1ihx: Difference between revisions

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New page: left|200px<br /><applet load="1ihx" size="450" color="white" frame="true" align="right" spinBox="true" caption="1ihx, resolution 2.80Å" /> '''Crystal structure of...
 
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[[Image:1ihx.jpg|left|200px]]<br /><applet load="1ihx" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1ihx, resolution 2.80&Aring;" />
'''Crystal structure of two D-glyceraldehyde-3-phosphate dehydrogenase complexes: a case of asymmetry'''<br />


==Overview==
==Crystal structure of two D-glyceraldehyde-3-phosphate dehydrogenase complexes: a case of asymmetry==
Crystal structures of GAPDH from Palinurus versicolor complexed with two, coenzyme analogues, SNAD(+) and ADP-ribose, were determined by molecular, replacement and refined at medium resolution to acceptable, crystallographic factors and reasonable stereochemistry. ADP-ribose in the, ADP-ribose-GAPDH complex adopts a rather extended conformation. The, interactions between ADP-ribose and GAPDH are extensive and in a fashion, dissimilar to the coenzyme NAD(+). This accounts for the strong inhibiting, ability of ADP-ribose. The conformational changes induced by ADP-ribose, binding are quite different to those induced by NAD(+) binding. This, presumably explains the non-cooperative behaviour of the ADP-ribose, binding. Unexpectedly, the SNAD(+)-GAPDH complex reveals pairwise, asymmetry. The asymmetry is significant, including the SNAD(+) molecule, active-site structure and domain motion induced by the coenzyme analogue., In the yellow or red subunits [nomenclature of subunits is as in Buehner, et al. (1974). J. Mol. Biol. 90, 25-49], SNAD(+) binds similarly, as does, NAD(+) in holo-GAPDH. While, in the green or blue subunit, the SNAD(+), binds in a non-productive manner, resulting in a disordered, thionicotinamide ring and rearranged active-site residues. The, conformation seen in the yellow and red subunits of SNAD(+)-GAPDH is, likely to represent the functional state of the enzyme complex in solution, and thus accounts for the substrate activity of SNAD(+). A novel type of, domain motion is observed for the binding of the coenzyme analogues to, GAPDH. The possible conformational transitions involved in the coenzyme, binding and the important role of the nicotinamide group are discussed.
<StructureSection load='1ihx' size='340' side='right'caption='[[1ihx]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1ihx]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Panulirus_versicolor Panulirus versicolor]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IHX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1IHX 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]] 2.8&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SND:THIONICOTINAMIDE-ADENINE-DINUCLEOTIDE'>SND</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=1ihx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ihx OCA], [https://pdbe.org/1ihx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ihx RCSB], [https://www.ebi.ac.uk/pdbsum/1ihx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ihx ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/G3P_PANVR G3P_PANVR]
== 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/ih/1ihx_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=1ihx ConSurf].
<div style="clear:both"></div>


==About this Structure==
==See Also==
1IHX is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Palinurus_versicolor Palinurus versicolor] with SO4 and SND as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Glyceraldehyde-3-phosphate_dehydrogenase_(phosphorylating) Glyceraldehyde-3-phosphate dehydrogenase (phosphorylating)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.2.1.12 1.2.1.12] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1IHX OCA].
*[[Aldehyde dehydrogenase 3D structures|Aldehyde dehydrogenase 3D structures]]
 
*[[Glyceraldehyde-3-phosphate dehydrogenase 3D structures|Glyceraldehyde-3-phosphate dehydrogenase 3D structures]]
==Reference==
__TOC__
Structures of D-glyceraldehyde-3-phosphate dehydrogenase complexed with coenzyme analogues., Shen YQ, Song SY, Lin ZJ, Acta Crystallogr D Biol Crystallogr. 2002 Aug;58(Pt 8):1287-97. Epub 2002, Jul 20. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12136140 12136140]
</StructureSection>
[[Category: Glyceraldehyde-3-phosphate dehydrogenase (phosphorylating)]]
[[Category: Large Structures]]
[[Category: Palinurus versicolor]]
[[Category: Panulirus versicolor]]
[[Category: Single protein]]
[[Category: Lin Z-J]]
[[Category: Lin, Z.J.]]
[[Category: Shen Y-Q]]
[[Category: Shen, Y.Q.]]
[[Category: Song S-Y]]
[[Category: Song, S.Y.]]
[[Category: SND]]
[[Category: SO4]]
[[Category: asymmetry]]
[[Category: gapdh]]
[[Category: snad]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 17:24:35 2007''

Latest revision as of 16:24, 13 March 2024

Crystal structure of two D-glyceraldehyde-3-phosphate dehydrogenase complexes: a case of asymmetryCrystal structure of two D-glyceraldehyde-3-phosphate dehydrogenase complexes: a case of asymmetry

Structural highlights

1ihx is a 4 chain structure with sequence from Panulirus versicolor. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.8Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

G3P_PANVR

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

1ihx, resolution 2.80Å

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OCA
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