1ihx: Difference between revisions

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<StructureSection load='1ihx' size='340' side='right'caption='[[1ihx]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
<StructureSection load='1ihx' size='340' side='right'caption='[[1ihx]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1ihx]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Palinurus_versicolor Palinurus 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>
<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='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>
</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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1ihy|1ihy]]</div></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='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Glyceraldehyde-3-phosphate_dehydrogenase_(phosphorylating) Glyceraldehyde-3-phosphate dehydrogenase (phosphorylating)], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.2.1.12 1.2.1.12] </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=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>
<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>
</table>
== Function ==
[https://www.uniprot.org/uniprot/G3P_PANVR G3P_PANVR]
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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</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].
</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>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
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.
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:12136140<ref>PMID:12136140</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1ihx" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Aldehyde dehydrogenase 3D structures|Aldehyde dehydrogenase 3D structures]]
*[[Aldehyde dehydrogenase 3D structures|Aldehyde dehydrogenase 3D structures]]
*[[Glyceraldehyde-3-phosphate dehydrogenase 3D structures|Glyceraldehyde-3-phosphate dehydrogenase 3D structures]]
*[[Glyceraldehyde-3-phosphate dehydrogenase 3D structures|Glyceraldehyde-3-phosphate dehydrogenase 3D structures]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Palinurus versicolor]]
[[Category: Panulirus versicolor]]
[[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: Asymmetry]]
[[Category: Gapdh]]
[[Category: Oxidoreductase]]
[[Category: Snad]]

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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