3o05: Difference between revisions

Latest revision as of 16:52, 1 November 2023

Crystal Structure of Yeast Pyridoxal 5-Phosphate Synthase Snz1 Complxed with Substrate PLP

Structural highlights

3o05 is a 3 chain structure with sequence from Saccharomyces cerevisiae. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.2Å
Ligands:	PLP
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

SNZ1_YEAST Required for the production of pyridoxine (vitamin B6). May be involved in growth arrest and cellular response to nutrient limitation. Required for growth in the presence of low level of intracellular pyridoxine.^[1] ^[2]

Publication Abstract from PubMed

In most eubacteria, fungi, apicomplexa, plants, and some metazoans, the active form of vitamin B6, pyridoxal 5-phosphate (PLP) is de novo synthesized from three substrates, ribose 5-phosphate (R5P), dihydroxyacetone phosphate (DHAP), and ammonia hydrolyzed from glutamine by a complexed glutaminase. Of the three active sites of deoxyxylulose 5-phosphate (DXP)-independent PLP synthase (Pdx1), the R5P isomerization site has been assigned, but the sites for DHAP isomerization and PLP formation remain unknown. Here, we present the crystal structures of yeast Pdx1/Snz1, in apo-, glyceraldehyde 3-phosphate (G3P)- and PLP-bound forms, at 2.30, 1.80, and 2.20 A, respectively. Structural and biochemical analysis enabled us to assign the PLP-formation site, a G3P-binding site and a G3P-transfer site. We propose a putative catalytic mechanism for Pdx1/Snz1 in which R5P and DHAP are isomerized at two distinct sites and transferred along well-defined routes to a final destination for PLP synthesis.

Structural insights into the catalytic mechanism of the yeast pyridoxal 5-phosphate synthase Snz1.,Zhang X, Teng YB, Liu JP, He YX, Zhou K, Chen Y, Zhou CZ Biochem J. 2010 Oct 5. PMID:20919991^[3]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Rodriguez-Navarro S, Llorente B, Rodriguez-Manzaneque MT, Ramne A, Uber G, Marchesan D, Dujon B, Herrero E, Sunnerhagen P, Perez-Ortin JE. Functional analysis of yeast gene families involved in metabolism of vitamins B1 and B6. Yeast. 2002 Oct;19(14):1261-76. PMID:12271461 doi:10.1002/yea.916
↑ Stolz J, Vielreicher M. Tpn1p, the plasma membrane vitamin B6 transporter of Saccharomyces cerevisiae. J Biol Chem. 2003 May 23;278(21):18990-6. Epub 2003 Mar 20. PMID:12649274 doi:10.1074/jbc.M300949200
↑ Zhang X, Teng YB, Liu JP, He YX, Zhou K, Chen Y, Zhou CZ. Structural insights into the catalytic mechanism of the yeast pyridoxal 5-phosphate synthase Snz1. Biochem J. 2010 Oct 5. PMID:20919991 doi:10.1042/BJ20101241

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OCA

[1] Rodriguez-Navarro S, Llorente B, Rodriguez-Manzaneque MT, Ramne A, Uber G, Marchesan D, Dujon B, Herrero E, Sunnerhagen P, Perez-Ortin JE. Functional analysis of yeast gene families involved in metabolism of vitamins B1 and B6. Yeast. 2002 Oct;19(14):1261-76. PMID:12271461 doi:10.1002/yea.916

[2] Stolz J, Vielreicher M. Tpn1p, the plasma membrane vitamin B6 transporter of Saccharomyces cerevisiae. J Biol Chem. 2003 May 23;278(21):18990-6. Epub 2003 Mar 20. PMID:12649274 doi:10.1074/jbc.M300949200

[3] Zhang X, Teng YB, Liu JP, He YX, Zhou K, Chen Y, Zhou CZ. Structural insights into the catalytic mechanism of the yeast pyridoxal 5-phosphate synthase Snz1. Biochem J. 2010 Oct 5. PMID:20919991 doi:10.1042/BJ20101241

[1]

[2]

[3]

@@ Line 3: / Line 3: @@
 <StructureSection load='3o05' size='340' side='right'caption='[[3o05]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3o05]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3O05 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3O05 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3o05]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3O05 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3O05 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</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]] 2.2&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3o06|3o06]], [[3o07|3o07]]</div></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">SNZ1 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</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=3o05 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3o05 OCA], [https://pdbe.org/3o05 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3o05 RCSB], [https://www.ebi.ac.uk/pdbsum/3o05 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3o05 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/SNZ1_YEAST SNZ1_YEAST]] Required for the production of pyridoxine (vitamin B6). May be involved in growth arrest and cellular response to nutrient limitation. Required for growth in the presence of low level of intracellular pyridoxine.<ref>PMID:12271461</ref> <ref>PMID:12649274</ref>
+[https://www.uniprot.org/uniprot/SNZ1_YEAST SNZ1_YEAST] Required for the production of pyridoxine (vitamin B6). May be involved in growth arrest and cellular response to nutrient limitation. Required for growth in the presence of low level of intracellular pyridoxine.<ref>PMID:12271461</ref> <ref>PMID:12649274</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 24: / Line 23: @@
 __TOC__
 </StructureSection>
-[[Category: Atcc 18824]]
 [[Category: Large Structures]]
-[[Category: He, Y X]]
+[[Category: Saccharomyces cerevisiae]]
-[[Category: Hu, H X]]
+[[Category: He YX]]
-[[Category: Teng, Y B]]
+[[Category: Hu HX]]
-[[Category: Zhang, X]]
+[[Category: Teng YB]]
-[[Category: Zhou, C Z]]
+[[Category: Zhang X]]
-[[Category: Beta slash alpha barrel]]
+[[Category: Zhou CZ]]
-[[Category: Biosynthetic protein]]
-[[Category: Plp g3p rbp sno1]]
-[[Category: Pyridoxal 5-phosphate synthase]]

3o05: Difference between revisions

Latest revision as of 16:52, 1 November 2023

Crystal Structure of Yeast Pyridoxal 5-Phosphate Synthase Snz1 Complxed with Substrate PLP

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

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