1k1d: Difference between revisions

← Older edit

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 3: / Line 3: @@
 <StructureSection load='1k1d' size='340' side='right'caption='[[1k1d]], [[Resolution|resolution]] 3.01&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1k1d]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_12980 Atcc 12980]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K1D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1K1D FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1k1d]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K1D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1K1D FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 3.01&#8491;</td></tr>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=1k1d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k1d OCA], [https://pdbe.org/1k1d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1k1d RCSB], [https://www.ebi.ac.uk/pdbsum/1k1d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1k1d ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/HYDA_GEOSE HYDA_GEOSE]] Catalyzes the stereospecific hydrolysis of the cyclic amide bond of D-hydantoin. Has no activity on dihydropyrimidines.
+[https://www.uniprot.org/uniprot/HYDA_GEOSE HYDA_GEOSE] Catalyzes the stereospecific hydrolysis of the cyclic amide bond of D-hydantoin. Has no activity on dihydropyrimidines.
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 20: / Line 20: @@
 </jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1k1d ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-Industrial production of antibiotics, such as semisynthetic penicillins and cephalosporins, requires optically pure D-p-hydroxylphenylglycine and its derivatives as important side-chain precursors. To produce optically pure D-amino acids, microbial D-hydantoinase (E.C. 3.5.2.2) is used for stereospecific hydrolysis of chemically synthesized cyclic hydantoins. We report the apo-crystal structure of D-hydantoinase from B. stearothermophilus SD1 at 3.0 A resolution. The structure has a classic TIM barrel fold. Despite an undetectable similarity in sequence, D-hydantoinase shares a striking structural similarity with the recently solved structure of dihydroorotase. A structural comparison of hydantoinase with dihydroorotase revealed that the catalytic chemistry is conserved, while the substrate recognition is not. This structure provides insight into the stereochemistry of enantioselectivity in hydrolysis and illustrates how the enzyme recognizes stereospecific exocyclic substituents and hydrolyzes hydantoins. It should also provide a rationale for further directed evolution of this enzyme for hydrolysis of new hydantoins with novel exocyclic substituents.
-Crystal structure of D-hydantoinase from Bacillus stearothermophilus: insight into the stereochemistry of enantioselectivity.,Cheon YH, Kim HS, Han KH, Abendroth J, Niefind K, Schomburg D, Wang J, Kim Y Biochemistry. 2002 Jul 30;41(30):9410-7. PMID:12135362<ref>PMID:12135362</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 1k1d" style="background-color:#fffaf0;"></div>
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Atcc 12980]]
+[[Category: Geobacillus stearothermophilus]]
 [[Category: Large Structures]]
-[[Category: Abendroth, J]]
+[[Category: Abendroth J]]
-[[Category: Cheon, Y H]]
+[[Category: Cheon YH]]
-[[Category: Han, K H]]
+[[Category: Han KH]]
-[[Category: Kim, H S]]
+[[Category: Kim HS]]
-[[Category: Kim, Y]]
+[[Category: Kim Y]]
-[[Category: Niefind, K]]
+[[Category: Niefind K]]
-[[Category: Schomburg, D]]
+[[Category: Schomburg D]]
-[[Category: Wang, J]]
+[[Category: Wang J]]
-[[Category: D-hydantoinase]]
-[[Category: Hydrolase]]