1pyi: Difference between revisions

From Proteopedia
Jump to navigation Jump to search
New page: left|200px<br /><applet load="1pyi" size="450" color="white" frame="true" align="right" spinBox="true" caption="1pyi, resolution 3.200Å" /> '''CRYSTAL STRUCTURE O...
 
No edit summary
 
(13 intermediate revisions by the same user not shown)
Line 1: Line 1:
[[Image:1pyi.gif|left|200px]]<br /><applet load="1pyi" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1pyi, resolution 3.200&Aring;" />
'''CRYSTAL STRUCTURE OF A PPR1-DNA COMPLEX: DNA RECOGNITION BY PROTEINS CONTAINING A ZN2CYS6 BINUCLEAR CLUSTER'''<br />


==Overview==
==CRYSTAL STRUCTURE OF A PPR1-DNA COMPLEX: DNA RECOGNITION BY PROTEINS CONTAINING A ZN2CYS6 BINUCLEAR CLUSTER==
PPR1 is a yeast transcription factor that contains a six-cysteine, two-zinc (Zn) domain, homologous to a similar structure in GAL4. Like, GAL4, it binds to DNA sites with conserved CGG triplets symmetrically, placed near each end. Whereas the GAL4 site has 11 intervening base pairs, the PPR1 site has 6. The crystal structure of a 95-residue fragment of, PPR1 in specific complex with DNA shows that the protein binds to a, symmetrical 14-bp recognition site as a nonsymmetrical homodimer. An, amino-terminal Zn domain interacts with a conserved CGG triplet near each, end of the site through major groove contacts, and the carboxy-terminal, residues mediate dimerization through a coiled-coil element and an, extended strand. A linker region, connecting the Zn domain and the, coiled-coil, folds into a beta-hairpin. This hairpin packs differently on, the two subunits and leads to a striking asymmetry, which is largely, restricted to the dimerization and linker regions of the protein., Comparison with the GAL4-DNA structure shows that their specificities for, sites of different length are determined by the preferred folds of their, respective linker segments and by residues at the amino-terminal ends of, their coiled-coils. None of these residues contact DNA in PPR1, and they, contact only the sugar phosphate backbone in GAL4. We propose that this, novel mode of DNA site selection is employed by other proteins that, contain a Zn2Cys6 binuclear cluster.
<StructureSection load='1pyi' size='340' side='right'caption='[[1pyi]], [[Resolution|resolution]] 3.20&Aring;' scene=''>
 
== Structural highlights ==
==About this Structure==
<table><tr><td colspan='2'>[[1pyi]] is a 4 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=1PYI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1PYI FirstGlance]. <br>
1PYI is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae] with ZN as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1PYI OCA].  
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.2&#8491;</td></tr>
 
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
==Reference==
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1pyi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pyi OCA], [https://pdbe.org/1pyi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1pyi RCSB], [https://www.ebi.ac.uk/pdbsum/1pyi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1pyi ProSAT]</span></td></tr>
Crystal structure of a PPR1-DNA complex: DNA recognition by proteins containing a Zn2Cys6 binuclear cluster., Marmorstein R, Harrison SC, Genes Dev. 1994 Oct 15;8(20):2504-12. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=7958913 7958913]
</table>
== Function ==
[https://www.uniprot.org/uniprot/PPR1_YEAST PPR1_YEAST] Positive regulator of URA1 and URA3 expression.
== 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/py/1pyi_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1pyi ConSurf].
<div style="clear:both"></div>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Saccharomyces cerevisiae]]
[[Category: Saccharomyces cerevisiae]]
[[Category: Single protein]]
[[Category: Harrison SC]]
[[Category: Harrison, S.C.]]
[[Category: Marmorstein R]]
[[Category: Marmorstein, R.]]
[[Category: ZN]]
[[Category: protein-dna complex]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 00:14:04 2007''

Latest revision as of 11:11, 14 February 2024

CRYSTAL STRUCTURE OF A PPR1-DNA COMPLEX: DNA RECOGNITION BY PROTEINS CONTAINING A ZN2CYS6 BINUCLEAR CLUSTERCRYSTAL STRUCTURE OF A PPR1-DNA COMPLEX: DNA RECOGNITION BY PROTEINS CONTAINING A ZN2CYS6 BINUCLEAR CLUSTER

Structural highlights

1pyi is a 4 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 3.2Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

PPR1_YEAST Positive regulator of URA1 and URA3 expression.

Evolutionary Conservation

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

1pyi, resolution 3.20Å

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA
Retrieved from "https://proteopedia.openfox.io/wiki/index.php?title=1pyi&oldid=4053525"