scene>, <scene name='pdbligand=HYP:4-HYDROXYPROLINE'>HYP</scene>, <scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene>, <scene name='pdbligand=LYO:4-HYDROXY-LYSINE'>LYO</scene>, <scene name='pdbligand=M3L:N-TRIMETHYLLYSINE'>M3L</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></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'>[https://proteopedia.org/fgij/fg.htm?mol=5n9z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5n9z OCA], [https://pdbe.org/5n9z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5n9z RCSB], [https://www.ebi.ac.uk/pdbsum/5n9z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5n9z ProSAT]</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=5n9z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5n9z OCA], [http://pdbe.org/5n9z PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5n9z RCSB], [http://www.ebi.ac.uk/pdbsum/5n9z PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5n9z ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/A0A384E0M2_9STRA A0A384E0M2_9STRA] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | </StructureSection> | | </StructureSection> |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Ribulose-bisphosphate carboxylase]] | |
| | [[Category: Thalassiosira hyalina]] | | [[Category: Thalassiosira hyalina]] |
| - | [[Category: Andersson, I]] | + | [[Category: Andersson I]] |
| - | [[Category: Valegard, K]] | + | [[Category: Valegard K]] |
| - | [[Category: Carbon dioxide fixation]]
| + | |
| - | [[Category: Photorespiration]]
| + | |
| - | [[Category: Photosynthesis]]
| + | |
| Structural highlights
5n9z is a 16 chain structure with sequence from Thalassiosira hyalina. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 1.899Å |
| Ligands: | , , , , , , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
A0A384E0M2_9STRA
Publication Abstract from PubMed
The catalytic performance of the major CO2-assimilating enzyme, ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco), restricts photosynthetic productivity. Natural diversity in the catalytic properties of Rubisco indicates possibilities for improvement. Oceanic phytoplankton contain some of the most efficient Rubisco enzymes, and diatoms in particular are responsible for a significant proportion of total marine primary production as well as being a major source of CO2 sequestration in polar cold waters. Until now, the biochemical properties and three-dimensional structures of Rubisco from diatoms were unknown. Here, diatoms from Arctic waters were collected, cultivated and analyzed for their CO2 fixing capability. We characterized the kinetic properties of five, and determined the crystal structures of four Rubiscos selected for their high CO2-fixing efficiency. The DNA sequences of the rbcL and rbcS genes of the selected diatoms were similar, reflecting their close phylogenetic relationship. The Vmax and KM for the oxygenase and carboxylase activities at 25 degrees C and the specificity factors (Sc/o) at 15, 25 and 35 degrees C, were determined. The Sc/o values were high, approaching those of mono- and dicot plants, thus exhibiting good selectivity for CO2 relative to O2 Structurally, diatom Rubiscos belong to Form I C/D, containing small subunits characterised by a short betaA-betaB loop and a carboxy-terminal extension that forms a beta-hairpin structure (betaE-betaF loop). Of note, the diatom Rubiscos featured a number of posttranslational modifications of the large subunit, including 4-hydroxy-proline, betahydroxyleucine, hydroxylated, and nitrosylated cysteine, mono-, and di-hydroxylated lysine, and tri-methylated lysine. Our studies suggest adaptation toward achieving efficient CO2-fixation in Arctic diatom Rubiscos.
Structural and functional analyses of Rubisco from arctic diatom species reveal unusual posttranslational modifications.,Valegard K, Andralojc PJ, Haslam RP, Pearce FG, Eriksen GK, Madgwick PJ, Kristoffersen AK, van Lun M, Klein U, Eilertsen HC, Parry MAJ, Andersson I J Biol Chem. 2018 Jun 20. pii: RA118.003518. doi: 10.1074/jbc.RA118.003518. PMID:29925588[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Valegard K, Andralojc PJ, Haslam RP, Pearce FG, Eriksen GK, Madgwick PJ, Kristoffersen AK, van Lun M, Klein U, Eilertsen HC, Parry MAJ, Andersson I. Structural and functional analyses of Rubisco from arctic diatom species reveal unusual posttranslational modifications. J Biol Chem. 2018 Jun 20. pii: RA118.003518. doi: 10.1074/jbc.RA118.003518. PMID:29925588 doi:http://dx.doi.org/10.1074/jbc.RA118.003518
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