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| | ==Crystal structure of D-Cysteine desulfhydrase from Salmonella typhimurium at 2.2 A resolution== | | ==Crystal structure of D-Cysteine desulfhydrase from Salmonella typhimurium at 2.2 A resolution== |
| - | <StructureSection load='4d8t' size='340' side='right' caption='[[4d8t]], [[Resolution|resolution]] 2.28Å' scene=''> | + | <StructureSection load='4d8t' size='340' side='right'caption='[[4d8t]], [[Resolution|resolution]] 2.28Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4d8t]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4D8T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4D8T FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4d8t]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_Typhimurium Salmonella enterica subsp. enterica serovar Typhimurium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4D8T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4D8T 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=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.28Å</td></tr> |
| - | <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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BEN:BENZAMIDINE'>BEN</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=LLP:(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC+ACID'>LLP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4d8u|4d8u]], [[4d8w|4d8w]], [[4d92|4d92]], [[4d96|4d96]], [[4d97|4d97]], [[4d99|4d99]], [[4d9b|4d9b]], [[4d9c|4d9c]], [[4d9e|4d9e]], [[4d9f|4d9f]]</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=4d8t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4d8t OCA], [https://pdbe.org/4d8t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4d8t RCSB], [https://www.ebi.ac.uk/pdbsum/4d8t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4d8t ProSAT]</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=4d8t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4d8t OCA], [http://pdbe.org/4d8t PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4d8t RCSB], [http://www.ebi.ac.uk/pdbsum/4d8t PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4d8t ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/DCYD_SALTY 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] | + | [https://www.uniprot.org/uniprot/DCYD_SALTY 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] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: D-cysteine desulfhydrase]] | + | [[Category: Large Structures]] |
| - | [[Category: Bharath, S R]] | + | [[Category: Salmonella enterica subsp. enterica serovar Typhimurium]] |
| - | [[Category: Murthy, M R.N]]
| + | [[Category: Bharath SR]] |
| - | [[Category: Rajesh, K H]] | + | [[Category: Murthy MRN]] |
| - | [[Category: Savithri, H S]] | + | [[Category: Rajesh KH]] |
| - | [[Category: Shveta, B]] | + | [[Category: Savithri HS]] |
| - | [[Category: Fold type ii plp-dependent enzyme]] | + | [[Category: Shveta B]] |
| - | [[Category: Lyase]] | + | |
| - | [[Category: Tryptophan synthase beta subunit-like plp-dependent enzymes superfamily]]
| + | |
| 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 PubMed
Salmonella 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
- ↑ Bharath SR, Bisht S, Harijan RK, Savithri HS, Murthy MR. Structural and Mutational Studies on Substrate Specificity and Catalysis of Salmonella typhimurium D-Cysteine Desulfhydrase. PLoS One. 2012;7(5):e36267. Epub 2012 May 4. PMID:22574144 doi:10.1371/journal.pone.0036267
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