2hru: Difference between revisions

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OCA

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-[[Image:2hru.jpg|left|200px]]<br /><applet load="2hru" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="2hru, resolution 2.80&Aring;" />
-'''T. maritima PurL complexed with ADP'''<br />
-==Overview==
+==T. maritima PurL complexed with ADP==
-Formylglycinamide ribonucleotide amidotransferase (FGAR-AT) catalyzes the, ATP-dependent synthesis of formylglycinamidine ribonucleotide (FGAM) from, formylglycinamide ribonucleotide (FGAR) and glutamine in the fourth step, of the purine biosynthetic pathway. FGAR-AT is encoded by the purL gene., Two types of PurL have been detected. The first type, found in eukaryotes, and Gram-negative bacteria, consists of a single 140 kDa polypeptide chain, and is designated large PurL (lgPurL). The second type, small PurL, (smPurL), is found in archaea and Gram-positive bacteria and consists of, an 80 kDa polypeptide chain. SmPurL requires two additional gene products, PurQ and PurS, for activity. PurL is a member of a protein superfamily, that contains a novel ATP-binding domain. Structures of several members of, this superfamily are available in the unliganded form. We determined five, different structures of FGAR-AT from Thermotoga maritima in the presence, of substrates, a substrate analogue, and a product. These complexes have, allowed a detailed description of the novel ATP-binding motif. The, availability of a ternary complex enabled mapping of the active site, thus, identifying potential residues involved in catalysis. The complexes show a, conformational change in the active site compared to the unliganded, structure. Surprising discoveries, an ATP molecule in an auxiliary site of, the protein and the conformational changes associated with its binding, provoke speculation about the regulatory role of the auxiliary site in, formation of the PurLSQ complex as well as the evolutionary relationship, of PurLs from different organisms.
+<StructureSection load='2hru' size='340' side='right'caption='[[2hru]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
+== Structural highlights ==
-==About this Structure==
+<table><tr><td colspan='2'>[[2hru]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HRU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2HRU FirstGlance]. <br>
-HRU is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima] with MG and ADP as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Phosphoribosylformylglycinamidine_synthase Phosphoribosylformylglycinamidine synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.5.3 6.3.5.3] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2HRU OCA].
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.8&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-==Reference==
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2hru FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hru OCA], [https://pdbe.org/2hru PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2hru RCSB], [https://www.ebi.ac.uk/pdbsum/2hru PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2hru ProSAT]</span></td></tr>
-Complexed structures of formylglycinamide ribonucleotide amidotransferase from Thermotoga maritima describe a novel ATP binding protein superfamily., Morar M, Anand R, Hoskins AA, Stubbe J, Ealick SE, Biochemistry. 2006 Dec 19;45(50):14880-95. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17154526 17154526]
+</table>
-[[Category: Phosphoribosylformylglycinamidine synthase]]
+== Function ==
-[[Category: Single protein]]
+[https://www.uniprot.org/uniprot/PURL_THEMA PURL_THEMA] Part of the phosphoribosylformylglycinamidine synthase complex involved in the purines biosynthetic pathway. Catalyzes the ATP-dependent conversion of formylglycinamide ribonucleotide (FGAR) and glutamine to yield formylglycinamidine ribonucleotide (FGAM) and glutamate. The FGAM synthase complex is composed of three subunits. PurQ produces an ammonia molecule by converting glutamine to glutamate. PurL transfers the ammonia molecule to FGAR to form FGAM in an ATP-dependent manner. PurS interacts with PurQ and PurL and is thought to assist in the transfer of the ammonia molecule from PurQ to PurL.
+== 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/hr/2hru_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=2hru ConSurf].
+<div style="clear:both"></div>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Thermotoga maritima]]
-[[Category: Ealick, S.E.]]
+[[Category: Ealick SE]]
-[[Category: Morar, M.]]
+[[Category: Morar M]]
-[[Category: ADP]]
-[[Category: MG]]
-[[Category: beta barrel; alpha-beta structure]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 11:56:11 2007''