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| | <StructureSection load='4p3m' size='340' side='right'caption='[[4p3m]], [[Resolution|resolution]] 1.85Å' scene=''> | | <StructureSection load='4p3m' size='340' side='right'caption='[[4p3m]], [[Resolution|resolution]] 1.85Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4p3m]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Psyin Psyin]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4P3M OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4P3M FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4p3m]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Psychromonas_ingrahamii_37 Psychromonas ingrahamii 37]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4P3M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4P3M FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <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]] 1.85Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">glyA, Ping_1438 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=357804 PSYIN])</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <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'>[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'>[https://proteopedia.org/fgij/fg.htm?mol=4p3m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4p3m OCA], [https://pdbe.org/4p3m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4p3m RCSB], [https://www.ebi.ac.uk/pdbsum/4p3m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4p3m ProSAT]</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=4p3m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4p3m OCA], [http://pdbe.org/4p3m PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4p3m RCSB], [http://www.ebi.ac.uk/pdbsum/4p3m PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4p3m ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/GLYA_PSYIN GLYA_PSYIN]] 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 (By similarity). | + | [https://www.uniprot.org/uniprot/GLYA_PSYIN GLYA_PSYIN] 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 (By similarity). |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | ==See Also== | | ==See Also== |
| - | *[[Serine hydroxymethyltransferase|Serine hydroxymethyltransferase]] | + | *[[Serine hydroxymethyltransferase 3D structures|Serine hydroxymethyltransferase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Glycine hydroxymethyltransferase]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Psyin]] | + | [[Category: Psychromonas ingrahamii 37]] |
| - | [[Category: Angelaccio, S]] | + | [[Category: Angelaccio S]] |
| - | [[Category: Capitani, G]] | + | [[Category: Capitani G]] |
| - | [[Category: Dworkowski, F]] | + | [[Category: Dworkowski F]] |
| - | [[Category: Pascarella, S]] | + | [[Category: Pascarella S]] |
| - | [[Category: Psychrophilic enzyme]]
| + | |
| - | [[Category: Pyridoxal phosphate]]
| + | |
| - | [[Category: Serine hydroxymethyltransferase]]
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| - | [[Category: Transferase]]
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| Structural highlights
Function
GLYA_PSYIN 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 (By similarity).
Publication Abstract from PubMed
Serine hydroxymethyltransferase (SHMT) is a pyridoxal-5'-phosphate (PLP)-dependent enzyme belonging to the fold type I superfamily which catalyzes in vivo the reversible conversion of l-serine and tetrahydropteroylglutamate (H4 PteGlu) to glycine and 5,10-methylenetetrahydropteroylglutamate (5,10-CH2 -H4 PteGlu). The SHMT from the psychrophilic bacterium Psychromonas ingrahamii (piSHMT) had been recently purified and characterized. This enzyme was shown to display catalytic and stability properties typical of psychrophilic enzymes, namely high catalytic activity at low temperature and thermolability. To gain deeper insights into the structure-function relationship of piSHMT, the three-dimensional structure of its apo form was determined by X-ray crystallography. Homology modelling techniques were applied to build a model of the piSHMT holo form. Comparison of the two forms unraveled the conformation modifications that take place when the apo enzyme binds its cofactor. Our results show that the apo form is in an "open" conformation and possesses four (or five, in chain A) disordered loops whose electron density is not visible by X-ray crystallography. These loops contain residues that interact with the PLP cofactor and three of them are localized in the major domain that, along with the small domain, constitutes the single subunit of the SHMT homodimer. Cofactor binding triggers a rearrangement of the small domain that moves toward the large domain and screens the PLP binding site at the solvent side. Comparison to the mesophilic apo SHMT from Salmonella typhimurium suggests that the backbone conformational changes are wider in psychrophilic SHMT. (c) Proteins 2014;. (c) 2014 Wiley Periodicals, Inc.
Conformational transitions driven by PLP uptake in the psychrophilic serine hydroxymethyltransferase from Psychromonas ingrahamii.,Angelaccio S, Dworkowski F, Di Bello A, Milano T, Capitani G, Pascarella S Proteins. 2014 Jul 15. doi: 10.1002/prot.24646. PMID:25044250[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Angelaccio S, Dworkowski F, Di Bello A, Milano T, Capitani G, Pascarella S. Conformational transitions driven by PLP uptake in the psychrophilic serine hydroxymethyltransferase from Psychromonas ingrahamii. Proteins. 2014 Jul 15. doi: 10.1002/prot.24646. PMID:25044250 doi:http://dx.doi.org/10.1002/prot.24646
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