3eh8

From Proteopedia

(Difference between revisions)

Revision as of 21:19, 4 August 2016

Crystal structure of Y2 I-AniI variant (F13Y/S111Y)/DNA complex with calcium

Structural highlights

3eh8 is a 9 chain structure with sequence from A. nidulans. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Gene:	AnCOB Intron Gene (A. 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

The LAGLIDADG homing endonuclease (LHE) I-AniI has adopted an extremely efficient secondary RNA splicing activity that is beneficial to its host, balanced against inefficient DNA cleavage. A selection experiment identified point mutations in the enzyme that act synergistically to improve endonuclease activity. The amino-acid substitutions increase target affinity, alter the thermal cleavage profile and significantly increase targeted recombination in transfected cells. The RNA splicing activity is not affected by these mutations. The improvement in DNA cleavage activity is largely focused on one of the enzyme's two active sites, corresponding to a rearrangement of a lysine residue hypothesized to act as a general base. Most of the constructs isolated in the screen contain one or more mutations that revert an amino-acid identity to a residue found in one or more close homologues of I-AniI. This implies that mutations that have previously reduced the endonuclease activity of I-AniI are identified and reversed, sometimes in combination with additional 'artificial' mutations, to optimize its in vivo activity.

Optimization of in vivo activity of a bifunctional homing endonuclease and maturase reverses evolutionary degradation.,Takeuchi R, Certo M, Caprara MG, Scharenberg AM, Stoddard BL Nucleic Acids Res. 2008 Dec 22. PMID:19103658^[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
↑ Takeuchi R, Certo M, Caprara MG, Scharenberg AM, Stoddard BL. Optimization of in vivo activity of a bifunctional homing endonuclease and maturase reverses evolutionary degradation. Nucleic Acids Res. 2008 Dec 22. PMID:19103658 doi:gkn1007

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3eh8"

@@ Line 1: / Line 1: @@
 ==Crystal structure of Y2 I-AniI variant (F13Y/S111Y)/DNA complex with calcium==
 <StructureSection load='3eh8' size='340' side='right' caption='[[3eh8]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3eh8]] is a 9 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=3EH8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3EH8 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3eh8]] is a 9 chain structure with sequence from [http://en.wikipedia.org/wiki/A._nidulans A. nidulans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EH8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3EH8 FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">AnCOB Intron Gene ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=162425 Emericella nidulans])</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">AnCOB Intron Gene ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=162425 A. 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=3eh8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3eh8 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3eh8 RCSB], [http://www.ebi.ac.uk/pdbsum/3eh8 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=3eh8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3eh8 OCA], [http://pdbe.org/3eh8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3eh8 RCSB], [http://www.ebi.ac.uk/pdbsum/3eh8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3eh8 ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 17: / Line 18: @@
     <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=3eh8 ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 27: / Line 28: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 3eh8" style="background-color:#fffaf0;"></div>
 ==See Also==
@@ Line 34: / Line 36: @@
 __TOC__
 </StructureSection>
-[[Category: Emericella nidulans]]
+[[Category: A. nidulans]]
 [[Category: Stoddard, B L]]
 [[Category: Takeuchi, R]]

3eh8

From Proteopedia

Revision as of 21:19, 4 August 2016

Crystal structure of Y2 I-AniI variant (F13Y/S111Y)/DNA complex with calcium

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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