2wcc: Difference between revisions
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< | ==phage lambda IntDBD1-64 complex with p prime 2 DNA== | ||
<StructureSection load='2wcc' size='340' side='right'caption='[[2wcc]], [[NMR_Ensembles_of_Models | 20 NMR models]]' scene=''> | |||
You may | == Structural highlights == | ||
<table><tr><td colspan='2'>[[2wcc]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacteriophage_lambda Bacteriophage lambda]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2WCC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2WCC FirstGlance]. <br> | |||
</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1z1g|1z1g]], [[1z1b|1z1b]], [[1kjk|1kjk]], [[1z19|1z19]], [[1ae9|1ae9]], [[1m97|1m97]], [[1p7d|1p7d]]</div></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=2wcc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2wcc OCA], [https://pdbe.org/2wcc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2wcc RCSB], [https://www.ebi.ac.uk/pdbsum/2wcc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2wcc ProSAT]</span></td></tr> | |||
</table> | |||
== 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. | |||
== 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/wc/2wcc_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=2wcc ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
The integrase protein (Int) from bacteriophage lambda is the archetypal member of the tyrosine recombinase family, a large group of enzymes that rearrange DNA in all domains of life. Int catalyzes the insertion and excision of the viral genome into and out of the Escherichia coli chromosome. Recombination transpires within higher-order nucleoprotein complexes that form when its amino-terminal domain binds to arm-type DNA sequences that are located distal to the site of strand exchange. Arm-site binding by Int is essential for catalysis, as it promotes Int-mediated bridge structures that stabilize the recombination machinery. We have elucidated how Int is able to sequence specifically recognize the arm-type site sequence by determining the solution structure of its amino-terminal domain (Int(N), residues Met1 to Leu64) in complex with its P'2 DNA binding site. Previous studies have shown that Int(N) adopts a rare monomeric DNA binding fold that consists of a three-stranded antiparallel beta-sheet that is packed against a carboxy-terminal alpha helix. A low-resolution crystal structure of the full-length protein also revealed that the sheet is inserted into the major groove of the arm-type site. The solution structure presented here reveals how Int(N) specifically recognizes the arm-type site sequence. A novel feature of the new solution structure is the use of an 11-residue tail that is located at the amino terminus. DNA binding induces the folding of a 3(10) helix in the tail that projects the amino terminus of the protein deep into the minor groove for stabilizing DNA contacts. This finding reveals the structural basis for the observation that the "unstructured" amino terminus is required for recombination. | |||
NMR structure of the amino-terminal domain of the lambda integrase protein in complex with DNA: immobilization of a flexible tail facilitates beta-sheet recognition of the major groove.,Fadeev EA, Sam MD, Clubb RT J Mol Biol. 2009 May 15;388(4):682-90. Epub 2009 Mar 24. PMID:19324050<ref>PMID:19324050</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 2wcc" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Retroviral integrase 3D structures|Retroviral integrase 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
== | [[Category: Bacteriophage lambda]] | ||
[[Category: Large Structures]] | |||
[[Category: Clubb, R T]] | |||
== | [[Category: Fadeev, E A]] | ||
< | [[Category: Sam, M D]] | ||
[[Category: | |||
[[Category: Clubb, R T | |||
[[Category: Fadeev, E A | |||
[[Category: Sam, M D | |||
[[Category: Dna integration]] | [[Category: Dna integration]] | ||
[[Category: Dna recombination]] | [[Category: Dna recombination]] | ||
| Line 34: | Line 46: | ||
[[Category: Phage lambda]] | [[Category: Phage lambda]] | ||
[[Category: Protein dna complex]] | [[Category: Protein dna complex]] | ||
[[Category: Protein-dna complex]] | |||
[[Category: Protein/dna]] | [[Category: Protein/dna]] | ||
[[Category: Recombination]] | [[Category: Recombination]] | ||
Latest revision as of 14:03, 6 April 2022
phage lambda IntDBD1-64 complex with p prime 2 DNAphage lambda IntDBD1-64 complex with p prime 2 DNA
Structural highlights
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. Publication Abstract from PubMedThe integrase protein (Int) from bacteriophage lambda is the archetypal member of the tyrosine recombinase family, a large group of enzymes that rearrange DNA in all domains of life. Int catalyzes the insertion and excision of the viral genome into and out of the Escherichia coli chromosome. Recombination transpires within higher-order nucleoprotein complexes that form when its amino-terminal domain binds to arm-type DNA sequences that are located distal to the site of strand exchange. Arm-site binding by Int is essential for catalysis, as it promotes Int-mediated bridge structures that stabilize the recombination machinery. We have elucidated how Int is able to sequence specifically recognize the arm-type site sequence by determining the solution structure of its amino-terminal domain (Int(N), residues Met1 to Leu64) in complex with its P'2 DNA binding site. Previous studies have shown that Int(N) adopts a rare monomeric DNA binding fold that consists of a three-stranded antiparallel beta-sheet that is packed against a carboxy-terminal alpha helix. A low-resolution crystal structure of the full-length protein also revealed that the sheet is inserted into the major groove of the arm-type site. The solution structure presented here reveals how Int(N) specifically recognizes the arm-type site sequence. A novel feature of the new solution structure is the use of an 11-residue tail that is located at the amino terminus. DNA binding induces the folding of a 3(10) helix in the tail that projects the amino terminus of the protein deep into the minor groove for stabilizing DNA contacts. This finding reveals the structural basis for the observation that the "unstructured" amino terminus is required for recombination. NMR structure of the amino-terminal domain of the lambda integrase protein in complex with DNA: immobilization of a flexible tail facilitates beta-sheet recognition of the major groove.,Fadeev EA, Sam MD, Clubb RT J Mol Biol. 2009 May 15;388(4):682-90. Epub 2009 Mar 24. PMID:19324050[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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