4d97: Difference between revisions
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<StructureSection load='4d97' size='340' side='right' caption='[[4d97]], [[Resolution|resolution]] 1.77Å' scene=''> | <StructureSection load='4d97' size='340' side='right' caption='[[4d97]], [[Resolution|resolution]] 1.77Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[4d97]] is a 4 chain structure | <table><tr><td colspan='2'>[[4d97]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4D97 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4D97 FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BEN:BENZAMIDINE'>BEN</scene>, <scene name='pdbligand=DSN:D-SERINE'>DSN</scene></td></tr> | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BEN:BENZAMIDINE'>BEN</scene>, <scene name='pdbligand=DSN:D-SERINE'>DSN</scene></td></tr> | ||
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand= | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=LLP:(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC+ACID'>LLP</scene></td></tr> | ||
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4d8t|4d8t]], [[4d8u|4d8u]], [[4d8w|4d8w]], [[4d92|4d92]], [[4d96|4d96]], [[4d99|4d99]], [[4d9b|4d9b]], [[4d9c|4d9c]], [[4d9e|4d9e]], [[4d9f|4d9f]]</td></tr> | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4d8t|4d8t]], [[4d8u|4d8u]], [[4d8w|4d8w]], [[4d92|4d92]], [[4d96|4d96]], [[4d99|4d99]], [[4d9b|4d9b]], [[4d9c|4d9c]], [[4d9e|4d9e]], [[4d9f|4d9f]]</td></tr> | ||
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/D-cysteine_desulfhydrase D-cysteine desulfhydrase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.4.1.15 4.4.1.15] </span></td></tr> | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/D-cysteine_desulfhydrase D-cysteine desulfhydrase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.4.1.15 4.4.1.15] </span></td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4d97 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4d97 OCA], [http://pdbe.org/4d97 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4d97 RCSB], [http://www.ebi.ac.uk/pdbsum/4d97 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4d97 ProSAT]</span></td></tr> | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4d97 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4d97 OCA], [http://pdbe.org/4d97 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4d97 RCSB], [http://www.ebi.ac.uk/pdbsum/4d97 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4d97 ProSAT]</span></td></tr> | ||
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__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: D-cysteine desulfhydrase]] | [[Category: D-cysteine desulfhydrase]] | ||
[[Category: Bharath, S R]] | [[Category: Bharath, S R]] | ||
Revision as of 09:26, 10 May 2017
Salmonella typhimurium D-Cysteine desulfhydrase with D-ser bound at active siteSalmonella typhimurium D-Cysteine desulfhydrase with D-ser bound at active site
Structural highlights
Function[DCYD_SALTY] Catalyzes the alpha,beta-elimination reaction of D-cysteine and of several D-cysteine derivatives. It could be a defense mechanism against D-cysteine.[HAMAP-Rule:MF_01045] Publication Abstract from PubMedSalmonella typhimurium DCyD (StDCyD) is a fold type II pyridoxal 5' phosphate (PLP)-dependent enzyme that catalyzes the degradation of D-Cys to H(2)S and pyruvate. It also efficiently degrades beta-chloro-D-alanine (betaCDA). D-Ser is a poor substrate while the enzyme is inactive with respect to L-Ser and 1-amino-1-carboxy cyclopropane (ACC). Here, we report the X-ray crystal structures of StDCyD and of crystals obtained in the presence of D-Cys, betaCDA, ACC, D-Ser, L-Ser, D-cycloserine (DCS) and L-cycloserine (LCS) at resolutions ranging from 1.7 to 2.6 A. The polypeptide fold of StDCyD consisting of a small domain (residues 48-161) and a large domain (residues 1-47 and 162-328) resembles other fold type II PLP dependent enzymes. The structures obtained in the presence of D-Cys and betaCDA show the product, pyruvate, bound at a site 4.0-6.0 A away from the active site. ACC forms an external aldimine complex while D- and L-Ser bind non-covalently suggesting that the reaction with these ligands is arrested at Calpha proton abstraction and transimination steps, respectively. In the active site of StDCyD cocrystallized with DCS or LCS, electron density for a pyridoxamine phosphate (PMP) was observed. Crystals soaked in cocktail containing these ligands show density for PLP-cycloserine. Spectroscopic observations also suggest formation of PMP by the hydrolysis of cycloserines. Mutational studies suggest that Ser78 and Gln77 are key determinants of enzyme specificity and the phenolate of Tyr287 is responsible for Calpha proton abstraction from D-Cys. Based on these studies, a probable mechanism for the degradation of D-Cys by StDCyD is proposed. Structural and Mutational Studies on Substrate Specificity and Catalysis of Salmonella typhimurium D-Cysteine Desulfhydrase.,Bharath SR, Bisht S, Harijan RK, Savithri HS, Murthy MR PLoS One. 2012;7(5):e36267. Epub 2012 May 4. PMID:22574144[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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