1cer: Difference between revisions

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==DETERMINANTS OF ENZYME THERMOSTABILITY OBSERVED IN THE MOLECULAR STRUCTURE OF THERMUS AQUATICUS D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE AT 2.5 ANGSTROMS RESOLUTION==
==DETERMINANTS OF ENZYME THERMOSTABILITY OBSERVED IN THE MOLECULAR STRUCTURE OF THERMUS AQUATICUS D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE AT 2.5 ANGSTROMS RESOLUTION==
<StructureSection load='1cer' size='340' side='right' caption='[[1cer]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
<StructureSection load='1cer' size='340' side='right'caption='[[1cer]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1cer]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_aquaticus Thermus aquaticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1CER OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1CER FirstGlance]. <br>
<table><tr><td colspan='2'>[[1cer]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_aquaticus Thermus aquaticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1CER OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1CER FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</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]] 2.5&#8491;</td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">THERMUS AQUATICUS GAPDH ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=271 Thermus aquaticus])</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></td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[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] </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=1cer FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1cer OCA], [https://pdbe.org/1cer PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1cer RCSB], [https://www.ebi.ac.uk/pdbsum/1cer PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1cer 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=1cer FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1cer OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1cer RCSB], [http://www.ebi.ac.uk/pdbsum/1cer PDBsum]</span></td></tr>
</table>
</table>
== Function ==
[https://www.uniprot.org/uniprot/G3P_THEAQ G3P_THEAQ]
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
Check<jmol>
   <jmolCheckbox>
   <jmolCheckbox>
     <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ce/1cer_consurf.spt"</scriptWhenChecked>
     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ce/1cer_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
   </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/chain_selection.php?pdb_ID=2ata 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=1cer ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The crystal structure of holo D-glyceraldehyde-3-phosphate dehydrogenase (GAPDH) from the extreme thermophile Thermus aquaticus has been solved at 2.5 Angstroms resolution. To study the determinants of thermostability, we compare our structure to four other GAPDHs. Salt links, hydrogen bonds, buried surface area, packing density, surface to volume ratio, and stabilization of alpha-helices and beta-turns are analyzed. We find a strong correlation between thermostability and the number of hydrogen bonds between charged side chains and neutral partners. These charged-neutral hydrogen bonds provide electrostatic stabilization without the heavy desolvation penalty of salt links. The stability of thermophilic GAPDHs is also correlated with the number of intrasubunit salt links and total hydrogen bonds. Charged residues, therefore, play a dual role in stabilization by participating not only in salt links but also in hydrogen bonds with a neutral partner. Hydrophobic effects allow for discrimination between thermophiles and psychrophiles, but not within the GAPDH thermophiles. There is, however, an association between thermostability and decreasing enzyme surface to volume ratio. Finally, we describe several interactions present in both our GAPDH and a hyperthermophilic GAPDH that are absent in the less thermostable GAPDHs. These include a four-residue salt link network, a hydrogen bond near the active site, an intersubunit salt link, and several buried Ile residues.
Determinants of enzyme thermostability observed in the molecular structure of Thermus aquaticus D-glyceraldehyde-3-phosphate dehydrogenase at 25 Angstroms Resolution.,Tanner JJ, Hecht RM, Krause KL Biochemistry. 1996 Feb 27;35(8):2597-609. PMID:8611563<ref>PMID:8611563</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>


==See Also==
==See Also==
*[[Glyceraldehyde-3-Phosphate Dehydrogenase|Glyceraldehyde-3-Phosphate Dehydrogenase]]
*[[Aldehyde dehydrogenase 3D structures|Aldehyde dehydrogenase 3D structures]]
== References ==
*[[Glyceraldehyde-3-phosphate dehydrogenase 3D structures|Glyceraldehyde-3-phosphate dehydrogenase 3D structures]]
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Thermus aquaticus]]
[[Category: Thermus aquaticus]]
[[Category: Hecht, R M]]
[[Category: Hecht RM]]
[[Category: Krause, K L]]
[[Category: Krause KL]]
[[Category: Tanner, J J]]
[[Category: Tanner JJ]]
[[Category: Glycolysis]]
[[Category: Nad]]
[[Category: Oxidoreductase]]

Latest revision as of 09:42, 7 February 2024

DETERMINANTS OF ENZYME THERMOSTABILITY OBSERVED IN THE MOLECULAR STRUCTURE OF THERMUS AQUATICUS D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE AT 2.5 ANGSTROMS RESOLUTIONDETERMINANTS OF ENZYME THERMOSTABILITY OBSERVED IN THE MOLECULAR STRUCTURE OF THERMUS AQUATICUS D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE AT 2.5 ANGSTROMS RESOLUTION

Structural highlights

1cer is a 8 chain structure with sequence from Thermus aquaticus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.5Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

G3P_THEAQ

Evolutionary Conservation

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

See Also

1cer, resolution 2.50Å

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