3k2b: Difference between revisions
New page: '''Unreleased structure''' The entry 3k2b is ON HOLD Authors: Fermani, S., Falini, G., Thumiger, A, Sparla, F., Marri, L., Trost, P. Description: Crystal structure of photosynthetic A4... |
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The | ==Crystal structure of photosynthetic A4 isoform glyceraldehyde-3-phosphate dehydrogenase complexed with NAD, from Arabidopsis thaliana== | ||
<StructureSection load='3k2b' size='340' side='right'caption='[[3k2b]], [[Resolution|resolution]] 2.60Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[3k2b]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3K2B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3K2B FirstGlance]. <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]] 2.6Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=3k2b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3k2b OCA], [https://pdbe.org/3k2b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3k2b RCSB], [https://www.ebi.ac.uk/pdbsum/3k2b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3k2b ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/G3PA1_ARATH G3PA1_ARATH] Involved in the photosynthetic reductive pentose phosphate pathway (Calvin-Benson cycle). Catalyzes the reduction of 1,3-diphosphoglycerate by NADPH (By similarity). | |||
== 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/k2/3k2b_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/main_output.php?pdb_ID=3k2b ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
The crystal structure of the A(4) isoform of photosynthetic glyceraldehyde-3-phosphate dehydrogenase (GAPDH) from Arabidopsis thaliana, expressed in recombinant form and complexed with NAD, is reported. The crystals, which were grown in 2.4 M ammonium sulfate and 0.1 M sodium citrate, belonged to space group I222. The asymmetric unit includes ten subunits, i.e. two independent tetramers plus a dimer that generates a third tetramer by a crystallographic symmetry operation. The crystal structure was solved by molecular replacement and refined to an R factor of 23.7% and an R(free) factor of 28.9% at 2.6 A resolution. In the final model, each subunit binds one NAD(+) molecule and two sulfates, which occupy the P(s) and the P(i) anion-binding sites. Detailed knowledge of this structure is instrumental for structural investigation of supramolecular complexes of A(4)-GAPDH, phosphoribulokinase and CP12, which are involved in the regulation of photosynthesis in the model plant A. thaliana. | |||
Structure of photosynthetic glyceraldehyde-3-phosphate dehydrogenase (isoform A4) from Arabidopsis thaliana in complex with NAD.,Fermani S, Sparla F, Marri L, Thumiger A, Pupillo P, Falini G, Trost P Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010 Jun 1;66(Pt 6):621-6. Epub, 2010 May 25. PMID:20516587<ref>PMID:20516587</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 3k2b" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Glyceraldehyde-3-phosphate dehydrogenase 3D structures|Glyceraldehyde-3-phosphate dehydrogenase 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Arabidopsis thaliana]] | |||
[[Category: Large Structures]] | |||
[[Category: Falini G]] | |||
[[Category: Fermani S]] | |||
[[Category: Marri L]] | |||
[[Category: Sparla F]] | |||
[[Category: Thumiger A]] | |||
[[Category: Trost P]] | |||