1jq3: Difference between revisions

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-[[Image:1jq3.png|left|200px]]
-<!--
+==Crystal Structure of Spermidine Synthase in Complex with Transition State Analogue AdoDATO==
-The line below this paragraph, containing "STRUCTURE_1jq3", creates the "Structure Box" on the page.
+<StructureSection load='1jq3' size='340' side='right'caption='[[1jq3]], [[Resolution|resolution]] 1.80&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'>[[1jq3]] is a 4 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=1JQ3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1JQ3 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]] 1.8&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AAT:S-ADENOSYL-1,8-DIAMINO-3-THIOOCTANE'>AAT</scene></td></tr>
-{{STRUCTURE_1jq3|  PDB=1jq3  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1jq3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jq3 OCA], [https://pdbe.org/1jq3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1jq3 RCSB], [https://www.ebi.ac.uk/pdbsum/1jq3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1jq3 ProSAT], [https://www.topsan.org/Proteins/MCSG/1jq3 TOPSAN]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/SPEE_THEMA SPEE_THEMA] Catalyzes the irreversible transfer of a propylamine group from the amino donor S-adenosylmethioninamine (decarboxy-AdoMet) to putrescine (1,4-diaminobutane) to yield spermidine. It has lower affinity and lower activity towards 1,3-diaminopropane, cadaverine (1,5-diaminopentane), agmatine, thermine and spermidine (in vitro).<ref>PMID:17585781</ref> <ref>PMID:11731804</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/jq/1jq3_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=1jq3 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Polyamines are essential in all branches of life. Spermidine synthase (putrescine aminopropyltransferase, PAPT) catalyzes the biosynthesis of spermidine, a ubiquitous polyamine. The crystal structure of the PAPT from Thermotoga maritima (TmPAPT) has been solved to 1.5 A resolution in the presence and absence of AdoDATO (S-adenosyl-1,8-diamino-3-thiooctane), a compound containing both substrate and product moieties. This, the first structure of an aminopropyltransferase, reveals deep cavities for binding substrate and cofactor, and a loop that envelops the active site. The AdoDATO binding site is lined with residues conserved in PAPT enzymes from bacteria to humans, suggesting a universal catalytic mechanism. Other conserved residues act sterically to provide a structural basis for polyamine specificity. The enzyme is tetrameric; each monomer consists of a C-terminal domain with a Rossmann-like fold and an N-terminal beta-stranded domain. The tetramer is assembled using a novel barrel-type oligomerization motif.
-===Crystal Structure of Spermidine Synthase in Complex with Transition State Analogue AdoDATO===
+The crystal structure of spermidine synthase with a multisubstrate adduct inhibitor.,Korolev S, Ikeguchi Y, Skarina T, Beasley S, Arrowsmith C, Edwards A, Joachimiak A, Pegg AE, Savchenko A Nat Struct Biol. 2002 Jan;9(1):27-31. PMID:11731804<ref>PMID:11731804</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1jq3" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_11731804}}, adds the Publication Abstract to the page
+*[[Spermidine synthase 3D structures|Spermidine synthase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 11731804 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_11731804}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-[[1jq3]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JQ3 OCA].
-==Reference==
-<ref group="xtra">PMID:011731804</ref><ref group="xtra">PMID:015340214</ref><references group="xtra"/>
-[[Category: Spermidine synthase]]
 [[Category: Thermotoga maritima]]
-[[Category: Beasley, S.]]
+[[Category: Beasley S]]
-[[Category: Edwards, A.]]
+[[Category: Edwards A]]
-[[Category: Ikeguchi, Y.]]
+[[Category: Ikeguchi Y]]
-[[Category: Joachimiak, A.]]
+[[Category: Joachimiak A]]
-[[Category: Korolev, S.]]
+[[Category: Korolev S]]
-[[Category: MCSG, Midwest Center for Structural Genomics.]]
+[[Category: Pegg AE]]
-[[Category: Pegg, A E.]]
+[[Category: Savchenko A]]
-[[Category: Savchenko, A.]]
+[[Category: Skarina T]]
-[[Category: Skarina, T.]]
-[[Category: Aminopropyltransferase]]
-[[Category: Beta-barrel]]
-[[Category: Homo-tetramer]]
-[[Category: Mcsg]]
-[[Category: Midwest center for structural genomic]]
-[[Category: Protein structure initiative]]
-[[Category: Psi]]
-[[Category: Structural genomic]]
-[[Category: Thermophyle]]
-[[Category: Transferase]]
-[[Category: Transition-state analogue]]