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[[Image:2iv0.jpg|left|200px]]


{{Structure
==Thermal stability of isocitrate dehydrogenase from Archaeoglobus fulgidus studied by crystal structure analysis and engineering of chimers==
|PDB= 2iv0 |SIZE=350|CAPTION= <scene name='initialview01'>2iv0</scene>, resolution 2.50&Aring;
<StructureSection load='2iv0' size='340' side='right'caption='[[2iv0]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
|SITE= <scene name='pdbsite=AC1:Cl+Binding+Site+For+Chain+B'>AC1</scene>
== Structural highlights ==
|LIGAND= <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>
<table><tr><td colspan='2'>[[2iv0]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Archaeoglobus_fulgidus Archaeoglobus fulgidus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IV0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2IV0 FirstGlance]. <br>
|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Isocitrate_dehydrogenase_(NADP(+)) Isocitrate dehydrogenase (NADP(+))], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.42 1.1.1.42] </span>
</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>
|GENE=
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
|DOMAIN=
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2iv0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2iv0 OCA], [https://pdbe.org/2iv0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2iv0 RCSB], [https://www.ebi.ac.uk/pdbsum/2iv0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2iv0 ProSAT]</span></td></tr>
|RELATEDENTRY=
</table>
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2iv0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2iv0 OCA], [http://www.ebi.ac.uk/pdbsum/2iv0 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2iv0 RCSB]</span>
== Function ==
}}
[https://www.uniprot.org/uniprot/IDH_ARCFU IDH_ARCFU]
== 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/iv/2iv0_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=2iv0 ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Isocitrate dehydrogenase from Archaeoglobus fulgidus (AfIDH) has an apparent melting temperature (T(m)) of 98.5 degrees C. To identify the structural features involved in thermal stabilization of AfIDH, the structure was solved to 2.5 A resolution. AfIDH was strikingly similar to mesophilic IDH from Escherichia coli (EcIDH) and displayed almost the same number of ion pairs and ionic networks. However, two unique inter-domain networks were present in AfIDH; one three-membered ionic network between the large and the small domain and one four-membered ionic network between the clasp and the small domain. The latter ionic network was presumably reduced in size when the clasp domain of AfIDH was swapped with that of EcIDH and the T (m) decreased by 18 degrees C. Contrarily, EcIDH was only stabilized by 4 degrees C by the clasp domain of AfIDH, a result probably due to the introduction of a unique inter-subunit aromatic cluster in AfIDH that may strengthen the dimeric interface in this enzyme. A unique aromatic cluster was identified close to the N-terminus of AfIDH that could provide additional stabilization of this region. Common and unique heat adaptive traits of AfIDH with those recently observed for hyperthermophilic IDH from Aeropyrum pernix (ApIDH) and Thermotoga maritima (TmIDH) are discussed herein.


'''THERMAL STABILITY OF ISOCITRATE DEHYDROGENASE FROM ARCHAEOGLOBUS FULGIDUS STUDIED BY CRYSTAL STRUCTURE ANALYSIS AND ENGINEERING OF CHIMERS'''
Thermal stability of isocitrate dehydrogenase from Archaeoglobus fulgidus studied by crystal structure analysis and engineering of chimers.,Stokke R, Karlstrom M, Yang N, Leiros I, Ladenstein R, Birkeland NK, Steen IH Extremophiles. 2007 May;11(3):481-93. Epub 2007 Mar 31. PMID:17401542<ref>PMID:17401542</ref>


From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 2iv0" style="background-color:#fffaf0;"></div>


==Overview==
==See Also==
Isocitrate dehydrogenase from Archaeoglobus fulgidus (AfIDH) has an apparent melting temperature (T(m)) of 98.5 degrees C. To identify the structural features involved in thermal stabilization of AfIDH, the structure was solved to 2.5 A resolution. AfIDH was strikingly similar to mesophilic IDH from Escherichia coli (EcIDH) and displayed almost the same number of ion pairs and ionic networks. However, two unique inter-domain networks were present in AfIDH; one three-membered ionic network between the large and the small domain and one four-membered ionic network between the clasp and the small domain. The latter ionic network was presumably reduced in size when the clasp domain of AfIDH was swapped with that of EcIDH and the T (m) decreased by 18 degrees C. Contrarily, EcIDH was only stabilized by 4 degrees C by the clasp domain of AfIDH, a result probably due to the introduction of a unique inter-subunit aromatic cluster in AfIDH that may strengthen the dimeric interface in this enzyme. A unique aromatic cluster was identified close to the N-terminus of AfIDH that could provide additional stabilization of this region. Common and unique heat adaptive traits of AfIDH with those recently observed for hyperthermophilic IDH from Aeropyrum pernix (ApIDH) and Thermotoga maritima (TmIDH) are discussed herein.
*[[Isocitrate dehydrogenase 3D structures|Isocitrate dehydrogenase 3D structures]]
 
== References ==
==About this Structure==
<references/>
2IV0 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Archaeoglobus_fulgidus Archaeoglobus fulgidus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IV0 OCA].
__TOC__
 
</StructureSection>
==Reference==
Thermal stability of isocitrate dehydrogenase from Archaeoglobus fulgidus studied by crystal structure analysis and engineering of chimers., Stokke R, Karlstrom M, Yang N, Leiros I, Ladenstein R, Birkeland NK, Steen IH, Extremophiles. 2007 May;11(3):481-93. Epub 2007 Mar 31. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17401542 17401542]
[[Category: Archaeoglobus fulgidus]]
[[Category: Archaeoglobus fulgidus]]
[[Category: Isocitrate dehydrogenase (NADP(+))]]
[[Category: Large Structures]]
[[Category: Single protein]]
[[Category: Birkeland NK]]
[[Category: Birkeland, N K.]]
[[Category: Karlstrom M]]
[[Category: Karlstrom, M.]]
[[Category: Ladenstein R]]
[[Category: Ladenstein, R.]]
[[Category: Leiros I]]
[[Category: Leiros, I.]]
[[Category: Steen IH]]
[[Category: Steen, I H.]]
[[Category: Stokke R]]
[[Category: Stokke, R.]]
[[Category: Yang N]]
[[Category: Yang, N.]]
[[Category: archaeoglobus fulgidus]]
[[Category: aromatic cluster]]
[[Category: domain swapping]]
[[Category: glyoxylate bypass]]
[[Category: ionic network]]
[[Category: isocitrate dehydrogenase]]
[[Category: nadp]]
[[Category: oxidoreductase]]
[[Category: phosphorylation]]
[[Category: thermal stability]]
[[Category: tricarboxylic acid cycle]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 03:49:02 2008''

Latest revision as of 17:26, 13 December 2023

Thermal stability of isocitrate dehydrogenase from Archaeoglobus fulgidus studied by crystal structure analysis and engineering of chimersThermal stability of isocitrate dehydrogenase from Archaeoglobus fulgidus studied by crystal structure analysis and engineering of chimers

Structural highlights

2iv0 is a 2 chain structure with sequence from Archaeoglobus fulgidus. 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

IDH_ARCFU

Evolutionary Conservation

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

Publication Abstract from PubMed

Isocitrate dehydrogenase from Archaeoglobus fulgidus (AfIDH) has an apparent melting temperature (T(m)) of 98.5 degrees C. To identify the structural features involved in thermal stabilization of AfIDH, the structure was solved to 2.5 A resolution. AfIDH was strikingly similar to mesophilic IDH from Escherichia coli (EcIDH) and displayed almost the same number of ion pairs and ionic networks. However, two unique inter-domain networks were present in AfIDH; one three-membered ionic network between the large and the small domain and one four-membered ionic network between the clasp and the small domain. The latter ionic network was presumably reduced in size when the clasp domain of AfIDH was swapped with that of EcIDH and the T (m) decreased by 18 degrees C. Contrarily, EcIDH was only stabilized by 4 degrees C by the clasp domain of AfIDH, a result probably due to the introduction of a unique inter-subunit aromatic cluster in AfIDH that may strengthen the dimeric interface in this enzyme. A unique aromatic cluster was identified close to the N-terminus of AfIDH that could provide additional stabilization of this region. Common and unique heat adaptive traits of AfIDH with those recently observed for hyperthermophilic IDH from Aeropyrum pernix (ApIDH) and Thermotoga maritima (TmIDH) are discussed herein.

Thermal stability of isocitrate dehydrogenase from Archaeoglobus fulgidus studied by crystal structure analysis and engineering of chimers.,Stokke R, Karlstrom M, Yang N, Leiros I, Ladenstein R, Birkeland NK, Steen IH Extremophiles. 2007 May;11(3):481-93. Epub 2007 Mar 31. PMID:17401542[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

See Also

References

  1. ↑ Stokke R, Karlstrom M, Yang N, Leiros I, Ladenstein R, Birkeland NK, Steen IH. Thermal stability of isocitrate dehydrogenase from Archaeoglobus fulgidus studied by crystal structure analysis and engineering of chimers. Extremophiles. 2007 May;11(3):481-93. Epub 2007 Mar 31. PMID:17401542 doi:10.1007/s00792-006-0060-z

2iv0, resolution 2.50Å

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