5lnw: Difference between revisions

Latest revision as of 18:36, 18 October 2023

Crystal structure of Arabidopsis thaliana Pdx1-I320-G3P complex

Structural highlights

5lnw is a 4 chain structure with sequence from Arabidopsis thaliana. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.9Å
Ligands:	GOL, HG3, K8P, RP5
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

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

Substrate channeling has emerged as a common mechanism for enzymatic intermediate transfer. A conspicuous gap in knowledge concerns the use of covalent lysine imines in the transfer of carbonyl-group-containing intermediates, despite their wideuse in enzymatic catalysis. Here we show how imine chemistry operates in the transfer of covalent intermediates in pyridoxal 5'-phosphate biosynthesis by the Arabidopsis thaliana enzyme Pdx1. An initial ribose 5-phosphate lysine imine is converted to the chromophoric I320 intermediate, simultaneously bound to two lysine residues and partially vacating the active site, which creates space for glyceraldehyde 3-phosphate to bind. Crystal structures show how substrate binding, catalysis and shuttling are coupled to conformational changes around strand beta6 of the Pdx1 (betaalpha)8-barrel. The dual-specificity active site and imine relay mechanism for migration of carbonyl intermediates provide elegant solutions to the challenge of coordinating a complex sequence of reactions that follow a path of over 20 A between substrate- and product-binding sites.

Lysine relay mechanism coordinates intermediate transfer in vitamin B6 biosynthesis.,Rodrigues MJ, Windeisen V, Zhang Y, Guedez G, Weber S, Strohmeier M, Hanes JW, Royant A, Evans G, Sinning I, Ealick SE, Begley TP, Tews I Nat Chem Biol. 2017 Jan 16. doi: 10.1038/nchembio.2273. PMID:28092359^[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:https://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:https://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:https://dx.doi.org/10.1104/pp.107.096784
↑ Rodrigues MJ, Windeisen V, Zhang Y, Guedez G, Weber S, Strohmeier M, Hanes JW, Royant A, Evans G, Sinning I, Ealick SE, Begley TP, Tews I. Lysine relay mechanism coordinates intermediate transfer in vitamin B6 biosynthesis. Nat Chem Biol. 2017 Jan 16. doi: 10.1038/nchembio.2273. PMID:28092359 doi:https://dx.doi.org/10.1038/nchembio.2273

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] 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:https://dx.doi.org/0506228102

[2] 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:https://dx.doi.org/TPJ2538

[3] 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:https://dx.doi.org/10.1104/pp.107.096784

[4] Rodrigues MJ, Windeisen V, Zhang Y, Guedez G, Weber S, Strohmeier M, Hanes JW, Royant A, Evans G, Sinning I, Ealick SE, Begley TP, Tews I. Lysine relay mechanism coordinates intermediate transfer in vitamin B6 biosynthesis. Nat Chem Biol. 2017 Jan 16. doi: 10.1038/nchembio.2273. PMID:28092359 doi:https://dx.doi.org/10.1038/nchembio.2273

[1]

[2]

[3]

[4]

@@ Line 3: / Line 3: @@
 <StructureSection load='5lnw' size='340' side='right'caption='[[5lnw]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5lnw]] 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=5LNW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5LNW FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5lnw]] 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=5LNW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5LNW FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HG3:[(2~{R})-2,3,3-TRIS(OXIDANYL)PROPYL]+DIHYDROGEN+PHOSPHATE'>HG3</scene>, <scene name='pdbligand=K8P:[(2~{R},3~{R})-2,3-BIS(OXIDANYL)-3-[[(2~{S})-3-OXIDANYLIDENEPENT-4-EN-2-YL]AMINO]PROPYL]+DIHYDROGEN+PHOSPHATE'>K8P</scene>, <scene name='pdbligand=RP5:5-O-PHOSPHONO-BETA-D-RIBOFURANOSE'>RP5</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]] 1.9&#8491;</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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HG3:[(2~{R})-2,3,3-TRIS(OXIDANYL)PROPYL]+DIHYDROGEN+PHOSPHATE'>HG3</scene>, <scene name='pdbligand=K8P:[(2~{R},3~{R})-2,3-BIS(OXIDANYL)-3-[[(2~{S})-3-OXIDANYLIDENEPENT-4-EN-2-YL]AMINO]PROPYL]+DIHYDROGEN+PHOSPHATE'>K8P</scene>, <scene name='pdbligand=RP5:5-O-PHOSPHONO-BETA-D-RIBOFURANOSE'>RP5</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=5lnw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5lnw OCA], [https://pdbe.org/5lnw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5lnw RCSB], [https://www.ebi.ac.uk/pdbsum/5lnw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5lnw 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=5lnw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5lnw OCA], [http://pdbe.org/5lnw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5lnw RCSB], [http://www.ebi.ac.uk/pdbsum/5lnw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5lnw ProSAT]</span></td></tr>
 </table>
 == 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;">
 == Publication Abstract from PubMed ==
@@ Line 24: / Line 23: @@
 __TOC__
 </StructureSection>
-[[Category: Arath]]
+[[Category: Arabidopsis thaliana]]
 [[Category: Large Structures]]
-[[Category: Begley, T P]]
+[[Category: Begley TP]]
-[[Category: Ealick, S E]]
+[[Category: Ealick SE]]
-[[Category: Evans, G]]
+[[Category: Evans G]]
-[[Category: Guedez, G]]
+[[Category: Guedez G]]
-[[Category: Hanes, J W]]
+[[Category: Hanes JW]]
-[[Category: Rodrigues, M J]]
+[[Category: Rodrigues MJ]]
-[[Category: Royant, A]]
+[[Category: Royant A]]
-[[Category: Sinning, I]]
+[[Category: Sinning I]]
-[[Category: Strohmeier, M]]
+[[Category: Strohmeier M]]
-[[Category: Tews, I]]
+[[Category: Tews I]]
-[[Category: Weber, S]]
+[[Category: Weber S]]
-[[Category: Windeisen, V]]
+[[Category: Windeisen V]]
-[[Category: Zhang, Y]]
+[[Category: Zhang Y]]
-[[Category: Beta/alpha barrel]]
-[[Category: Glutamine amidotransferase]]
-[[Category: Lyase]]
-[[Category: Pyridoxal phosphate synthase]]
-[[Category: Vitamin b6 biosythesis]]

5lnw: Difference between revisions

Latest revision as of 18:36, 18 October 2023

Crystal structure of Arabidopsis thaliana Pdx1-I320-G3P complex

Structural highlights

Function

Publication Abstract from PubMed

References

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