3uj3

From Proteopedia

(Difference between revisions)

Current revision

Crystal Structure of the synaptic tetramer of the G-Segment Invertase (Gin)

Structural highlights

3uj3 is a 1 chain structure with sequence from Escherichia virus Mu. This structure supersedes the now removed PDB entry 3plo. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 3.51Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

GIN_BPMU Performs inversion of a viral 3 kp segment (G-segment) that encodes two alternate pairs of tail fiber proteins thereby modifying the host specificity of the virus. Binds as a dimer to the viral gix sites which are 34-bp palindromic sequences that flank the invertible G-segment. Catalyzes site-specific recombination in the presence of the host factor Fis. Gin dimers bound to each of the gix sites and host factor Fis bound to the enhancer come together to form the synaptic complex. Each Gin monomer introduces a nick and becomes covalently attached to the 5'-phosphate of the DNA, resulting in double-stranded staggered breaks at both recombination sites. A 180 degrees rotation of one of the two Gin dimers followed by religation of the DNA leads to the inversion of the G-segment (G+ or G- orientation).^[1] ^[2] ^[3] ^[4]

References

↑ Ritacco CJ, Kamtekar S, Wang J, Steitz TA. Crystal structure of an intermediate of rotating dimers within the synaptic tetramer of the G-segment invertase. Nucleic Acids Res. 2013 Feb 1;41(4):2673-82. doi: 10.1093/nar/gks1303. Epub 2012 , Dec 28. PMID:23275567 doi:10.1093/nar/gks1303
↑ Klippel A, Cloppenborg K, Kahmann R. Isolation and characterization of unusual gin mutants. EMBO J. 1988 Dec 1;7(12):3983-9. doi: 10.1002/j.1460-2075.1988.tb03286.x. PMID:2974801 doi:http://dx.doi.org/10.1002/j.1460-2075.1988.tb03286.x
↑ Kahmann R, Rudt F, Koch C, Mertens G. G inversion in bacteriophage Mu DNA is stimulated by a site within the invertase gene and a host factor. Cell. 1985 Jul;41(3):771-80. doi: 10.1016/s0092-8674(85)80058-1. PMID:3159478 doi:http://dx.doi.org/10.1016/s0092-8674(85)80058-1
↑ Plasterk RH, Kanaar R, van de Putte P. A genetic switch in vitro: DNA inversion by Gin protein of phage Mu. Proc Natl Acad Sci U S A. 1984 May;81(9):2689-92. doi: 10.1073/pnas.81.9.2689. PMID:6232613 doi:http://dx.doi.org/10.1073/pnas.81.9.2689

1 Structural highlights
2 Function
3 See Also
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3uj3"

@@ Line 3: / Line 3: @@
 <StructureSection load='3uj3' size='340' side='right'caption='[[3uj3]], [[Resolution|resolution]] 3.51&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3uj3]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bpmu Bpmu]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3plo 3plo]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3UJ3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3UJ3 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3uj3]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_virus_Mu Escherichia virus Mu]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3plo 3plo]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3UJ3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3UJ3 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;'>[[3plo|3plo]], [[1zr2|1zr2]], [[1zr4|1zr4]], [[3pkz|3pkz]]</div></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]] 3.51&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">gin, 51 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10677 BPMU])</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=3uj3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3uj3 OCA], [https://pdbe.org/3uj3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3uj3 RCSB], [https://www.ebi.ac.uk/pdbsum/3uj3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3uj3 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/DNIV_BPMU DNIV_BPMU]] This protein catalyzes the inversion of a 3000-bp segment of phage DNA. The inversion results in a modification of the 3'-end of the tail fiber gene and alters the host specificity.
+[https://www.uniprot.org/uniprot/GIN_BPMU GIN_BPMU] Performs inversion of a viral 3 kp segment (G-segment) that encodes two alternate pairs of tail fiber proteins thereby modifying the host specificity of the virus. Binds as a dimer to the viral gix sites which are 34-bp palindromic sequences that flank the invertible G-segment. Catalyzes site-specific recombination in the presence of the host factor Fis. Gin dimers bound to each of the gix sites and host factor Fis bound to the enhancer come together to form the synaptic complex. Each Gin monomer introduces a nick and becomes covalently attached to the 5'-phosphate of the DNA, resulting in double-stranded staggered breaks at both recombination sites. A 180 degrees rotation of one of the two Gin dimers followed by religation of the DNA leads to the inversion of the G-segment (G+ or G- orientation).<ref>PMID:23275567</ref> <ref>PMID:2974801</ref> <ref>PMID:3159478</ref> <ref>PMID:6232613</ref>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-The serine family of site-specific DNA recombination enzymes accomplishes strand cleavage, exchange and religation using a synaptic protein tetramer. A double-strand break intermediate in which each protein subunit is covalently linked to the target DNA substrate ensures that the recombination event will not damage the DNA. The previous structure of a tetrameric synaptic complex of gammadelta resolvase linked to two cleaved DNA strands had suggested a rotational mechanism of recombination in which one dimer rotates 180 degrees about the flat exchange interface for strand exchange. Here, we report the crystal structure of a synaptic tetramer of an unliganded activated mutant (M114V) of the G-segment invertase (Gin) in which one dimer half is rotated by 26 degrees or 154 degrees relative to the other dimer when compared with the dimers in the synaptic complex of gammadelta resolvase. Modeling shows that this rotational orientation of Gin is not compatible with its being able to bind uncleaved DNA, implying that this structure represents an intermediate in the process of strand exchange. Thus, our structure provides direct evidence for the proposed rotational mechanism of site-specific recombination.
-Crystal structure of an intermediate of rotating dimers within the synaptic tetramer of the G-segment invertase.,Ritacco CJ, Kamtekar S, Wang J, Steitz TA Nucleic Acids Res. 2013 Feb 1;41(4):2673-82. doi: 10.1093/nar/gks1303. Epub 2012 , Dec 28. PMID:23275567<ref>PMID:23275567</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 3uj3" style="background-color:#fffaf0;"></div>
 ==See Also==
@@ Line 26: / Line 16: @@
 __TOC__
 </StructureSection>
-[[Category: Bpmu]]
+[[Category: Escherichia virus Mu]]
 [[Category: Large Structures]]
-[[Category: Kamtekar, S]]
+[[Category: Kamtekar S]]
-[[Category: Ritacco, C J]]
+[[Category: Ritacco CJ]]
-[[Category: Steitz, T A]]
+[[Category: Steitz TA]]
-[[Category: Wang, J]]
+[[Category: Wang J]]
-[[Category: Helix-turn-helix]]
-[[Category: Recombination]]
-[[Category: Site-specific recombinase]]

3uj3

From Proteopedia

Current revision

Crystal Structure of the synaptic tetramer of the G-Segment Invertase (Gin)

Structural highlights

Function

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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