6ymd: Difference between revisions
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==Crystal structure of serine hydroxymethyltransferase from Aphanothece halophytica in the covalent complex with malonate== | ==Crystal structure of serine hydroxymethyltransferase from Aphanothece halophytica in the covalent complex with malonate== | ||
<StructureSection load='6ymd' size='340' side='right'caption='[[6ymd]]' scene=''> | <StructureSection load='6ymd' size='340' side='right'caption='[[6ymd]], [[Resolution|resolution]] 1.25Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6YMD OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6YMD FirstGlance]. <br> | <table><tr><td colspan='2'>[[6ymd]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Aphha Aphha]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6YMD OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6YMD FirstGlance]. <br> | ||
</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6ymd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ymd OCA], [http://pdbe.org/6ymd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ymd RCSB], [http://www.ebi.ac.uk/pdbsum/6ymd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ymd ProSAT]</span></td></tr> | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MLI:MALONATE+ION'>MLI</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PMP:4-DEOXY-4-AMINOPYRIDOXAL-5-PHOSPHATE'>PMP</scene></td></tr> | ||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">glyrA, glyA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=72020 APHHA])</td></tr> | |||
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glycine_hydroxymethyltransferase Glycine hydroxymethyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.2.1 2.1.2.1] </span></td></tr> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6ymd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ymd OCA], [http://pdbe.org/6ymd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ymd RCSB], [http://www.ebi.ac.uk/pdbsum/6ymd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ymd ProSAT]</span></td></tr> | |||
</table> | </table> | ||
== Function == | |||
[[http://www.uniprot.org/uniprot/I7H6W6_APHHA I7H6W6_APHHA]] Catalyzes the reversible interconversion of serine and glycine with tetrahydrofolate (THF) serving as the one-carbon carrier. This reaction serves as the major source of one-carbon groups required for the biosynthesis of purines, thymidylate, methionine, and other important biomolecules. Also exhibits THF-independent aldolase activity toward beta-hydroxyamino acids, producing glycine and aldehydes, via a retro-aldol mechanism.[HAMAP-Rule:MF_00051] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Serine hydroxymethyltransferase (SHMT) is a pyridoxal 5'-phosphate-dependent enzyme that plays a pivotal role in cellular onecarbon metabolism. In plants and cyanobacteria, this enzyme is also involved in photorespiration and confers salt tolerance, as in the case of SHMT from the halophilic cyanobacterium Aphanothece halophytica (AhSHMT). We have characterized the catalytic properties of AhSHMT in different salt and pH conditions. Although the kinetic properties of AhSHMT correlate with those of the mesophilic orthologue from Escherichia coli, AhSHMT appears more catalytically efficient, especially in presence of salt. Our studies also reveal substrate inhibition, previously unobserved in AhSHMT. Furthermore, addition of the osmoprotectant glycine betaine under salt conditions has a distinct positive effect on AhSHMT activity. The crystal structures of AhSHMT in three forms, as internal aldimine, as external aldimine with the l-serine substrate, and as a covalent complex with malonate, give structural insights on the possible role of specific amino acid residues implicated in the halophilic features of AhSHMT. Importantly, we observed that overexpression of the gene encoding SHMT, independently from its origin, increases the capability of E. coli to grow in high salt conditions, suggesting that the catalytic activity of this enzyme in itself plays a fundamental role in salt tolerance. | |||
Structural and kinetic properties of serine hydroxymethyltransferase from the halophytic cyanobacterium Aphanothece halophytica provide a rationale for salt tolerance.,Nogues I, Tramonti A, Angelaccio S, Ruszkowski M, Sekula B, Contestabile R Int J Biol Macromol. 2020 May 15;159:517-529. doi:, 10.1016/j.ijbiomac.2020.05.081. PMID:32417544<ref>PMID:32417544</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 6ymd" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Aphha]] | |||
[[Category: Glycine hydroxymethyltransferase]] | |||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Ruszkowski, M | [[Category: Angelaccio, S]] | ||
[[Category: Contestabile, R]] | |||
[[Category: Nogues, I]] | |||
[[Category: Ruszkowski, M]] | |||
[[Category: Sekula, B]] | |||
[[Category: Tramonti, A]] | |||
[[Category: Glycine]] | |||
[[Category: One-carbon metabolism]] | |||
[[Category: Plp]] | |||
[[Category: Serine biosynthesis]] | |||
[[Category: Tetrahydrofolate]] | |||
[[Category: Transferase]] | |||
Revision as of 09:54, 10 June 2020
Crystal structure of serine hydroxymethyltransferase from Aphanothece halophytica in the covalent complex with malonateCrystal structure of serine hydroxymethyltransferase from Aphanothece halophytica in the covalent complex with malonate
Structural highlights
Function[I7H6W6_APHHA] Catalyzes the reversible interconversion of serine and glycine with tetrahydrofolate (THF) serving as the one-carbon carrier. This reaction serves as the major source of one-carbon groups required for the biosynthesis of purines, thymidylate, methionine, and other important biomolecules. Also exhibits THF-independent aldolase activity toward beta-hydroxyamino acids, producing glycine and aldehydes, via a retro-aldol mechanism.[HAMAP-Rule:MF_00051] Publication Abstract from PubMedSerine hydroxymethyltransferase (SHMT) is a pyridoxal 5'-phosphate-dependent enzyme that plays a pivotal role in cellular onecarbon metabolism. In plants and cyanobacteria, this enzyme is also involved in photorespiration and confers salt tolerance, as in the case of SHMT from the halophilic cyanobacterium Aphanothece halophytica (AhSHMT). We have characterized the catalytic properties of AhSHMT in different salt and pH conditions. Although the kinetic properties of AhSHMT correlate with those of the mesophilic orthologue from Escherichia coli, AhSHMT appears more catalytically efficient, especially in presence of salt. Our studies also reveal substrate inhibition, previously unobserved in AhSHMT. Furthermore, addition of the osmoprotectant glycine betaine under salt conditions has a distinct positive effect on AhSHMT activity. The crystal structures of AhSHMT in three forms, as internal aldimine, as external aldimine with the l-serine substrate, and as a covalent complex with malonate, give structural insights on the possible role of specific amino acid residues implicated in the halophilic features of AhSHMT. Importantly, we observed that overexpression of the gene encoding SHMT, independently from its origin, increases the capability of E. coli to grow in high salt conditions, suggesting that the catalytic activity of this enzyme in itself plays a fundamental role in salt tolerance. Structural and kinetic properties of serine hydroxymethyltransferase from the halophytic cyanobacterium Aphanothece halophytica provide a rationale for salt tolerance.,Nogues I, Tramonti A, Angelaccio S, Ruszkowski M, Sekula B, Contestabile R Int J Biol Macromol. 2020 May 15;159:517-529. doi:, 10.1016/j.ijbiomac.2020.05.081. PMID:32417544[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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