1jq3: Difference between revisions
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< | ==Crystal Structure of Spermidine Synthase in Complex with Transition State Analogue AdoDATO== | ||
<StructureSection load='1jq3' size='340' side='right'caption='[[1jq3]], [[Resolution|resolution]] 1.80Å' scene=''> | |||
You may | == Structural highlights == | ||
<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> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.8Å</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> | ||
<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. | |||
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®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 1jq3" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Spermidine synthase 3D structures|Spermidine synthase 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
== | [[Category: Large Structures]] | ||
[[ | |||
== | |||
< | |||
[[Category: | |||
[[Category: Thermotoga maritima]] | [[Category: Thermotoga maritima]] | ||
[[Category: Beasley | [[Category: Beasley S]] | ||
[[Category: Edwards | [[Category: Edwards A]] | ||
[[Category: Ikeguchi | [[Category: Ikeguchi Y]] | ||
[[Category: Joachimiak | [[Category: Joachimiak A]] | ||
[[Category: Korolev | [[Category: Korolev S]] | ||
[[Category: Pegg AE]] | |||
[[Category: Pegg | [[Category: Savchenko A]] | ||
[[Category: Savchenko | [[Category: Skarina T]] | ||
[[Category: Skarina | |||
Latest revision as of 11:44, 16 August 2023
Crystal Structure of Spermidine Synthase in Complex with Transition State Analogue AdoDATOCrystal Structure of Spermidine Synthase in Complex with Transition State Analogue AdoDATO
Structural highlights
FunctionSPEE_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).[1] [2] Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedPolyamines 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. 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[3] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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