1mdo: 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: @@
-[[Image:1mdo.gif|left|200px]]
-<!--
-The line below this paragraph, containing "STRUCTURE_1mdo", creates the "Structure Box" on the page.
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-or leave the SCENE parameter empty for the default display.
--->
-{{STRUCTURE_1mdo|  PDB=1mdo  |  SCENE=  }}
-'''Crystal structure of ArnB aminotransferase with pyridomine 5' phosphate'''
+==Crystal structure of ArnB aminotransferase with pyridomine 5' phosphate==
+<StructureSection load='1mdo' size='340' side='right'caption='[[1mdo]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1mdo]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_Typhimurium Salmonella enterica subsp. enterica serovar Typhimurium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1MDO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1MDO FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.7&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=PMP:4-DEOXY-4-AMINOPYRIDOXAL-5-PHOSPHATE'>PMP</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=1mdo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1mdo OCA], [https://pdbe.org/1mdo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1mdo RCSB], [https://www.ebi.ac.uk/pdbsum/1mdo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1mdo ProSAT]</span></td></tr>
+</table>
+== 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/md/1mdo_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=1mdo ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Lipid A modification with 4-amino-4-deoxy-L-arabinose confers on certain pathogenic bacteria, such as Salmonella, resistance to cationic antimicrobial peptides, including those derived from the innate immune system. ArnB catalysis of amino group transfer from glutamic acid to the 4"-position of a UDP-linked ketopyranose molecule to form UDP-4-amino-4-deoxy-L-arabinose represents a key step in the lipid A modification pathway. Structural and functional studies of the ArnB aminotransferase were undertaken by combining X-ray crystallography with biochemical analyses. High-resolution crystal structures were solved for two native forms and one covalently inhibited form of S. typhimurium ArnB. These structures permitted identification of key residues involved in substrate binding and catalysis, including a rarely observed nonprolyl cis peptide bond in the active site.
-==Overview==
+Structural studies of Salmonella typhimurium ArnB (PmrH) aminotransferase: a 4-amino-4-deoxy-L-arabinose lipopolysaccharide-modifying enzyme.,Noland BW, Newman JM, Hendle J, Badger J, Christopher JA, Tresser J, Buchanan MD, Wright TA, Rutter ME, Sanderson WE, Muller-Dieckmann HJ, Gajiwala KS, Buchanan SG Structure. 2002 Nov;10(11):1569-80. PMID:12429098<ref>PMID:12429098</ref>
-Lipid A modification with 4-amino-4-deoxy-L-arabinose confers on certain pathogenic bacteria, such as Salmonella, resistance to cationic antimicrobial peptides, including those derived from the innate immune system. ArnB catalysis of amino group transfer from glutamic acid to the 4"-position of a UDP-linked ketopyranose molecule to form UDP-4-amino-4-deoxy-L-arabinose represents a key step in the lipid A modification pathway. Structural and functional studies of the ArnB aminotransferase were undertaken by combining X-ray crystallography with biochemical analyses. High-resolution crystal structures were solved for two native forms and one covalently inhibited form of S. typhimurium ArnB. These structures permitted identification of key residues involved in substrate binding and catalysis, including a rarely observed nonprolyl cis peptide bond in the active site.
-==About this Structure==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-MDO is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Salmonella_typhimurium Salmonella typhimurium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1MDO OCA].
+</div>
+<div class="pdbe-citations 1mdo" style="background-color:#fffaf0;"></div>
-==Reference==
+==See Also==
-Structural studies of Salmonella typhimurium ArnB (PmrH) aminotransferase: a 4-amino-4-deoxy-L-arabinose lipopolysaccharide-modifying enzyme., Noland BW, Newman JM, Hendle J, Badger J, Christopher JA, Tresser J, Buchanan MD, Wright TA, Rutter ME, Sanderson WE, Muller-Dieckmann HJ, Gajiwala KS, Buchanan SG, Structure. 2002 Nov;10(11):1569-80. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12429098 12429098]
+*[[Aminotransferase 3D structures|Aminotransferase 3D structures]]
-[[Category: Salmonella typhimurium]]
+== References ==
-[[Category: Single protein]]
+<references/>
-[[Category: Badger, J.]]
+__TOC__
-[[Category: Buchanan, M D.]]
+</StructureSection>
-[[Category: Buchanan, S G.]]
+[[Category: Large Structures]]
-[[Category: Christopher, J A.]]
+[[Category: Salmonella enterica subsp. enterica serovar Typhimurium]]
-[[Category: Gajiwala, K.]]
+[[Category: Badger J]]
-[[Category: Hendle, J.]]
+[[Category: Buchanan MD]]
-[[Category: Muller-Dieckmann, H J.]]
+[[Category: Buchanan SG]]
-[[Category: Newman, J M.]]
+[[Category: Christopher JA]]
-[[Category: Noland, B W.]]
+[[Category: Gajiwala K]]
-[[Category: Rutter, M E.]]
+[[Category: Hendle J]]
-[[Category: Sanderson, W E.]]
+[[Category: Muller-Dieckmann H-J]]
-[[Category: Tresser, J.]]
+[[Category: Newman JM]]
-[[Category: Wright, T.]]
+[[Category: Noland BW]]
-[[Category: Type 1 aminotransferase fold]]
+[[Category: Rutter ME]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May  3 00:55:02 2008''
+[[Category: Sanderson WE]]
+[[Category: Sauder JM]]
+[[Category: Tresser J]]
+[[Category: Wright T]]