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1jq3

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Crystal Structure of Spermidine Synthase in Complex with Transition State Analogue AdoDATO

Structural highlights

1jq3 is a 4 chain structure with sequence from Thermotoga maritima. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.8Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT, TOPSAN

Function

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).^[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 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^[3]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Wu H, Min J, Ikeguchi Y, Zeng H, Dong A, Loppnau P, Pegg AE, Plotnikov AN. Structure and mechanism of spermidine synthases. Biochemistry. 2007 Jul 17;46(28):8331-9. Epub 2007 Jun 22. PMID:17585781 doi:http://dx.doi.org/10.1021/bi602498k
↑ Korolev S, Ikeguchi Y, Skarina T, Beasley S, Arrowsmith C, Edwards A, Joachimiak A, Pegg AE, Savchenko A. The crystal structure of spermidine synthase with a multisubstrate adduct inhibitor. Nat Struct Biol. 2002 Jan;9(1):27-31. PMID:11731804 doi:10.1038/nsb737
↑ Korolev S, Ikeguchi Y, Skarina T, Beasley S, Arrowsmith C, Edwards A, Joachimiak A, Pegg AE, Savchenko A. The crystal structure of spermidine synthase with a multisubstrate adduct inhibitor. Nat Struct Biol. 2002 Jan;9(1):27-31. PMID:11731804 doi:10.1038/nsb737

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1jq3"

@@ Line 1: / Line 1: @@
 ==Crystal Structure of Spermidine Synthase in Complex with Transition State Analogue AdoDATO==
-<StructureSection load='1jq3' size='340' side='right' caption='[[1jq3]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
+<StructureSection load='1jq3' size='340' side='right'caption='[[1jq3]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1jq3]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_43589 Atcc 43589]. 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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1JQ3 FirstGlance]. <br>
+<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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AAT:S-ADENOSYL-1,8-DIAMINO-3-THIOOCTANE'>AAT</scene></td></tr>
+</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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1inl|1inl]]</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='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Spermidine_synthase Spermidine synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.16 2.5.1.16] </span></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>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1jq3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jq3 OCA], [http://pdbe.org/1jq3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1jq3 RCSB], [http://www.ebi.ac.uk/pdbsum/1jq3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1jq3 ProSAT], [http://www.topsan.org/Proteins/MCSG/1jq3 TOPSAN]</span></td></tr>
 </table>
 == Function ==
-[[http://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>
+[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>
+    <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>
@@ Line 32: / Line 31: @@
 ==See Also==
-*[[Spermidine Synthase|Spermidine Synthase]]
+*[[Spermidine synthase 3D structures|Spermidine synthase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Atcc 43589]]
+[[Category: Large Structures]]
-[[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: Structural genomic]]
+[[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: PSI, Protein structure initiative]]
-[[Category: Thermophyle]]
-[[Category: Transferase]]
-[[Category: Transition-state analogue]]

1jq3

From Proteopedia

Current revision

Crystal Structure of Spermidine Synthase in Complex with Transition State Analogue AdoDATO

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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