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2qoj

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Revision as of 07:31, 25 October 2017

Coevolution of a homing endonuclease and its host target sequence

Structural highlights

2qoj is a 3 chain structure with sequence from Emericella nidulans. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
NonStd Res:
Related:	1p8k
Gene:	I-AniI (Emericella nidulans)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[ANI1_EMEND] Mitochondrial DNA endonuclease and mRNA maturase involved in intron homing and required for splicing of the cytochrome b (cobA) gene intron, containing its own coding sequence. The protein stimulates the intrinsic ribozyme activity of the intron through binding to and stabilizing specific secondary and tertiary structure elements in the RNA. As an endonuclease it introduces a specific double-strand break at the junction of the two exons the cobA gene and thus mediates the insertion of an intron, containing its own coding sequence (group I intron), into an intronless gene. Recognizes with limited specificity and cleaves the sequence 5'-GAGGAGGTTTCTCTGTA-3'. The proteins RNA and DNA recognition and binding surfaces are independent.^[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

We have determined the specificity profile of the homing endonuclease I-AniI and compared it to the conservation of its host gene. Homing endonucleases are encoded within intervening sequences such as group I introns. They initiate the transfer of such elements by cleaving cognate alleles lacking the intron, leading to their transfer via homologous recombination. Each structural homing endonuclease family has arrived at an appropriate balance of specificity and fidelity that avoids toxicity while maximizing target recognition and invasiveness. I-AniI recognizes a strongly conserved target sequence in a host gene encoding apocytochrome B and has fine-tuned its specificity to correlate with wobble versus nonwobble positions across that sequence and to the amount of degeneracy inherent in individual codons. The physiological target site in the host gene is not the optimal substrate for recognition and cleavage: at least one target variant identified during a screen is bound more tightly and cleaved more rapidly. This is a result of the periodic cycle of intron homing, which at any time can present nonoptimal combinations of endonuclease specificity and insertion site sequences in a biological host.

Coevolution of a homing endonuclease and its host target sequence.,Scalley-Kim M, McConnell-Smith A, Stoddard BL J Mol Biol. 2007 Oct 5;372(5):1305-19. Epub 2007 Aug 2. PMID:17720189^[4]

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

References

↑ Ho Y, Kim SJ, Waring RB. A protein encoded by a group I intron in Aspergillus nidulans directly assists RNA splicing and is a DNA endonuclease. Proc Natl Acad Sci U S A. 1997 Aug 19;94(17):8994-9. PMID:9256423
↑ Ho Y, Waring RB. The maturase encoded by a group I intron from Aspergillus nidulans stabilizes RNA tertiary structure and promotes rapid splicing. J Mol Biol. 1999 Oct 8;292(5):987-1001. PMID:10512698 doi:10.1006/jmbi.1999.3070
↑ Chatterjee P, Brady KL, Solem A, Ho Y, Caprara MG. Functionally distinct nucleic acid binding sites for a group I intron encoded RNA maturase/DNA homing endonuclease. J Mol Biol. 2003 May 30;329(2):239-51. PMID:12758073
↑ Scalley-Kim M, McConnell-Smith A, Stoddard BL. Coevolution of a homing endonuclease and its host target sequence. J Mol Biol. 2007 Oct 5;372(5):1305-19. Epub 2007 Aug 2. PMID:17720189 doi:10.1016/j.jmb.2007.07.052

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/2qoj"

@@ Line 1: / Line 1: @@
 ==Coevolution of a homing endonuclease and its host target sequence==
 <StructureSection load='2qoj' size='340' side='right' caption='[[2qoj]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2qoj]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Aspergillus_nidulans Aspergillus nidulans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QOJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2QOJ FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2qoj]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Emericella_nidulans Emericella nidulans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QOJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2QOJ FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
 <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1p8k|1p8k]]</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">I-AniI ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=162425 Aspergillus nidulans])</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">I-AniI ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=162425 Emericella nidulans])</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=2qoj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qoj OCA], [http://pdbe.org/2qoj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2qoj RCSB], [http://www.ebi.ac.uk/pdbsum/2qoj 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=2qoj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qoj OCA], [http://pdbe.org/2qoj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2qoj RCSB], [http://www.ebi.ac.uk/pdbsum/2qoj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2qoj ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 19: / Line 20: @@
     <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/chain_selection.php?pdb_ID=2ata 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=2qoj ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 30: / Line 31: @@
 </div>
 <div class="pdbe-citations 2qoj" style="background-color:#fffaf0;"></div>
-==See Also==
-*[[Endonuclease|Endonuclease]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Aspergillus nidulans]]
+[[Category: Emericella nidulans]]
 [[Category: Scalley-Kim, M]]
 [[Category: Smith, A McConnell]]

2qoj

From Proteopedia

Revision as of 07:31, 25 October 2017

Coevolution of a homing endonuclease and its host target sequence

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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