|
|
| (One intermediate revision not shown.) |
| Line 1: |
Line 1: |
| | | | |
| | ==Crystal structure of Arabidopsis thaliana phosphoserine aminotransferase isoform 1 (AtPSAT1) in complex with PLP-phosphoserine geminal diamine intermediate== | | ==Crystal structure of Arabidopsis thaliana phosphoserine aminotransferase isoform 1 (AtPSAT1) in complex with PLP-phosphoserine geminal diamine intermediate== |
| - | <StructureSection load='6czz' size='340' side='right' caption='[[6czz]], [[Resolution|resolution]] 1.70Å' scene=''> | + | <StructureSection load='6czz' size='340' side='right'caption='[[6czz]], [[Resolution|resolution]] 1.70Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[6czz]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Arath Arath]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CZZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6CZZ FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6czz]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CZZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6CZZ FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene>, <scene name='pdbligand=SEP:PHOSPHOSERINE'>SEP</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]] 1.7Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PSAT1, At4g35630, F8D20.140 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 ARATH])</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene>, <scene name='pdbligand=SEP:PHOSPHOSERINE'>SEP</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Phosphoserine_transaminase Phosphoserine transaminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.6.1.52 2.6.1.52] </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=6czz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6czz OCA], [https://pdbe.org/6czz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6czz RCSB], [https://www.ebi.ac.uk/pdbsum/6czz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6czz 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=6czz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6czz OCA], [http://pdbe.org/6czz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6czz RCSB], [http://www.ebi.ac.uk/pdbsum/6czz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6czz ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/SERB1_ARATH SERB1_ARATH]] Involved in the plastidial phosphorylated pathway of serine biosynthesis (PPSB). Catalyzes the reversible conversion of 3-phosphohydroxypyruvate to phosphoserine.<ref>PMID:16289358</ref> <ref>PMID:9881164</ref> | + | [https://www.uniprot.org/uniprot/SERB1_ARATH SERB1_ARATH] Involved in the plastidial phosphorylated pathway of serine biosynthesis (PPSB). Catalyzes the reversible conversion of 3-phosphohydroxypyruvate to phosphoserine.<ref>PMID:16289358</ref> <ref>PMID:9881164</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
| Line 20: |
Line 19: |
| | </div> | | </div> |
| | <div class="pdbe-citations 6czz" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 6czz" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[Phosphoserine aminotransferase|Phosphoserine aminotransferase]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Arath]] | + | [[Category: Arabidopsis thaliana]] |
| - | [[Category: Phosphoserine transaminase]] | + | [[Category: Large Structures]] |
| - | [[Category: Dauter, Z]] | + | [[Category: Dauter Z]] |
| - | [[Category: Ruszkowski, M]] | + | [[Category: Ruszkowski M]] |
| - | [[Category: Sekula, B]] | + | [[Category: Sekula B]] |
| - | [[Category: Plp]]
| + | |
| - | [[Category: Psat]]
| + | |
| - | [[Category: Pyridoxal 5'-phosphate]]
| + | |
| - | [[Category: Serine biosynthesis]]
| + | |
| - | [[Category: Transaminase]]
| + | |
| - | [[Category: Transferase]]
| + | |
| Structural highlights
Function
SERB1_ARATH Involved in the plastidial phosphorylated pathway of serine biosynthesis (PPSB). Catalyzes the reversible conversion of 3-phosphohydroxypyruvate to phosphoserine.[1] [2]
Publication Abstract from PubMed
Phosphoserine aminotransferase (PSAT) is a pyridoxal 5'-phosphate (PLP)-dependent enzyme that catalyzes the conversion of 3-phosphohydroxypyruvate (3-PHP) to 3-phosphoserine (PSer) in an L-glutamate (Glu)-linked reversible transamination reaction. This process proceeds through a bimolecular ping-pong mechanism and in plants takes place in plastids. It is a part of the phosphorylated pathway of serine biosynthesis, one of three routes recognized in plant organisms that yield serine. In this three-step biotransformation, 3-phosphoglycerate (3-PGA) delivered from plastidial glycolysis and Calvin cycle is oxidized by 3-PGA dehydrogenase. Then, 3-PHP is subjected to transamination with Glu to yield PSer and alpha-ketoglutarate (AKG). In the last step of the pathway, serine is produced by the action of phosphoserine phosphatase. Here we present the structural characterization of PSAT isoform 1 from Arabidopsis thaliana (AtPSAT1), a dimeric S-shaped protein that truncated of its 71-residue-long chloroplast-targeting signal peptide. Three crystal structures of AtPSAT1 captured at different stages of the reaction: (i) internal aldimine state with PLP covalently bound to the catalytic K265, (ii) holoenzyme in complex with pyridoxamine-5'-phosphate (PMP) after transfer of the amino group from glutamate and (iii) the geminal diamine intermediate state wherein the cofactor is covalently bound to both, K265 and PSer. These snapshots over the course of the reaction present detailed architecture of AtPSAT1 and allow for the comparison of this plant enzyme with other PSATs. Conformational changes of the protein during the catalytic event concern (i) the neighborhood of K265 when the amino group is transferred to the cofactor to form PMP and (ii) movement of the gate-keeping loop (residues 391-401) upon binding of 3-PHP and PSer. The latter conformational change of the loop may likely be one of key elements that regulate catalytic activity of PSATs.
Structural Analysis of Phosphoserine Aminotransferase (Isoform 1) From Arabidopsis thaliana- the Enzyme Involved in the Phosphorylated Pathway of Serine Biosynthesis.,Sekula B, Ruszkowski M, Dauter Z Front Plant Sci. 2018 Jul 6;9:876. doi: 10.3389/fpls.2018.00876. eCollection, 2018. PMID:30034403[3]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Ali V, Nozaki T. Biochemical and functional characterization of phosphoserine aminotransferase from Entamoeba histolytica, which possesses both phosphorylated and non-phosphorylated serine metabolic pathways. Mol Biochem Parasitol. 2006 Jan;145(1):71-83. doi:, 10.1016/j.molbiopara.2005.09.008. Epub 2005 Oct 5. PMID:16289358 doi:http://dx.doi.org/10.1016/j.molbiopara.2005.09.008
- ↑ Ho CL, Noji M, Saito M, Yamazaki M, Saito K. Molecular characterization of plastidic phosphoserine aminotransferase in serine biosynthesis from Arabidopsis. Plant J. 1998 Nov;16(4):443-52. PMID:9881164
- ↑ Sekula B, Ruszkowski M, Dauter Z. Structural Analysis of Phosphoserine Aminotransferase (Isoform 1) From Arabidopsis thaliana- the Enzyme Involved in the Phosphorylated Pathway of Serine Biosynthesis. Front Plant Sci. 2018 Jul 6;9:876. doi: 10.3389/fpls.2018.00876. eCollection, 2018. PMID:30034403 doi:http://dx.doi.org/10.3389/fpls.2018.00876
|
