View source for 4d9b


==Pyridoxamine 5' phosphate (PMP) bound form of Salmonella typhimurium D-Cysteine desulfhydrase obtained after co-crystallization with D-cycloserine==
<StructureSection load='4d9b' size='340' side='right' caption='[[4d9b]], [[Resolution|resolution]] 1.67&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[4d9b]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_typhimurium"_loeffler_1892 "bacillus typhimurium" loeffler 1892]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4D9B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4D9B 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=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=PMP:4-DEOXY-4-AMINOPYRIDOXAL-5-PHOSPHATE'>PMP</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]], [[4d97|4d97]], [[4d99|4d99]], [[4d9c|4d9c]], [[4d9e|4d9e]], [[4d9f|4d9f]]</td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">dcyD, STM1953 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=90371 "Bacillus typhimurium" Loeffler 1892])</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=4d9b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4d9b OCA], [http://pdbe.org/4d9b PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4d9b RCSB], [http://www.ebi.ac.uk/pdbsum/4d9b PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4d9b ProSAT]</span></td></tr>
</table>
== 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] 
<div style="background-color:#fffaf0;">
== 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<ref>PMID:22574144</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 4d9b" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Bacillus typhimurium loeffler 1892]]
[[Category: D-cysteine desulfhydrase]]
[[Category: Bharath, S R]]
[[Category: Murthy, M R.N]]
[[Category: Rajesh, K H]]
[[Category: Savithri, H S]]
[[Category: Shveta, B]]
[[Category: Fold type ii plp-dependent enzyme or tryptophan synthase beta subunit like family]]
[[Category: Lyase]]
[[Category: Plp dependent enzyme]]