1twi: Difference between revisions

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-{{Seed}}
-[[Image:1twi.png|left|200px]]
-<!--
+==Crystal structure of Diaminopimelate Decarboxylase from m. jannaschii in co-complex with L-lysine==
-The line below this paragraph, containing "STRUCTURE_1twi", creates the "Structure Box" on the page.
+<StructureSection load='1twi' size='340' side='right'caption='[[1twi]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[1twi]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii Methanocaldococcus jannaschii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TWI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1TWI FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=LYS:LYSINE'>LYS</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr>
-{{STRUCTURE_1twi|  PDB=1twi  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1twi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1twi OCA], [https://pdbe.org/1twi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1twi RCSB], [https://www.ebi.ac.uk/pdbsum/1twi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1twi ProSAT], [https://www.topsan.org/Proteins/NYSGXRC/1twi TOPSAN]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/DCDA_METJA DCDA_METJA] Specifically catalyzes the decarboxylation of meso-diaminopimelate (meso-DAP) to L-lysine.<ref>PMID:12429091</ref>
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/tw/1twi_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</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=1twi ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Cocrystal structures of Methanococcus jannaschii diaminopimelate decarboxylase (DAPDC) bound to a substrate analog, azelaic acid, and its L-lysine product have been determined at 2.6 A and 2.0 A, respectively. This PLP-dependent enzyme is responsible for the final step of L-lysine biosynthesis in bacteria and plays a role in beta-lactam antibiotic resistance in Staphylococcus aureus. Substrate specificity derives from recognition of the L-chiral center of diaminopimelate and a system of ionic "molecular rulers" that dictate substrate length. A coupled-enzyme assay system permitted measurement of kinetic parameters for recombinant DAPDCs and inhibition constants (K(i)) for azelaic acid (89 microM) and other substrate analogs. Implications for rational design of broad-spectrum antimicrobial agents targeted against DAPDCs of drug-resistant strains of bacterial pathogens, such as Staphylococcus aureus, are discussed.
-===Crystal structure of Diaminopimelate Decarboxylase from m. jannaschii in co-complex with L-lysine===
+Cocrystal structures of diaminopimelate decarboxylase: mechanism, evolution, and inhibition of an antibiotic resistance accessory factor.,Ray SS, Bonanno JB, Rajashankar KR, Pinho MG, He G, De Lencastre H, Tomasz A, Burley SK Structure. 2002 Nov;10(11):1499-508. PMID:12429091<ref>PMID:12429091</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_12429091}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 1twi" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 12429091 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_12429091}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-TWI is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii Methanocaldococcus jannaschii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TWI OCA].
-==Reference==
-Cocrystal structures of diaminopimelate decarboxylase: mechanism, evolution, and inhibition of an antibiotic resistance accessory factor., Ray SS, Bonanno JB, Rajashankar KR, Pinho MG, He G, De Lencastre H, Tomasz A, Burley SK, Structure. 2002 Nov;10(11):1499-508. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12429091 12429091]
-[[Category: Diaminopimelate decarboxylase]]
 [[Category: Methanocaldococcus jannaschii]]
-[[Category: Single protein]]
+[[Category: Bonanno JB]]
-[[Category: Bonanno, J B.]]
+[[Category: Burley SK]]
-[[Category: Burley, S K.]]
+[[Category: De Lencastre H]]
-[[Category: He, G.]]
+[[Category: He G]]
-[[Category: Lencastre, H De.]]
+[[Category: Pinho MG]]
-[[Category: NYSGXRC, New York Structural GenomiX Research Consortium.]]
+[[Category: Rajashankar KR]]
-[[Category: Pinho, M G.]]
+[[Category: Ray SS]]
-[[Category: Rajashankar, K R.]]
+[[Category: Tomasz A]]
-[[Category: Ray, S S.]]
-[[Category: Tomasz, A.]]
-[[Category: Antibiotic resistance]]
-[[Category: Diaminopimelate decarboxylase]]
-[[Category: Lysine biosynthesis]]
-[[Category: New york structural genomix research consortium]]
-[[Category: Nysgxrc]]
-[[Category: Protein structure initiative]]
-[[Category: Psi]]
-[[Category: Structural genomic]]
-[[Category: T135]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 14:38:01 2008''