2vf5: Difference between revisions

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-[[Image:2vf5.png|left|200px]]
-<!--
+==Glucosamine-6-phosphate synthase in complex with glucosamine-6- phosphate==
-The line below this paragraph, containing "STRUCTURE_2vf5", creates the "Structure Box" on the page.
+<StructureSection load='2vf5' size='340' side='right'caption='[[2vf5]], [[Resolution|resolution]] 2.90&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'>[[2vf5]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VF5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VF5 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]] 2.9&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GLP:GLUCOSAMINE+6-PHOSPHATE'>GLP</scene></td></tr>
-{{STRUCTURE_2vf5|  PDB=2vf5  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2vf5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vf5 OCA], [https://pdbe.org/2vf5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2vf5 RCSB], [https://www.ebi.ac.uk/pdbsum/2vf5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2vf5 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/GLMS_ECOLI GLMS_ECOLI] Catalyzes the first step in hexosamine metabolism, converting fructose-6P into glucosamine-6P using glutamine as a nitrogen source.
+== 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/vf/2vf5_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=2vf5 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Glucosamine-6-phosphate synthase (GlmS) channels ammonia from glutamine at the glutaminase site to fructose 6-phosphate (Fru6P) at the synthase site. Escherichia coli GlmS is composed of two C-terminal synthase domains that form the dimer interface and two N-terminal glutaminase domains at its periphery. We report the crystal structures of GlmS alone and in complex with the glucosamine-6-phosphate product at 2.95 A and 2.9 A resolution, respectively. Surprisingly, although the whole protein is present in this crystal form, no electron density for the glutaminase domain was observed, indicating its mobility. Comparison of the two structures with that of the previously reported GlmS-Fru6P complex shows that, upon sugar binding, the C-terminal loop, which forms the major part of the channel walls, becomes ordered and covers the synthase site. The ordering of the glutaminase domains likely follows Fru6P binding by the anchoring of Trp74, which acts as the gate of the channel, on the closed C-terminal loop. This is accompanied by a major conformational change of the side chain of Lys503# of the neighboring synthase domain that strengthens the interactions of the synthase domain with the C-terminal loop and completely shields the synthase site. The concomitant conformational change of the Lys503#-Gly505# tripeptide places catalytic His504# in the proper position to open the sugar and buries the linear sugar, which is now in the vicinity of the catalytic groups involved in the sugar isomerization reaction. Together with the previously reported structures of GlmS in complex with Fru6P or glucose 6-phosphate and a glutamine analogue, the new structures reveal the structural changes occurring during the whole catalytic cycle.
-===GLUCOSAMINE-6-PHOSPHATE SYNTHASE IN COMPLEX WITH GLUCOSAMINE-6-PHOSPHATE===
+Ordering of C-terminal loop and glutaminase domains of glucosamine-6-phosphate synthase promotes sugar ring opening and formation of the ammonia channel.,Mouilleron S, Badet-Denisot MA, Golinelli-Pimpaneau B J Mol Biol. 2008 Apr 4;377(4):1174-85. Epub 2008 Feb 4. PMID:18295797<ref>PMID:18295797</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2vf5" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_18295797}}, adds the Publication Abstract to the page
+*[[Glucosamine 6-phosphate synthase|Glucosamine 6-phosphate synthase]]
-(as it appears on PubMed at http://www.pubmed.gov), where 18295797 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_18295797}}
+__TOC__
+</StructureSection>
-==About this Structure==
-[[2vf5]] is a 1 chain structure with 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=2VF5 OCA].
-==Reference==
-<ref group="xtra">PMID:18295797</ref><ref group="xtra">PMID:16339762</ref><references group="xtra"/>
 [[Category: Escherichia coli]]
-[[Category: Golinelli-Pimpaneau, B.]]
+[[Category: Large Structures]]
-[[Category: Mouilleron, S.]]
+[[Category: Golinelli-Pimpaneau B]]
-[[Category: Amidotransferase]]
+[[Category: Mouilleron S]]
-[[Category: Aminotransferase]]
-[[Category: Ammonia-channeling]]
-[[Category: Cytoplasm]]
-[[Category: Glucosamine-6- phosphate synthase]]
-[[Category: Glutamine amidotransferase]]
-[[Category: N terminal nucleophile]]
-[[Category: Transferase]]