3o4f: Difference between revisions

Latest revision as of 16:53, 1 November 2023

Crystal Structure of Spermidine Synthase from E. coli

Structural highlights

3o4f is a 8 chain structure with sequence from Escherichia coli K-12. This structure supersedes the now removed PDB entries 3adn and 3hh9. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.9Å
Ligands:	SO4
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

SPEE_ECOLI Involved in the biosynthesis of polyamines which play a significant role in the structural and functional organization in the chromoid of E.coli by compacting DNA and neutralizing negative charges. Catalyzes the irreversible transfer of a propylamine group from the amino donor S-adenosylmethioninamine (decarboxy-AdoMet) to putrescine (1,4-diaminobutane) to yield spermidine. Cadaverine (1,5-diaminopentane) and spermidine can replace putrescine as the propylamine acceptor.^[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. Biosynthesis of spermidine, one of the most ubiquitous polyamines, is catalyzed by spermidine synthase (SpeE). Although the function of this enzyme from Escherichia coli has been thoroughly characterised, its structural details remain unknown. Here, we report the crystal structure of E. coli SpeE and study its interaction with the ligands by isothermal titration calorimetry and computational modelling. SpeE consists of two domains - a small N-terminal beta-strand domain, and a C-terminal catalytic domain that adopts a canonical methyltransferase (MTase) Rossmann fold. The protein forms a dimer in the crystal and in solution. Structural comparison of E. coli SpeE to its homologs reveals that it has a large and unique substrate-binding cleft that may account for its lower amine substrate specificity.

The crystal structure of Escherichia coli spermidine synthase SpeE reveals a unique substrate-binding pocket.,Zhou X, Chua TK, Tkaczuk KL, Bujnicki JM, Sivaraman J J Struct Biol. 2010 Mar;169(3):277-85. Epub 2010 Jan 4. PMID:20051267^[3]

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

References

↑ Lee MJ, Yang YT, Lin V, Huang H. Site-directed mutations of the gatekeeping loop region affect the activity of Escherichia coli spermidine synthase. Mol Biotechnol. 2013 Jun;54(2):572-80. doi: 10.1007/s12033-012-9599-3. PMID:23001854 doi:https://dx.doi.org/10.1007/s12033-012-9599-3
↑ Bowman WH, Tabor CW, Tabor H. Spermidine biosynthesis. Purification and properties of propylamine transferase from Escherichia coli. J Biol Chem. 1973 Apr 10;248(7):2480-6. PMID:4572733
↑ Zhou X, Chua TK, Tkaczuk KL, Bujnicki JM, Sivaraman J. The crystal structure of Escherichia coli spermidine synthase SpeE reveals a unique substrate-binding pocket. J Struct Biol. 2010 Mar;169(3):277-85. Epub 2010 Jan 4. PMID:20051267 doi:10.1016/j.jsb.2009.12.024

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Lee MJ, Yang YT, Lin V, Huang H. Site-directed mutations of the gatekeeping loop region affect the activity of Escherichia coli spermidine synthase. Mol Biotechnol. 2013 Jun;54(2):572-80. doi: 10.1007/s12033-012-9599-3. PMID:23001854 doi:https://dx.doi.org/10.1007/s12033-012-9599-3

[2] Bowman WH, Tabor CW, Tabor H. Spermidine biosynthesis. Purification and properties of propylamine transferase from Escherichia coli. J Biol Chem. 1973 Apr 10;248(7):2480-6. PMID:4572733

[3] Zhou X, Chua TK, Tkaczuk KL, Bujnicki JM, Sivaraman J. The crystal structure of Escherichia coli spermidine synthase SpeE reveals a unique substrate-binding pocket. J Struct Biol. 2010 Mar;169(3):277-85. Epub 2010 Jan 4. PMID:20051267 doi:10.1016/j.jsb.2009.12.024

[1]

[2]

[3]

@@ Line 3: / Line 3: @@
 <StructureSection load='3o4f' size='340' side='right'caption='[[3o4f]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3o4f]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Ecoli Ecoli]. This structure supersedes the now removed PDB entries [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3adn 3adn] and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3hh9 3hh9]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3O4F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3O4F FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3o4f]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. This structure supersedes the now removed PDB entries [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3adn 3adn] and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3hh9 3hh9]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3O4F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3O4F FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.9&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">SPEE ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Spermidine_synthase Spermidine synthase], with EC number [https://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=3o4f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3o4f OCA], [https://pdbe.org/3o4f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3o4f RCSB], [https://www.ebi.ac.uk/pdbsum/3o4f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3o4f ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/SPEE_ECOLI SPEE_ECOLI]] Involved in the biosynthesis of polyamines which play a significant role in the structural and functional organization in the chromoid of E.coli by compacting DNA and neutralizing negative charges. Catalyzes the irreversible transfer of a propylamine group from the amino donor S-adenosylmethioninamine (decarboxy-AdoMet) to putrescine (1,4-diaminobutane) to yield spermidine. Cadaverine (1,5-diaminopentane) and spermidine can replace putrescine as the propylamine acceptor.<ref>PMID:23001854</ref> <ref>PMID:4572733</ref>
+[https://www.uniprot.org/uniprot/SPEE_ECOLI SPEE_ECOLI] Involved in the biosynthesis of polyamines which play a significant role in the structural and functional organization in the chromoid of E.coli by compacting DNA and neutralizing negative charges. Catalyzes the irreversible transfer of a propylamine group from the amino donor S-adenosylmethioninamine (decarboxy-AdoMet) to putrescine (1,4-diaminobutane) to yield spermidine. Cadaverine (1,5-diaminopentane) and spermidine can replace putrescine as the propylamine acceptor.<ref>PMID:23001854</ref> <ref>PMID:4572733</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 37: / Line 36: @@
 __TOC__
 </StructureSection>
-[[Category: Ecoli]]
+[[Category: Escherichia coli K-12]]
 [[Category: Large Structures]]
-[[Category: Spermidine synthase]]
+[[Category: Chruszcz M]]
-[[Category: Chruszcz, M]]
+[[Category: Chua TK]]
-[[Category: Chua, T K]]
+[[Category: Minor W]]
-[[Category: Minor, W]]
+[[Category: Sivaraman J]]
-[[Category: Sivaraman, J]]
+[[Category: Tkaczuk KL]]
-[[Category: Tkaczuk, K L]]
+[[Category: Zhou X]]
-[[Category: Zhou, X]]
-[[Category: Aminopropyltransferase]]
-[[Category: Polyamine biosynthesis]]
-[[Category: Polyamine synthase]]
-[[Category: Rossmann fold]]
-[[Category: Spermidine biosynthesis]]
-[[Category: Transferase]]

3o4f: Difference between revisions

Latest revision as of 16:53, 1 November 2023

Crystal Structure of Spermidine Synthase from E. coli

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

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