2oxo: Difference between revisions

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== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[2oxo]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacteriophage_sp. Bacteriophage sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OXO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2OXO FirstGlance]. <br>
<table><tr><td colspan='2'>[[2oxo]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacteriophage_sp. Bacteriophage sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OXO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2OXO FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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&#8491;</td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">int ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=38018 Bacteriophage sp.])</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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'>[https://proteopedia.org/fgij/fg.htm?mol=2oxo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2oxo OCA], [https://pdbe.org/2oxo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2oxo RCSB], [https://www.ebi.ac.uk/pdbsum/2oxo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2oxo 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=2oxo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2oxo OCA], [https://pdbe.org/2oxo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2oxo RCSB], [https://www.ebi.ac.uk/pdbsum/2oxo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2oxo ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[https://www.uniprot.org/uniprot/VINT_LAMBD VINT_LAMBD]] Integrase is necessary for integration of the phage into the host genome by site-specific recombination. In conjunction with excisionase, integrase is also necessary for excision of the prophage from the host genome.  
[https://www.uniprot.org/uniprot/VINT_LAMBD VINT_LAMBD] Integrase is necessary for integration of the phage into the host genome by site-specific recombination. In conjunction with excisionase, integrase is also necessary for excision of the prophage from the host genome.
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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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=2oxo ConSurf].
</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=2oxo ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Bacteriophage lambda integrase catalyzes site-specific DNA recombination. A helical bundle domain in the enzyme, called the core-binding domain (Int(CB)), promotes the catalysis of an intermediate DNA-cleavage reaction that is critical for recombination and is not well folded in solution in the absence of DNA. To gain structural insights into the mechanism behind the accessory role of this domain in catalysis, an attempt was made to crystallize an Int(CB)-DNA complex, but crystals of free Int(CB) were fortuitously obtained. The three-dimensional structure of DNA-free Int(CB) was solved at 2.0 A resolution by molecular replacement using as the search model the previously available DNA-bound 2.8 A structure of the Int(CB) domain in a larger construct of lambda integrase. The crystal structure of DNA-free Int(CB) resembles the DNA-bound structure of Int(CB), but exhibits subtle differences in the DNA-binding face and lacks electron density for ten residues in the C-terminus that form a portion of a linker connecting Int(CB) to the C-terminal catalytic domain of the enzyme. Thus, this work reveals the domain in the absence of DNA and allows comparison with the DNA-bound form of this catalytically activating domain.
Crystallization and structure determination of the core-binding domain of bacteriophage lambda integrase.,Kamadurai HB, Jain R, Foster MP Acta Crystallogr Sect F Struct Biol Cryst Commun. 2008 Jun 1;64(Pt, 6):470-3. Epub 2008 May 17. PMID:18540053<ref>PMID:18540053</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 2oxo" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Retroviral integrase 3D structures|Retroviral integrase 3D structures]]
*[[Retroviral integrase 3D structures|Retroviral integrase 3D structures]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Bacteriophage sp]]
[[Category: Bacteriophage sp]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Foster, M P]]
[[Category: Foster MP]]
[[Category: Jain, R]]
[[Category: Jain R]]
[[Category: Kamadurai, H B]]
[[Category: Kamadurai HB]]
[[Category: Dna binding protein]]
[[Category: Dna-binding protein]]
[[Category: Four-helix bundle]]

Latest revision as of 12:06, 21 February 2024

Crystallization and structure determination of the core-binding domain of bacteriophage lambda integraseCrystallization and structure determination of the core-binding domain of bacteriophage lambda integrase

Structural highlights

2oxo is a 1 chain structure with sequence from Bacteriophage sp.. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

VINT_LAMBD Integrase is necessary for integration of the phage into the host genome by site-specific recombination. In conjunction with excisionase, integrase is also necessary for excision of the prophage from the host genome.

Evolutionary Conservation

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

See Also

2oxo, resolution 2.00Å

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