3ss9: Difference between revisions
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==Crystal structure of holo D-serine dehydratase from Escherichia coli at 1.97 A resolution== | ==Crystal structure of holo D-serine dehydratase from Escherichia coli at 1.97 A resolution== | ||
<StructureSection load='3ss9' size='340' side='right' caption='[[3ss9]], [[Resolution|resolution]] 1.97Å' scene=''> | <StructureSection load='3ss9' size='340' side='right' caption='[[3ss9]], [[Resolution|resolution]] 1.97Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[3ss9]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/ | <table><tr><td colspan='2'>[[3ss9]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3SS9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3SS9 FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr> | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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">[[3ss7|3ss7]], [[3awo|3awo]], [[3awn|3awn]], [[3anv|3anv]], [[3rox|3rox]], [[3roz|3roz]]</td></tr> | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3ss7|3ss7]], [[3awo|3awo]], [[3awn|3awn]], [[3anv|3anv]], [[3rox|3rox]], [[3roz|3roz]]</td></tr> | ||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">b2366, dsdA, dsdA b2366JW2393, JW2363 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id= | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">b2366, dsdA, dsdA b2366JW2393, JW2363 ([http://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'>[http://en.wikipedia.org/wiki/D-serine_ammonia-lyase D-serine ammonia-lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.3.1.18 4.3.1.18] </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-serine_ammonia-lyase D-serine ammonia-lyase], with EC number [http://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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3ss9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ss9 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ss9 RCSB], [http://www.ebi.ac.uk/pdbsum/3ss9 PDBsum]</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=3ss9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ss9 OCA], [http://pdbe.org/3ss9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3ss9 RCSB], [http://www.ebi.ac.uk/pdbsum/3ss9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3ss9 ProSAT]</span></td></tr> | ||
</table> | </table> | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
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From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
</div> | </div> | ||
<div class="pdbe-citations 3ss9" style="background-color:#fffaf0;"></div> | |||
==See Also== | ==See Also== | ||
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</StructureSection> | </StructureSection> | ||
[[Category: D-serine ammonia-lyase]] | [[Category: D-serine ammonia-lyase]] | ||
[[Category: | [[Category: Ecoli]] | ||
[[Category: Antonyuk, S V]] | [[Category: Antonyuk, S V]] | ||
[[Category: Bartunik, H D]] | [[Category: Bartunik, H D]] | ||
Revision as of 18:16, 11 August 2016
Crystal structure of holo D-serine dehydratase from Escherichia coli at 1.97 A resolutionCrystal structure of holo D-serine dehydratase from Escherichia coli at 1.97 A resolution
Structural highlights
Publication Abstract from PubMedD-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[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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