3a3u: Difference between revisions

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-{{Seed}}
-[[Image:3a3u.jpg|left|200px]]
-<!--
+==Crystal structure of MqnD (TTHA1568), a menaquinone biosynthetic enzyme from Thermus thermophilus HB8==
-The line below this paragraph, containing "STRUCTURE_3a3u", creates the "Structure Box" on the page.
+<StructureSection load='3a3u' size='340' side='right'caption='[[3a3u]], [[Resolution|resolution]] 1.65&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'>[[3a3u]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB8 Thermus thermophilus HB8]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2dbp 2dbp]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3A3U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3A3U 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]] 1.65&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=7PE:2-(2-(2-(2-(2-(2-ETHOXYETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHANOL'>7PE</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=TLA:L(+)-TARTARIC+ACID'>TLA</scene></td></tr>
-{{STRUCTURE_3a3u|  PDB=3a3u  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3a3u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3a3u OCA], [https://pdbe.org/3a3u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3a3u RCSB], [https://www.ebi.ac.uk/pdbsum/3a3u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3a3u ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/MQND_THET8 MQND_THET8] Catalyzes the conversion of cyclic dehypoxanthine futalosine (cyclic DHFL) into 1,4-dihydroxy-6-naphthoate, a step in the biosynthesis of menaquinone (MK, vitamin K2).[HAMAP-Rule:MF_00996]<ref>PMID:18801996</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/a3/3a3u_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=3a3u ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+In many microorganisms, menaquinone is an essential lipid-soluble electron carrier. Recently, an alternative menaquinone biosynthetic pathway was found in some microorganisms [Hiratsuka, T., Furihata, K., Ishikawa, J., Yamashita, H., Itoh, N., Seto, H., Dairi, T., 2008. An alternative menaquinone biosynthetic pathway operating in microorganisms. Science 321, 1670-1673]. Here, we report the 1.55 A crystal structure of MqnD (TTHA1568) from Thermus thermophilus HB8, an enzyme within the alternative menaquinone biosynthetic pathway. The structure comprises two domains with alpha/beta structures, a large domain and a small domain. L(+)-Tartaric acid was bound to the pocket between the two domains, suggesting that this pocket is a putative active site. The conserved glycine residues at positions 78, 80 and 82 seem to act as hinges, allowing the substrate to access the pocket. Highly conserved residues, such as Asp14, Asp38, Asn43, Ser57, Thr107, Ile144, His145, Glu146, Leu176 and Tyr234, are located at this pocket, suggesting that these residues are involved in substrate binding and/or catalysis, and especially, His145 could function as a catalytic base. Since humans and their commensal intestinal bacteria, including lactobacilli, lack the alternative menaquinone biosynthetic pathway, this enzyme in pathogenic species, such as Helicobacter pylori and Campylobacter jejuni, is an attractive target for the development of chemotherapeutics. This high-resolution structure may contribute toward the development of its inhibitors.
-===Crystal structure of MqnD (TTHA1568), a menaquinone biosynthetic enzyme from Thermus thermophilus HB8===
+Crystal structure of MqnD (TTHA1568), a menaquinone biosynthetic enzyme from Thermus thermophilus HB8.,Arai R, Murayama K, Uchikubo-Kamo T, Nishimoto M, Toyama M, Kuramitsu S, Terada T, Shirouzu M, Yokoyama S J Struct Biol. 2009 Dec;168(3):575-81. Epub 2009 Jul 12. PMID:19602440<ref>PMID:19602440</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-==About this Structure==
+</div>
-A3U is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus_hb8 Thermus thermophilus hb8]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2dbp 2dbp]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3A3U OCA].
+<div class="pdbe-citations 3a3u" style="background-color:#fffaf0;"></div>
-[[Category: Thermus thermophilus hb8]]
+== References ==
-[[Category: Arai, R.]]
+<references/>
-[[Category: Katsura, K.]]
+__TOC__
-[[Category: Kuramitsu, S.]]
+</StructureSection>
-[[Category: Murayama, K.]]
+[[Category: Large Structures]]
-[[Category: Nagano, K.]]
+[[Category: Thermus thermophilus HB8]]
-[[Category: Nishimoto, M.]]
+[[Category: Arai R]]
-[[Category: Nishino, A.]]
+[[Category: Katsura K]]
-[[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]]
+[[Category: Kuramitsu S]]
-[[Category: Shirouzu, M.]]
+[[Category: Murayama K]]
-[[Category: Terada, T.]]
+[[Category: Nagano K]]
-[[Category: Toyama, M.]]
+[[Category: Nishimoto M]]
-[[Category: Uchikubo-Kamo, T.]]
+[[Category: Nishino A]]
-[[Category: Yokoyama, S.]]
+[[Category: Shirouzu M]]
-[[Category: Alpha/beta structure]]
+[[Category: Terada T]]
-[[Category: Biosynthetic protein]]
+[[Category: Toyama M]]
-[[Category: National project on protein structural and functional analyse]]
+[[Category: Uchikubo-Kamo T]]
-[[Category: Nppsfa]]
+[[Category: Yokoyama S]]
-[[Category: Riken structural genomics/proteomics initiative]]
-[[Category: Rsgi]]
-[[Category: Structural genomic]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jul 15 08:38:27 2009''