3vfl: Difference between revisions

← Older edit

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

OCA

@@ Line 1: / Line 1: @@
 ==Structure, Function, Stability and Knockout Phenotype of Dihydrodipicolinate Synthase from Streptococcus pneumoniae==
-<StructureSection load='3vfl' size='340' side='right' caption='[[3vfl]], [[Resolution|resolution]] 1.91&Aring;' scene=''>
+<StructureSection load='3vfl' size='340' side='right'caption='[[3vfl]], [[Resolution|resolution]] 1.91&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3vfl]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Streptococcus_pneumoniae_sp3-bs71 Streptococcus pneumoniae sp3-bs71]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3h5d 3h5d]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VFL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3VFL FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3vfl]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptococcus_pneumoniae_SP3-BS71 Streptococcus pneumoniae SP3-BS71]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3h5d 3h5d]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VFL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3VFL FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</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]] 1.91&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3bi8|3bi8]], [[3du0|3du0]], [[3hij|3hij]]</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=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">CGSSp3BS71_00085, dapA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=406556 Streptococcus pneumoniae SP3-BS71])</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=3vfl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vfl OCA], [https://pdbe.org/3vfl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3vfl RCSB], [https://www.ebi.ac.uk/pdbsum/3vfl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3vfl 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/4-hydroxy-tetrahydrodipicolinate_synthase 4-hydroxy-tetrahydrodipicolinate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.3.3.7 4.3.3.7] </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=3vfl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vfl OCA], [http://pdbe.org/3vfl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3vfl RCSB], [http://www.ebi.ac.uk/pdbsum/3vfl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3vfl ProSAT]</span></td></tr>
 </table>
-== Function ==
-[[http://www.uniprot.org/uniprot/A5LD17_STREE A5LD17_STREE]] Catalyzes the condensation of (S)-aspartate-beta-semialdehyde [(S)-ASA] and pyruvate to 4-hydroxy-tetrahydrodipicolinate (HTPA) (By similarity).[HAMAP-Rule:MF_00418][SAAS:SAAS005263_004_011311]
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-Dihydrodipicolinate synthase (DHDPS; EC 4.2.1.52) catalyzes the rate-limiting step in the (S)-lysine biosynthesis pathway of bacteria and plants. Here, the cloning of the DHDPS gene from a clinical isolate of Streptococcus pneumoniae (OXC141 strain) and the strategy used to express, purify and crystallize the recombinant enzyme are described. Diffracting crystals were grown in high-molecular-weight PEG precipitants using the hanging-drop vapour-diffusion method. The best crystal, from which data were collected, diffracted to beyond 2.0 A resolution. Initially, the crystals were thought to belong to space group P4(2)2(1)2, with unit-cell parameters a = 105.5, b = 105.5, c = 62.4 A. However, the R factors remained high following initial processing of the data. It was subsequently shown that the data set was twinned and it was thus reprocessed in space group P2, resulting in a significant reduction in the R factors. Determination of the structure will provide insight into the design of novel antimicrobial agents targeting this important enzyme from S. pneumoniae.
-Crystallization of dihydrodipicolinate synthase from a clinical isolate of Streptococcus pneumoniae.,Sibarani NE, Gorman MA, Dogovski C, Parker MW, Perugini MA Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010 Jan 1;66(Pt, 1):32-6. Epub 2009 Dec 25. PMID:20057065<ref>PMID:20057065</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 3vfl" style="background-color:#fffaf0;"></div>
 ==See Also==
 *[[Dihydrodipicolinate synthase|Dihydrodipicolinate synthase]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: 4-hydroxy-tetrahydrodipicolinate synthase]]
+[[Category: Large Structures]]
-[[Category: Streptococcus pneumoniae sp3-bs71]]
+[[Category: Streptococcus pneumoniae SP3-BS71]]
-[[Category: Gorman, M A]]
+[[Category: Gorman MA]]
-[[Category: Dihydrodipicolinate synthase]]
-[[Category: Lyase]]
-[[Category: Lysine biosynthesis]]