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1dq3

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(New page: 200px<br /><applet load="1dq3" size="450" color="white" frame="true" align="right" spinBox="true" caption="1dq3, resolution 2.10&Aring;" /> '''CRYSTAL STRUCTURE OF...)
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[[Image:1dq3.gif|left|200px]]<br /><applet load="1dq3" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1dq3, resolution 2.10&Aring;" />
 
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'''CRYSTAL STRUCTURE OF AN ARCHAEAL INTEIN-ENCODED HOMING ENDONUCLEASE PI-PFUI'''<br />
 
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==Overview==
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==CRYSTAL STRUCTURE OF AN ARCHAEAL INTEIN-ENCODED HOMING ENDONUCLEASE PI-PFUI==
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Inteins possess two different enzymatic activities, self-catalyzed protein, splicing and site-specific DNA cleavage. These endonucleases, which are, classified as part of the homing endonuclease family, initiate the, mobility of their genetic elements into homologous alleles. They recognize, long asymmetric nucleotide sequences and cleave both DNA strands in a, monomer form. We present here the 2.1 A crystal structure of the archaeal, PI-PfuI intein from Pyroccocus furiosus. The structure reveals a unique, domain, designated here as the Stirrup domain, which is inserted between, the Hint domain and an endonuclease domain. The horseshoe-shaped Hint, domain contains a catalytic center for protein splicing, which involves, both N and C-terminal residues. The endonuclease domain, which is inserted, into the Hint domain, consists of two copies of substructure related by an, internal pseudo 2-fold axis. In contrast with the I-CreI homing, endonuclease, PI-PfuI possibly has two asymmetric catalytic sites at the, center of a putative DNA-binding cleft formed by a pair of four-stranded, beta-sheets. DNase I footprinting experiments showed that PI-PfuI covers, more than 30 bp of the substrate asymmetrically across the cleavage site., A docking model of the DNA-enzyme complex suggests that the endonuclease, domain covers the 20 bp DNA duplex encompassing the cleavage site, whereas, the Stirrup domain could make an additional contact with another upstream, 10 bp region. For the double-strand break, the two strands in the DNA, duplex were cleaved by PI-PfuI with different efficiencies. We suggest, that the cleavage of each strand is catalyzed by each of the two, non-equivalent active sites.
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<StructureSection load='1dq3' size='340' side='right'caption='[[1dq3]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1dq3]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_furiosus Pyrococcus furiosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DQ3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DQ3 FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.1&#8491;</td></tr>
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<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>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1dq3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dq3 OCA], [https://pdbe.org/1dq3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dq3 RCSB], [https://www.ebi.ac.uk/pdbsum/1dq3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dq3 ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/NDRZ_PYRFU NDRZ_PYRFU] Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides.<ref>PMID:9012808</ref>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dq/1dq3_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=1dq3 ConSurf].
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<div style="clear:both"></div>
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==About this Structure==
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==See Also==
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1DQ3 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Pyrococcus_furiosus Pyrococcus furiosus] 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=1DQ3 OCA].
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*[[Endonuclease 3D structures|Endonuclease 3D structures]]
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== References ==
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==Reference==
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<references/>
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Crystal structure of an archaeal intein-encoded homing endonuclease PI-PfuI., Ichiyanagi K, Ishino Y, Ariyoshi M, Komori K, Morikawa K, J Mol Biol. 2000 Jul 21;300(4):889-901. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10891276 10891276]
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__TOC__
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</StructureSection>
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[[Category: Large Structures]]
[[Category: Pyrococcus furiosus]]
[[Category: Pyrococcus furiosus]]
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[[Category: Single protein]]
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[[Category: Ichiyanagi K]]
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[[Category: Ichiyanagi, K.]]
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[[Category: Ishino Y]]
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[[Category: Ishino, Y.]]
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[[Category: Morikawa K]]
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[[Category: Morikawa, K.]]
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[[Category: ZN]]
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[[Category: endonuclease]]
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[[Category: intein-encoded]]
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[[Category: pi-pfui]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sun Nov 25 03:30:38 2007''
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Current revision

CRYSTAL STRUCTURE OF AN ARCHAEAL INTEIN-ENCODED HOMING ENDONUCLEASE PI-PFUI

PDB ID 1dq3

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