3fem

From Proteopedia

(Difference between revisions)

Current revision

Structure of the synthase subunit Pdx1.1 (Snz1) of PLP synthase from Saccharomyces cerevisiae

Structural highlights

3fem is a 6 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 3.02Å
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]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

The universal enzymatic cofactor vitamin B6 can be synthesized as pyridoxal 5-phosphate (PLP) by the glutamine amidotransferase Pdx1. We show that Saccharomyces cerevisiae Pdx1 is hexameric by analytical ultracentrifugation and by crystallographic 3D structure determination. Bacterial homologues were previously reported to exist in hexamer:dodecamer equilibrium. A small sequence insertion found in yeast Pdx1 elevates the dodecamer dissociation constant when introduced into Bacillus subtilis Pdx1. Further, we demonstrate that the yeast Pdx1 C-terminus contacts an adjacent subunit, and deletion of this segment decreases enzymatic activity 3.5-fold, suggesting a role in catalysis.

X-ray crystal structure of Saccharomyces cerevisiae Pdx1 provides insights into the oligomeric nature of PLP synthases.,Neuwirth M, Strohmeier M, Windeisen V, Wallner S, Deller S, Rippe K, Sinning I, Macheroux P, Tews I FEBS Lett. 2009 Jul 7;583(13):2179-86. Epub 2009 Jun 11. PMID:19523954^[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
↑ Neuwirth M, Strohmeier M, Windeisen V, Wallner S, Deller S, Rippe K, Sinning I, Macheroux P, Tews I. X-ray crystal structure of Saccharomyces cerevisiae Pdx1 provides insights into the oligomeric nature of PLP synthases. FEBS Lett. 2009 Jul 7;583(13):2179-86. Epub 2009 Jun 11. PMID:19523954 doi:10.1016/j.febslet.2009.06.009

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3fem"

@@ Line 1: / Line 1: @@
 ==Structure of the synthase subunit Pdx1.1 (Snz1) of PLP synthase from Saccharomyces cerevisiae==
-<StructureSection load='3fem' size='340' side='right' caption='[[3fem]], [[Resolution|resolution]] 3.02&Aring;' scene=''>
+<StructureSection load='3fem' size='340' side='right'caption='[[3fem]], [[Resolution|resolution]] 3.02&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3fem]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FEM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3FEM FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3fem]] is a 6 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=3FEM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3FEM FirstGlance]. <br>
-</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2nv1|2nv1]], [[1znn|1znn]], [[2nv2|2nv2]], [[2iss|2iss]]</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]] 3.02&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">SNZ1, Snz1p, YM6543.03, YMR096W ([http://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=3fem FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fem OCA], [https://pdbe.org/3fem PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3fem RCSB], [https://www.ebi.ac.uk/pdbsum/3fem PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3fem 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=3fem FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fem OCA], [http://pdbe.org/3fem PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3fem RCSB], [http://www.ebi.ac.uk/pdbsum/3fem PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3fem ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://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>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/fe/3fem_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/fe/3fem_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 33: / Line 32: @@
 __TOC__
 </StructureSection>
-[[Category: Atcc 18824]]
+[[Category: Large Structures]]
-[[Category: Sinning, I]]
+[[Category: Saccharomyces cerevisiae]]
-[[Category: Strohmeier, M]]
+[[Category: Sinning I]]
-[[Category: Tews, I]]
+[[Category: Strohmeier M]]
-[[Category: Windeisen, V]]
+[[Category: Tews I]]
-[[Category: Biosynthetic protein]]
+[[Category: Windeisen V]]
-[[Category: Pyridoxine biosynthesis]]
-[[Category: Synthase]]
-[[Category: Transferase]]

3fem

From Proteopedia

Current revision

Structure of the synthase subunit Pdx1.1 (Snz1) of PLP synthase from Saccharomyces cerevisiae

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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