1n31: Difference between revisions
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< | ==Structure of A Catalytically Inactive Mutant (K223A) of C-DES with a Substrate (Cystine) Linked to the Co-Factor== | ||
<StructureSection load='1n31' size='340' side='right'caption='[[1n31]], [[Resolution|resolution]] 2.20Å' scene=''> | |||
You may | == Structural highlights == | ||
<table><tr><td colspan='2'>[[1n31]] 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=1N31 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1N31 FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.2Å</td></tr> | |||
-- | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CYS:CYSTEINE'>CYS</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=1n31 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1n31 OCA], [https://pdbe.org/1n31 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1n31 RCSB], [https://www.ebi.ac.uk/pdbsum/1n31 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1n31 ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/Q9ZHG9_SYNY4 Q9ZHG9_SYNY4] | |||
== 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/n3/1n31_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=1n31 ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
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. | |||
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:12386155<ref>PMID:12386155</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 1n31" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
== | [[Category: Large Structures]] | ||
[[Category: Synechocystis sp. PCC 6714]] | |||
[[Category: Bruno S]] | |||
== | [[Category: Clausen T]] | ||
[[Category: Huber R]] | |||
[[Category: | [[Category: Kaiser JT]] | ||
[[Category: Synechocystis sp. | [[Category: Kessler D]] | ||
[[Category: Bruno | [[Category: Mozzarelli A]] | ||
[[Category: Clausen | [[Category: Schiaretti F]] | ||
[[Category: Huber | |||
[[Category: Kaiser | |||
[[Category: Kessler | |||
[[Category: Mozzarelli | |||
[[Category: Schiaretti | |||
Latest revision as of 15:28, 13 December 2023
Structure of A Catalytically Inactive Mutant (K223A) of C-DES with a Substrate (Cystine) Linked to the Co-FactorStructure of A Catalytically Inactive Mutant (K223A) of C-DES with a Substrate (Cystine) Linked to the Co-Factor
Structural highlights
FunctionEvolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedThe 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. 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:12386155[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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