6vdg: Difference between revisions
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==Crystal Structure of the Y182A HisF Mutant from Thermotoga maritima== | ==Crystal Structure of the Y182A HisF Mutant from Thermotoga maritima== | ||
<StructureSection load='6vdg' size='340' side='right'caption='[[6vdg]]' scene=''> | <StructureSection load='6vdg' size='340' side='right'caption='[[6vdg]], [[Resolution|resolution]] 2.79Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6VDG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6VDG FirstGlance]. <br> | <table><tr><td colspan='2'>[[6vdg]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6VDG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6VDG FirstGlance]. <br> | ||
</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=6vdg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6vdg OCA], [https://pdbe.org/6vdg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6vdg RCSB], [https://www.ebi.ac.uk/pdbsum/6vdg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6vdg ProSAT]</span></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]] 2.79Å</td></tr> | ||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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=6vdg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6vdg OCA], [https://pdbe.org/6vdg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6vdg RCSB], [https://www.ebi.ac.uk/pdbsum/6vdg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6vdg ProSAT]</span></td></tr> | |||
</table> | </table> | ||
== Function == | |||
[https://www.uniprot.org/uniprot/HIS6_THEMA HIS6_THEMA] IGPS catalyzes the conversion of PRFAR and glutamine to IGP, AICAR and glutamate. The HisF subunit catalyzes the cyclization activity that produces IGP and AICAR from PRFAR using the ammonia provided by the HisH subunit.[HAMAP-Rule:MF_01013] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Centralities determined from Residue Interaction Networks (RIN) in proteins have been used to predict aspects of their structure and dynamics. Here, we correlate the Eigenvector Centrality (Ec) with the rate constant for thermal denaturation (kden) of the HisF protein from Thermotoga maritima based on 12 single alanine substitution mutants. The molecular basis for this correlation was further explored by studying a mutant containing a replacement of a high Ec residue, Y182A, which displayed increased kden at 80 degrees C. The crystallographic structure of this mutant showed few changes, mostly in two flexible loops. The (1)H-(15)N -HSQC showed only subtle changes of cross peak positions for residues located near the mutation site and scattered throughout the structure. However, the comparison of the RIN showed that Y182 is the vertex of a set of high centrality residues that spreads throughout the HisF structure, which is lacking in the mutant. Cross-correlation displacements of Calpha calculated from a molecular dynamics simulation at different temperatures showed that the Y182A mutation reduced the correlated movements in the HisF structure above 70 degrees C. (1)H-(15)N NMR chemical shift covariance using temperature as perturbation were consistent with these results. In conclusion the increase in temperature drives the structure of the mutant HisF-Y182A into a less connected state, richer in non-concerted motions, located predominantly in the C-terminal half of the protein where Y182 is placed. Conversely, wild-type HisF responds to increased temperature as a single unit. Hence the replacement of a high Ec residue alters the distribution of thermal energy through HisF structure. | |||
Role of a high centrality residue in protein dynamics and thermal stability.,Medeiros Almeida V, Chaudhuri A, Cangussu Cardoso MV, Matsuyama BY, Monteiro Ferreira G, Goulart Trossini GH, Salinas RK, Loria JP, Marana SR J Struct Biol. 2021 Sep;213(3):107773. doi: 10.1016/j.jsb.2021.107773. Epub 2021 , Jul 25. PMID:34320379<ref>PMID:34320379</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 6vdg" style="background-color:#fffaf0;"></div> | |||
==See Also== | ==See Also== | ||
*[[ | *[[IGPS 3D structures|IGPS 3D structures]] | ||
== References == | |||
<references/> | |||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Thermotoga maritima]] | |||
[[Category: Almeida VM]] | [[Category: Almeida VM]] | ||
[[Category: Farah CS]] | [[Category: Farah CS]] | ||
[[Category: Marana SR]] | [[Category: Marana SR]] | ||
[[Category: Matsuyama BY]] | [[Category: Matsuyama BY]] | ||
Latest revision as of 11:09, 11 October 2023
Crystal Structure of the Y182A HisF Mutant from Thermotoga maritimaCrystal Structure of the Y182A HisF Mutant from Thermotoga maritima
Structural highlights
FunctionHIS6_THEMA IGPS catalyzes the conversion of PRFAR and glutamine to IGP, AICAR and glutamate. The HisF subunit catalyzes the cyclization activity that produces IGP and AICAR from PRFAR using the ammonia provided by the HisH subunit.[HAMAP-Rule:MF_01013] Publication Abstract from PubMedCentralities determined from Residue Interaction Networks (RIN) in proteins have been used to predict aspects of their structure and dynamics. Here, we correlate the Eigenvector Centrality (Ec) with the rate constant for thermal denaturation (kden) of the HisF protein from Thermotoga maritima based on 12 single alanine substitution mutants. The molecular basis for this correlation was further explored by studying a mutant containing a replacement of a high Ec residue, Y182A, which displayed increased kden at 80 degrees C. The crystallographic structure of this mutant showed few changes, mostly in two flexible loops. The (1)H-(15)N -HSQC showed only subtle changes of cross peak positions for residues located near the mutation site and scattered throughout the structure. However, the comparison of the RIN showed that Y182 is the vertex of a set of high centrality residues that spreads throughout the HisF structure, which is lacking in the mutant. Cross-correlation displacements of Calpha calculated from a molecular dynamics simulation at different temperatures showed that the Y182A mutation reduced the correlated movements in the HisF structure above 70 degrees C. (1)H-(15)N NMR chemical shift covariance using temperature as perturbation were consistent with these results. In conclusion the increase in temperature drives the structure of the mutant HisF-Y182A into a less connected state, richer in non-concerted motions, located predominantly in the C-terminal half of the protein where Y182 is placed. Conversely, wild-type HisF responds to increased temperature as a single unit. Hence the replacement of a high Ec residue alters the distribution of thermal energy through HisF structure. Role of a high centrality residue in protein dynamics and thermal stability.,Medeiros Almeida V, Chaudhuri A, Cangussu Cardoso MV, Matsuyama BY, Monteiro Ferreira G, Goulart Trossini GH, Salinas RK, Loria JP, Marana SR J Struct Biol. 2021 Sep;213(3):107773. doi: 10.1016/j.jsb.2021.107773. Epub 2021 , Jul 25. PMID:34320379[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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