5iit

From Proteopedia

(Difference between revisions)

Current revision

Structure of SPX domain of the yeast inorganic polyphophate polymerase Vtc4 crystallized by carrier-driven crystallization in fusion with the macro domain of human histone macroH2A1.1

Structural highlights

5iit is a 4 chain structure with sequence from Homo sapiens and Saccharomyces cerevisiae S288C. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.134Å
Ligands:	, , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

H2AY_HUMAN Variant histone H2A which replaces conventional H2A in a subset of nucleosomes where it represses transcription. Nucleosomes wrap and compact DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication and chromosomal stability. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called histone code, and nucleosome remodeling. Involved in stable X chromosome inactivation. Inhibits the binding of transcription factors and interferes with the activity of remodeling SWI/SNF complexes. Inhibits histone acetylation by EP300 and recruits class I HDACs, which induces a hypoacetylated state of chromatin. In addition, isoform 1, but not isoform 2, binds ADP-ribose and O-acetyl-ADP-ribose, and may be involved in ADP-ribose-mediated chromatin modulation.^[1] ^[2] ^[3] ^[4] ^[5] VTC4_YEAST Component of the vacuolar transporter chaperone (VTC) complex, which plays a role in vacuolar membrane fusion. Required for SEC18/NSF activity in SNARE priming, membrane binding of LMA1 and V(0) trans-complex formation.^[6] ^[7] ^[8]

Publication Abstract from PubMed

Phosphorus is a macronutrient taken up by cells as inorganic phosphate (Pi). How cells sense cellular Pilevels is poorly characterized. Here we report that SPX domains, which are found in eukaryotic phosphate transporters, signaling proteins and inorganic polyphosphate polymerases, provide a basic binding surface for inositol polyphosphate signaling molecules (InsPs), whose concentrations change in response to Piavailability. Substitutions of critical binding surface residues impair InsP binding in vitro, inorganic polyphosphate synthesis in yeast and Pitransport inArabidopsis In plants, InsPs trigger the association of SPX proteins with transcription factors to regulate Pistarvation responses. We propose that InsPs communicate cytosolic Pilevels to SPX domains and enable them to interact with a multitude of proteins to regulate Piuptake, transport and storage in fungi, plants and animals.

Control of eukaryotic phosphate homeostasis by inositol polyphosphate sensor domains.,Wild R, Gerasimaite R, Jung JY, Truffault V, Pavlovic I, Schmidt A, Saiardi A, Jessen HJ, Poirier Y, Hothorn M, Mayer A Science. 2016 Apr 14. pii: aad9858. PMID:27080106^[9]

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

References

↑ Angelov D, Molla A, Perche PY, Hans F, Cote J, Khochbin S, Bouvet P, Dimitrov S. The histone variant macroH2A interferes with transcription factor binding and SWI/SNF nucleosome remodeling. Mol Cell. 2003 Apr;11(4):1033-41. PMID:12718888
↑ Zhang R, Poustovoitov MV, Ye X, Santos HA, Chen W, Daganzo SM, Erzberger JP, Serebriiskii IG, Canutescu AA, Dunbrack RL, Pehrson JR, Berger JM, Kaufman PD, Adams PD. Formation of MacroH2A-containing senescence-associated heterochromatin foci and senescence driven by ASF1a and HIRA. Dev Cell. 2005 Jan;8(1):19-30. PMID:15621527 doi:S1534580704004083
↑ Hernandez-Munoz I, Lund AH, van der Stoop P, Boutsma E, Muijrers I, Verhoeven E, Nusinow DA, Panning B, Marahrens Y, van Lohuizen M. Stable X chromosome inactivation involves the PRC1 Polycomb complex and requires histone MACROH2A1 and the CULLIN3/SPOP ubiquitin E3 ligase. Proc Natl Acad Sci U S A. 2005 May 24;102(21):7635-40. Epub 2005 May 16. PMID:15897469 doi:0408918102
↑ Doyen CM, An W, Angelov D, Bondarenko V, Mietton F, Studitsky VM, Hamiche A, Roeder RG, Bouvet P, Dimitrov S. Mechanism of polymerase II transcription repression by the histone variant macroH2A. Mol Cell Biol. 2006 Feb;26(3):1156-64. PMID:16428466 doi:10.1128/MCB.26.3.1156-1164.2006
↑ Chakravarthy S, Gundimella SK, Caron C, Perche PY, Pehrson JR, Khochbin S, Luger K. Structural characterization of the histone variant macroH2A. Mol Cell Biol. 2005 Sep;25(17):7616-24. PMID:16107708 doi:http://dx.doi.org/25/17/7616
↑ Ogawa N, DeRisi J, Brown PO. New components of a system for phosphate accumulation and polyphosphate metabolism in Saccharomyces cerevisiae revealed by genomic expression analysis. Mol Biol Cell. 2000 Dec;11(12):4309-21. PMID:11102525
↑ Muller O, Bayer MJ, Peters C, Andersen JS, Mann M, Mayer A. The Vtc proteins in vacuole fusion: coupling NSF activity to V(0) trans-complex formation. EMBO J. 2002 Feb 1;21(3):259-69. PMID:11823419 doi:http://dx.doi.org/10.1093/emboj/21.3.259
↑ Muller O, Neumann H, Bayer MJ, Mayer A. Role of the Vtc proteins in V-ATPase stability and membrane trafficking. J Cell Sci. 2003 Mar 15;116(Pt 6):1107-15. PMID:12584253
↑ Wild R, Gerasimaite R, Jung JY, Truffault V, Pavlovic I, Schmidt A, Saiardi A, Jessen HJ, Poirier Y, Hothorn M, Mayer A. Control of eukaryotic phosphate homeostasis by inositol polyphosphate sensor domains. Science. 2016 Apr 14. pii: aad9858. PMID:27080106 doi:http://dx.doi.org/10.1126/science.aad9858

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5iit"

Categories: Homo sapiens | Large Structures | Saccharomyces cerevisiae S288C | Hothorn M | Wild R

@@ Line 3: / Line 3: @@
 <StructureSection load='5iit' size='340' side='right'caption='[[5iit]], [[Resolution|resolution]] 2.13&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5iit]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IIT OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5IIT FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5iit]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_S288C Saccharomyces cerevisiae S288C]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IIT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5IIT FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 2.134&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">H2AFY, MACROH2A1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=5iit FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5iit OCA], [http://pdbe.org/5iit PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5iit RCSB], [http://www.ebi.ac.uk/pdbsum/5iit PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5iit ProSAT]</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=5iit FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5iit OCA], [https://pdbe.org/5iit PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5iit RCSB], [https://www.ebi.ac.uk/pdbsum/5iit PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5iit ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/VTC4_YEAST VTC4_YEAST]] Component of the vacuolar transporter chaperone (VTC) complex, which plays a role in vacuolar membrane fusion. Required for SEC18/NSF activity in SNARE priming, membrane binding of LMA1 and V(0) trans-complex formation.<ref>PMID:11102525</ref> <ref>PMID:11823419</ref> <ref>PMID:12584253</ref>
+[https://www.uniprot.org/uniprot/H2AY_HUMAN H2AY_HUMAN] Variant histone H2A which replaces conventional H2A in a subset of nucleosomes where it represses transcription. Nucleosomes wrap and compact DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication and chromosomal stability. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called histone code, and nucleosome remodeling. Involved in stable X chromosome inactivation. Inhibits the binding of transcription factors and interferes with the activity of remodeling SWI/SNF complexes. Inhibits histone acetylation by EP300 and recruits class I HDACs, which induces a hypoacetylated state of chromatin. In addition, isoform 1, but not isoform 2, binds ADP-ribose and O-acetyl-ADP-ribose, and may be involved in ADP-ribose-mediated chromatin modulation.<ref>PMID:12718888</ref> <ref>PMID:15621527</ref> <ref>PMID:15897469</ref> <ref>PMID:16428466</ref> <ref>PMID:16107708</ref> [https://www.uniprot.org/uniprot/VTC4_YEAST VTC4_YEAST] Component of the vacuolar transporter chaperone (VTC) complex, which plays a role in vacuolar membrane fusion. Required for SEC18/NSF activity in SNARE priming, membrane binding of LMA1 and V(0) trans-complex formation.<ref>PMID:11102525</ref> <ref>PMID:11823419</ref> <ref>PMID:12584253</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 23: / Line 23: @@
 __TOC__
 </StructureSection>
-[[Category: Human]]
+[[Category: Homo sapiens]]
 [[Category: Large Structures]]
-[[Category: Hothorn, M]]
+[[Category: Saccharomyces cerevisiae S288C]]
-[[Category: Wild, R]]
+[[Category: Hothorn M]]
-[[Category: Alpha-helical hairpin]]
+[[Category: Wild R]]
-[[Category: Chaperone]]
-[[Category: Helical bundle]]
-[[Category: Inositol phosphate binding protein]]
-[[Category: Protein-protein interaction]]

5iit

From Proteopedia

Current revision

Structure of SPX domain of the yeast inorganic polyphophate polymerase Vtc4 crystallized by carrier-driven crystallization in fusion with the macro domain of human histone macroH2A1.1

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox