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| | <StructureSection load='5k2z' size='340' side='right'caption='[[5k2z]], [[Resolution|resolution]] 1.80Å' scene=''> | | <StructureSection load='5k2z' size='340' side='right'caption='[[5k2z]], [[Resolution|resolution]] 1.80Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5k2z]] 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=5K2Z OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5K2Z FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5k2z]] 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=5K2Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5K2Z FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=6R3:2-AZANYLPENTA-1,4-DIEN-3-ONE'>6R3</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</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]] 1.8Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PDX13, GIP2, PDX1L3, RSR4, At5g01410, T10O8.120 ([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=6R3:2-AZANYLPENTA-1,4-DIEN-3-ONE'>6R3</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</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/Pyridoxal_5'-phosphate_synthase_(glutamine_hydrolyzing) Pyridoxal 5'-phosphate synthase (glutamine hydrolyzing)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.3.3.6 4.3.3.6] </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=5k2z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k2z OCA], [https://pdbe.org/5k2z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5k2z RCSB], [https://www.ebi.ac.uk/pdbsum/5k2z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5k2z ProSAT]</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=5k2z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k2z OCA], [http://pdbe.org/5k2z PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5k2z RCSB], [http://www.ebi.ac.uk/pdbsum/5k2z PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5k2z ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/PDX13_ARATH PDX13_ARATH]] Catalyzes the formation of pyridoxal 5'-phosphate from ribose 5-phosphate (RBP), glyceraldehyde 3-phosphate (G3P) and ammonia. The ammonia is provided by PDX2. Can also use ribulose 5-phosphate and dihydroxyacetone phosphate as substrates, resulting from enzyme-catalyzed isomerization of RBP and G3P, respectively. Also plays an indirect role in resistance to singlet oxygen-generating photosensitizers.<ref>PMID:16157873</ref> <ref>PMID:16236150</ref> <ref>PMID:17468224</ref> | + | [https://www.uniprot.org/uniprot/PDX13_ARATH PDX13_ARATH] Catalyzes the formation of pyridoxal 5'-phosphate from ribose 5-phosphate (RBP), glyceraldehyde 3-phosphate (G3P) and ammonia. The ammonia is provided by PDX2. Can also use ribulose 5-phosphate and dihydroxyacetone phosphate as substrates, resulting from enzyme-catalyzed isomerization of RBP and G3P, respectively. Also plays an indirect role in resistance to singlet oxygen-generating photosensitizers.<ref>PMID:16157873</ref> <ref>PMID:16236150</ref> <ref>PMID:17468224</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Arath]] | + | [[Category: Arabidopsis thaliana]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Fitzpatrick, T B]] | + | [[Category: Fitzpatrick TB]] |
| - | [[Category: Kaufmann, M]] | + | [[Category: Kaufmann M]] |
| - | [[Category: Robinson, G C]] | + | [[Category: Robinson GC]] |
| - | [[Category: Roux, C]] | + | [[Category: Roux C]] |
| - | [[Category: Biosynthetic protein]]
| + | |
| - | [[Category: Pyridoxal 5'-phosphate]]
| + | |
| - | [[Category: Ribose 5-phosphate]]
| + | |
| - | [[Category: Vitamin b6 biosynthesis]]
| + | |
| Structural highlights
Function
PDX13_ARATH Catalyzes the formation of pyridoxal 5'-phosphate from ribose 5-phosphate (RBP), glyceraldehyde 3-phosphate (G3P) and ammonia. The ammonia is provided by PDX2. Can also use ribulose 5-phosphate and dihydroxyacetone phosphate as substrates, resulting from enzyme-catalyzed isomerization of RBP and G3P, respectively. Also plays an indirect role in resistance to singlet oxygen-generating photosensitizers.[1] [2] [3]
Publication Abstract from PubMed
Vitamin B6 is indispensible for all organisms, notably as the coenzyme form pyridoxal 5'-phosphate. Plants make the compound de novo using a relatively simple pathway comprising pyridoxine synthase (PDX1) and pyridoxine glutaminase (PDX2). PDX1 is remarkable given its multifaceted synthetic ability to carry out isomerization, imine formation, ammonia addition, aldol-type condensation, cyclization, and aromatization, all in the absence of coenzymes or recruitment of specialized domains. Two active sites (P1 and P2) facilitate the plethora of reactions, but it is not known how the two are coordinated and, moreover, if intermediates are tunneled between active sites. Here we present X-ray structures of PDX1.3 from Arabidopsis thaliana, the overall architecture of which is a dodecamer of (beta/alpha)8 barrels, similar to the majority of its homologs. An apoenzyme structure revealed that features around the P1 active site in PDX1.3 have adopted inward conformations consistent with a catalytically primed state and delineated a substrate accessible cavity above this active site, not noted in other reported structures. Comparison with the structure of PDX1.3 with an intermediate along the catalytic trajectory demonstrated that a lysine residue swings from the distinct P2 site to the P1 site at this stage of catalysis and is held in place by a molecular catch and pin, positioning it for transfer of serviced substrate back to P2. The study shows that a simple lysine swinging arm coordinates use of chemically disparate sites, dispensing with the need for additional factors, and provides an elegant example of solving complex chemistry to generate an essential metabolite.
Structural definition of the lysine swing in Arabidopsis thaliana PDX1: Intermediate channeling facilitating vitamin B6 biosynthesis.,Robinson GC, Kaufmann M, Roux C, Fitzpatrick TB Proc Natl Acad Sci U S A. 2016 Sep 19. pii: 201608125. PMID:27647886[4]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Tambasco-Studart M, Titiz O, Raschle T, Forster G, Amrhein N, Fitzpatrick TB. Vitamin B6 biosynthesis in higher plants. Proc Natl Acad Sci U S A. 2005 Sep 20;102(38):13687-92. Epub 2005 Sep 12. PMID:16157873 doi:http://dx.doi.org/0506228102
- ↑ Chen H, Xiong L. Pyridoxine is required for post-embryonic root development and tolerance to osmotic and oxidative stresses. Plant J. 2005 Nov;44(3):396-408. PMID:16236150 doi:http://dx.doi.org/TPJ2538
- ↑ Tambasco-Studart M, Tews I, Amrhein N, Fitzpatrick TB. Functional analysis of PDX2 from Arabidopsis, a glutaminase involved in vitamin B6 biosynthesis. Plant Physiol. 2007 Jun;144(2):915-25. Epub 2007 Apr 27. PMID:17468224 doi:http://dx.doi.org/10.1104/pp.107.096784
- ↑ Robinson GC, Kaufmann M, Roux C, Fitzpatrick TB. Structural definition of the lysine swing in Arabidopsis thaliana PDX1: Intermediate channeling facilitating vitamin B6 biosynthesis. Proc Natl Acad Sci U S A. 2016 Sep 19. pii: 201608125. PMID:27647886 doi:http://dx.doi.org/10.1073/pnas.1608125113
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