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The | ==Crystal structure of holo D-serine dehydratase from Escherichia coli at 1.55 A resolution== | ||
<StructureSection load='3ss7' size='340' side='right'caption='[[3ss7]], [[Resolution|resolution]] 1.55Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[3ss7]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3SS7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3SS7 FirstGlance]. <br> | |||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr> | |||
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3ss9|3ss9]], [[3gwq|3gwq]], [[3awo|3awo]], [[3awn|3awn]], [[3anv|3anv]], [[3anu|3anu]], [[3roz|3roz]]</div></td></tr> | |||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">b2366, dsdA, dsdA b2366JW2393, JW2363 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr> | |||
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/D-serine_ammonia-lyase D-serine ammonia-lyase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.3.1.18 4.3.1.18] </span></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=3ss7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ss7 OCA], [https://pdbe.org/3ss7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ss7 RCSB], [https://www.ebi.ac.uk/pdbsum/3ss7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ss7 ProSAT]</span></td></tr> | |||
</table> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
D-Serine dehydratase from Escherichia coli is a member of the beta-family (fold-type II) of the pyridoxal 5'-phosphate-dependent enzymes, catalyzing the conversion of D-serine to pyruvate and ammonia. The crystal structure of monomeric D-serine dehydratase has been solved to 1.97A-resolution for an orthorhombic data set by molecular replacement. In addition, the structure was refined in a monoclinic data set to 1.55A resolution. The structure of DSD reveals a larger pyridoxal 5'-phosphate-binding domain and a smaller domain. The active site of DSD is very similar to those of the other members of the beta-family. Lys118 forms the Schiff base to PLP, the cofactor phosphate group is liganded to a tetraglycine cluster Gly279-Gly283, and the 3-hydroxyl group of PLP is liganded to Asn170 and N1 to Thr424, respectively. In the closed conformation the movement of the small domain blocks the entrance to active site of DSD. The domain movement plays an important role in the formation of the substrate recognition site and the catalysis of the enzyme. Modeling of D-serine into the active site of DSD suggests that the hydroxyl group of D-serine is coordinated to the carboxyl group of Asp238. The carboxyl oxygen of D-serine is coordinated to the hydroxyl group of Ser167 and the amide group of Leu171 (O1), whereas the O2 of the carboxyl group of D-serine is hydrogen-bonded to the hydroxyl group of Ser167 and the amide group of Thr168. A catalytic mechanism very similar to that proposed for L-serine dehydratase is discussed. | |||
Crystal structure of D-serine dehydratase from Escherichia coli.,Urusova DV, Isupov MN, Antonyuk S, Kachalova GS, Oblomova G, Vagin AA, Lebedev AA, Bourenko GP, Dauter Z, Bartunik HD, Lamzin VS, Melik-Adamyan WR, Mueller TD, Schnackerz KD Biochim Biophys Acta. 2011 Nov 27. PMID:22197591<ref>PMID:22197591</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 3ss7" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Deaminase 3D structures|Deaminase 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: D-serine ammonia-lyase]] | |||
[[Category: Ecoli]] | |||
[[Category: Large Structures]] | |||
[[Category: Antonyuk, S V]] | |||
[[Category: Bartunik, H D]] | |||
[[Category: Bourenkov, G P]] | |||
[[Category: Dauter, Z]] | |||
[[Category: Isupov, M N]] | |||
[[Category: Kachalova, G S]] | |||
[[Category: Lebedev, A A]] | |||
[[Category: Melik-Adamyan, W R]] | |||
[[Category: Mueller, T D]] | |||
[[Category: Schnackerz, K D]] | |||
[[Category: Urusova, D V]] | |||
[[Category: Vagin, A A]] | |||
[[Category: Alfa]] | |||
[[Category: Beta-elimination]] | |||
[[Category: D-serine dehydratase]] | |||
[[Category: Lyase]] | |||
[[Category: Pyridoxal-5'-phosphate]] | |||
[[Category: Type ii fold]] | |||