3bm2: Difference between revisions

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-{{Seed}}
-[[Image:3bm2.png|left|200px]]
-<!--
+==Crystal structure of a minimal nitroreductase ydjA from Escherichia coli K12 with and without FMN cofactor==
-The line below this paragraph, containing "STRUCTURE_3bm2", creates the "Structure Box" on the page.
+<StructureSection load='3bm2' size='340' side='right'caption='[[3bm2]], [[Resolution|resolution]] 2.10&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'>[[3bm2]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BM2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3BM2 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]] 2.1&#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></td></tr>
-{{STRUCTURE_3bm2|  PDB=3bm2  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3bm2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bm2 OCA], [https://pdbe.org/3bm2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3bm2 RCSB], [https://www.ebi.ac.uk/pdbsum/3bm2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3bm2 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/YDJA_ECOLI YDJA_ECOLI]
+== 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/bm/3bm2_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=3bm2 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Nitroreductases (NTR) are enzymes that reduce hazardous nitroaromatic compounds and are of special interest due to their potential use in bioremediation and their activation of prodrugs in directed anticancer therapies. We elucidated the crystal structures of ydjA from Escherichia coli (Ec_ydjA), one of the smallest NTRs, in its flavin mononucleotide (FMN)-bound and cofactor-free forms. The alpha+beta mixed monomeric Ec_ydjA forms a homodimeric structure through the interactions of the long central helices and the extended regions at both termini. Two FMN molecules are bound at the dimeric interface. The absence of the 30 internal amino acids in Ec_ydjA, which forms two helices and restricts the cofactor and substrate binding in other NTR family members, creates a wider and more flexible active site. Unlike the bent FMN ring structures present in most NTR complexes currently known, the flavin system in the Ec_ydjA structure maintains a flat ring conformation, which is sandwiched between a Trp and a His residue from each monomer. The analysis of our Ec_ydjA structure explains its specificity for larger substrates and provides structural information for the rational design of novel prodrugs with the ability to reduce nitrogen-containing hazardous molecules.
-===Crystal structure of a minimal nitroreductase ydjA from Escherichia coli K12 with and without FMN cofactor===
+Crystal structure of a minimal nitroreductase, ydjA, from Escherichia coli K12 with and without FMN cofactor.,Choi JW, Lee J, Nishi K, Kim YS, Jung CH, Kim JS J Mol Biol. 2008 Mar 14;377(1):258-67. Epub 2008 Jan 11. PMID:18241886<ref>PMID:18241886</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3bm2" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_18241886}}, adds the Publication Abstract to the page
+*[[Nitroreductase 3D structures|Nitroreductase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 18241886 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_18241886}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Escherichia coli K-12]]
-BM2 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BM2 OCA].
+[[Category: Large Structures]]
+[[Category: Choi JW]]
-==Reference==
+[[Category: Kim JS]]
-Crystal structure of a minimal nitroreductase, ydjA, from Escherichia coli K12 with and without FMN cofactor., Choi JW, Lee J, Nishi K, Kim YS, Jung CH, Kim JS, J Mol Biol. 2008 Mar 14;377(1):258-67. Epub 2008 Jan 11. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18241886 18241886]
-[[Category: 6,7-dihydropteridine reductase]]
-[[Category: Escherichia coli]]
-[[Category: Single protein]]
-[[Category: Choi, J W.]]
-[[Category: Kim, J S.]]
-[[Category: Nitroreductase]]
-[[Category: Oxidoreductase]]
-[[Category: Ydja]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Jul 27 18:40:48 2008''