This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

1p4e

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Revision as of 07:36, 15 February 2018

Flpe W330F mutant-DNA Holliday Junction Complex

Structural highlights

1p4e is a 10 chain structure with sequence from Atcc 18824. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
NonStd Res:
Gene:	FLP1 (ATCC 18824)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[FLP_YEAST] Part of the plasmid amplification system, which corrects any decrease in copy number caused by a rare missegregation event. Catalyzes the recombination between the large inverted repetitions of the 2-micron plasmid during plasmid replication. This recombination event changes the direction of one of the two replication forks in the bidirectionally replicating molecule, effectively resulting in multiple rounds of replication from a single initiation event. Binds specifically to the FLP recognition target (FRT) site where it induces DNA to bend. Three types of bend exist. Type I is approximately 60 degrees and results from 1 FLP molecule binding to 1 symmetry element. Type II is >144 degrees and results from FLP molecules binding to symmetry elements a and b. Type III is approximately 65 degrees and results from FLP molecules binding to symmetry elements b and c.^[1] ^[2] ^[3]

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 PubMed

The active site of Flp contains, in addition to a transdonated nucleophilic tyrosine, five other residues that are highly conserved within the lambda-integrase family of site-specific recombinases and the type IB topoisomerases. We have used site-directed mutagenesis and x-ray crystallography to investigate the roles of two such residues, Lys223 and Trp330. Our findings agree with studies on related enzymes showing the importance of Lys223 in catalysis but demonstrate that in Flp-mediated recombination the primary role of Trp330 is architectural rather than catalytic. Eliminating the hydrogen bonding potential of Trp330 by phenylalanine substitution results in surprisingly small changes in reaction rates, compared with dramatic decreases in the activities of W330A, W330H, and W330Q. The structure of a W330F mutant-DNA complex reveals an active site nearly identical to that of the wild type. The phenylalanine side chain preserves most of the van der Waals interactions Trp330 forms with the Tyr343-containing trans helix, which may be particularly important for the docking of this helix. Our studies of Trp330 provide the first detailed examination of this conserved residue in the lambda-integrase family, suggesting that the relative importance of active site residues may differ among Flp and related enzymes.

The role of the conserved Trp330 in Flp-mediated recombination. Functional and structural analysis.,Chen Y, Rice PA J Biol Chem. 2003 Jul 4;278(27):24800-7. Epub 2003 Apr 27. PMID:12716882^[4]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Pan H, Clary D, Sadowski PD. Identification of the DNA-binding domain of the FLP recombinase. J Biol Chem. 1991 Jun 15;266(17):11347-54. PMID:2040639
↑ Reynolds AE, Murray AW, Szostak JW. Roles of the 2 microns gene products in stable maintenance of the 2 microns plasmid of Saccharomyces cerevisiae. Mol Cell Biol. 1987 Oct;7(10):3566-73. PMID:3316982
↑ Schwartz CJ, Sadowski PD. FLP protein of 2 mu circle plasmid of yeast induces multiple bends in the FLP recognition target site. J Mol Biol. 1990 Nov 20;216(2):289-98. PMID:2254930
↑ Chen Y, Rice PA. The role of the conserved Trp330 in Flp-mediated recombination. Functional and structural analysis. J Biol Chem. 2003 Jul 4;278(27):24800-7. Epub 2003 Apr 27. PMID:12716882 doi:10.1074/jbc.M300853200

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1p4e"

@@ Line 1: / Line 1: @@
 ==Flpe W330F mutant-DNA Holliday Junction Complex==
 <StructureSection load='1p4e' size='340' side='right' caption='[[1p4e]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
@@ Line 6: / Line 7: @@
 <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=PTR:O-PHOSPHOTYROSINE'>PTR</scene></td></tr>
 <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">FLP1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1p4e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1p4e OCA], [http://pdbe.org/1p4e PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1p4e RCSB], [http://www.ebi.ac.uk/pdbsum/1p4e PDBsum]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1p4e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1p4e OCA], [http://pdbe.org/1p4e PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1p4e RCSB], [http://www.ebi.ac.uk/pdbsum/1p4e PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1p4e ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 14: / Line 15: @@
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/p4/1p4e_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/p4/1p4e_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 29: / Line 30: @@
 </div>
 <div class="pdbe-citations 1p4e" style="background-color:#fffaf0;"></div>
-==See Also==
-*[[Resolvase|Resolvase]]
 == References ==
 <references/>

1p4e

From Proteopedia

Revision as of 07:36, 15 February 2018

Flpe W330F mutant-DNA Holliday Junction Complex

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox