1n2t: Difference between revisions

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[[Image:1n2t.jpg|left|200px]]


{{Structure
==C-DES Mutant K223A with GLY Covalenty Linked to the PLP-cofactor==
|PDB= 1n2t |SIZE=350|CAPTION= <scene name='initialview01'>1n2t</scene>, resolution 2.00&Aring;
<StructureSection load='1n2t' size='340' side='right'caption='[[1n2t]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
|SITE=  
== Structural highlights ==
|LIGAND= <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5&#39;-PHOSPHATE'>PLP</scene> and <scene name='pdbligand=GLY:GLYCINE'>GLY</scene>
<table><tr><td colspan='2'>[[1n2t]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Synechocystis_sp._PCC_6714 Synechocystis sp. PCC 6714]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1N2T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1N2T FirstGlance]. <br>
|ACTIVITY=  
</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&#8491;</td></tr>
|GENE= C-DES ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1148 Synechocystis sp. PCC 6803])
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GLY:GLYCINE'>GLY</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</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=1n2t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1n2t OCA], [https://pdbe.org/1n2t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1n2t RCSB], [https://www.ebi.ac.uk/pdbsum/1n2t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1n2t ProSAT]</span></td></tr>
 
</table>
'''C-DES Mutant K223A with GLY Covalenty Linked to the PLP-cofactor'''
== Function ==
 
[https://www.uniprot.org/uniprot/Q9ZHG9_SYNY4 Q9ZHG9_SYNY4]
 
== Evolutionary Conservation ==
==Overview==
[[Image:Consurf_key_small.gif|200px|right]]
The cystine lyase (C-DES) of Synechocystis is a pyridoxal-5'-phosphate-dependent enzyme distantly related to the family of NifS-like proteins. The crystal structure of an N-terminal modified variant has recently been determined. Herein, the reactivity of this enzyme variant was investigated spectroscopically in solution and in the crystalline state to follow the course of the reaction and to determine the catalytic mechanism on a molecular level. Using the stopped-flow technique, the reaction with the preferred substrate cystine was found to follow biphasic kinetics leading to the formation of absorbing species at 338 and 470 nm, attributed to the external aldimine and the alpha-aminoacrylate; the reaction with cysteine also exhibited biphasic behavior but only the external aldimine accumulated. The same reaction intermediates were formed in crystals as seen by polarized absorption microspectrophotometry, thus indicating that C-DES is catalytically competent in the crystalline state. The three-dimensional structure of the catalytically inactive mutant C-DES(K223A) in the presence of cystine showed the formation of an external aldimine species, in which two alternate conformations of the substrate were observed. The combined results allow a catalytic mechanism to be proposed involving interactions between cystine and the active site residues Arg-360, Arg-369, and Trp-251*; these residues reorient during the beta-elimination reaction, leading to the formation of a hydrophobic pocket that stabilizes the enolimine tautomer of the aminoacrylate and the cysteine persulfide product.
Check<jmol>
 
  <jmolCheckbox>
==About this Structure==
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/n2/1n2t_consurf.spt"</scriptWhenChecked>
1N2T is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Synechocystis_sp._pcc_6803 Synechocystis sp. pcc 6803]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1N2T OCA].  
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
 
    <text>to colour the structure by Evolutionary Conservation</text>
==Reference==
  </jmolCheckbox>
Snapshots of the cystine lyase C-DES during catalysis. Studies in solution and in the crystalline state., Kaiser JT, Bruno S, Clausen T, Huber R, Schiaretti F, Mozzarelli A, Kessler D, J Biol Chem. 2003 Jan 3;278(1):357-65. Epub 2002 Oct 16. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12386155 12386155]
</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=1n2t ConSurf].
[[Category: Single protein]]
<div style="clear:both"></div>
[[Category: Synechocystis sp. pcc 6803]]
__TOC__
[[Category: Bruno, S.]]
</StructureSection>
[[Category: Clausen, T.]]
[[Category: Large Structures]]
[[Category: Huber, R.]]
[[Category: Synechocystis sp. PCC 6714]]
[[Category: Kaiser, J T.]]
[[Category: Bruno S]]
[[Category: Kessler, D.]]
[[Category: Clausen T]]
[[Category: Mozzarelli, A.]]
[[Category: Huber R]]
[[Category: Schiaretti, F.]]
[[Category: Kaiser JT]]
[[Category: GLY]]
[[Category: Kessler D]]
[[Category: K]]
[[Category: Mozzarelli A]]
[[Category: PLP]]
[[Category: Schiaretti F]]
[[Category: fes cluster biosynthesis]]
[[Category: inactive mutant]]
[[Category: nif]]
[[Category: pyridoxal 5'-phosphate]]
 
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Retrieved from "https://proteopedia.org/1n2t"