1cw4: Difference between revisions

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[[Image:1cw4.gif|left|200px]]


{{Structure
==CRYSTAL STRUCTURE OF K230M ISOCITRATE DEHYDROGENASE IN COMPLEX WITH ALPHA-KETOGLUTARATE==
|PDB= 1cw4 |SIZE=350|CAPTION= <scene name='initialview01'>1cw4</scene>, resolution 2.10&Aring;
<StructureSection load='1cw4' size='340' side='right'caption='[[1cw4]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
|SITE=  
== Structural highlights ==
|LIGAND= <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene> and <scene name='pdbligand=AKG:2-OXYGLUTARIC ACID'>AKG</scene>
<table><tr><td colspan='2'>[[1cw4]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1CW4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1CW4 FirstGlance]. <br>
|ACTIVITY= [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]  
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.1&#8491;</td></tr>
|GENE=  
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AKG:2-OXOGLUTARIC+ACID'>AKG</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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=1cw4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1cw4 OCA], [https://pdbe.org/1cw4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1cw4 RCSB], [https://www.ebi.ac.uk/pdbsum/1cw4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1cw4 ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/IDH_ECOLI IDH_ECOLI]
== 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/cw/1cw4_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=1cw4 ConSurf].
<div style="clear:both"></div>


'''CRYSTAL STRUCTURE OF K230M ISOCITRATE DEHYDROGENASE IN COMPLEX WITH ALPHA-KETOGLUTARATE'''
==See Also==
 
*[[Isocitrate dehydrogenase 3D structures|Isocitrate dehydrogenase 3D structures]]
 
__TOC__
==Overview==
</StructureSection>
Isocitrate dehydrogenase catalyses the two step, acid base, oxidative decarboxylation of isocitrate to alpha-ketoglutarate. Lysine 230 was suggested to act as proton donor based on geometry and spatial proximity to isocitrate. To clarify further the role of lysine 230, we co-crystallized the lysine-to-methionine mutant (K230M) with isocitrate and with alpha-ketoglutarate. Crystals were flash-frozen and the two structures were determined and refined to 2. 1 A. Several new features were identified relative to the wild-type structure. Seven side-chains previously unplaced in the wild-type structure were identified and included in the model, and the amino acid terminus was extended by an alanine residue. Many additional water molecules were identified.Examination of the K230M active sites (K230M isocitrate and K230M-ketoglutarate) revealed that tyrosine 160 protrudes further into the active site in the presence of either isocitrate or alpha-ketoglutarate in K230 M than it does in the wild-type structure. Also, methionine 230 was not as fully extended, and asparagine 232 rotates approximately 30 degrees toward the ligand permitting polar interactions. Outside the active site cleft a tetragonal volume of density was identified as a sulfate molecule. Its location and interactions suggest it may influence the equilibrium between the tetragonal and the orthorhombic forms of isocitrate dehydrogenase. Differences observed in the active site water structure between the wild-type and K230M structures were due to a single point mutation. A water molecule was located in the position equivalent to that occupied by the wild-type epsilon-amine of lysine 230; a water molecule in that location in K230M suggests it may influence catalysis in the mutant. Comparison of K230M complexed with isocitrate and alpha-ketoglutarate illuminates the influence a ligand has on active site water structure.
 
==About this Structure==
1CW4 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1CW4 OCA].
 
==Reference==
Active site water molecules revealed in the 2.1 A resolution structure of a site-directed mutant of isocitrate dehydrogenase., Cherbavaz DB, Lee ME, Stroud RM, Koshland DE Jr, J Mol Biol. 2000 Jan 21;295(3):377-85. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/10623532 10623532]
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
[[Category: Isocitrate dehydrogenase (NADP(+))]]
[[Category: Large Structures]]
[[Category: Single protein]]
[[Category: Finer-Moore J]]
[[Category: Finer-Moore, J.]]
[[Category: Stroud MR]]
[[Category: Stroud, M R.]]
[[Category: AKG]]
[[Category: MN]]
[[Category: SO4]]
[[Category: isocitrate dehydrogenase]]
[[Category: mutant]]
[[Category: oxidoreductase]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 10:29:38 2008''

Latest revision as of 09:46, 7 February 2024

CRYSTAL STRUCTURE OF K230M ISOCITRATE DEHYDROGENASE IN COMPLEX WITH ALPHA-KETOGLUTARATECRYSTAL STRUCTURE OF K230M ISOCITRATE DEHYDROGENASE IN COMPLEX WITH ALPHA-KETOGLUTARATE

Structural highlights

1cw4 is a 1 chain structure with sequence from Escherichia coli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.1Å
Ligands:, ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

IDH_ECOLI

Evolutionary Conservation

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

See Also

1cw4, resolution 2.10Å

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