3a3u: Difference between revisions
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==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== | ||
<StructureSection load='3a3u' size='340' side='right' caption='[[3a3u]], [[Resolution|resolution]] 1.65Å' scene=''> | <StructureSection load='3a3u' size='340' side='right'caption='[[3a3u]], [[Resolution|resolution]] 1.65Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[3a3u]] is a 1 chain structure with sequence from [ | <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> | ||
</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.65Å</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> | |||
<tr | <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> | |||
<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 == | == Evolutionary Conservation == | ||
[[Image:Consurf_key_small.gif|200px|right]] | [[Image:Consurf_key_small.gif|200px|right]] | ||
Check<jmol> | Check<jmol> | ||
<jmolCheckbox> | <jmolCheckbox> | ||
<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/a3/3a3u_consurf.spt"</scriptWhenChecked> | <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> | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | ||
<text>to colour the structure by Evolutionary Conservation</text> | <text>to colour the structure by Evolutionary Conservation</text> | ||
</jmolCheckbox> | </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/ | </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="clear:both"></div> | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
| Line 26: | Line 28: | ||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
</div> | </div> | ||
<div class="pdbe-citations 3a3u" style="background-color:#fffaf0;"></div> | |||
== References == | == References == | ||
<references/> | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Thermus thermophilus]] | [[Category: Large Structures]] | ||
[[Category: Arai | [[Category: Thermus thermophilus HB8]] | ||
[[Category: Katsura | [[Category: Arai R]] | ||
[[Category: Kuramitsu | [[Category: Katsura K]] | ||
[[Category: Murayama | [[Category: Kuramitsu S]] | ||
[[Category: Nagano | [[Category: Murayama K]] | ||
[[Category: Nishimoto | [[Category: Nagano K]] | ||
[[Category: Nishino | [[Category: Nishimoto M]] | ||
[[Category: Nishino A]] | |||
[[Category: Shirouzu | [[Category: Shirouzu M]] | ||
[[Category: Terada | [[Category: Terada T]] | ||
[[Category: Toyama | [[Category: Toyama M]] | ||
[[Category: Uchikubo-Kamo | [[Category: Uchikubo-Kamo T]] | ||
[[Category: Yokoyama | [[Category: Yokoyama S]] | ||