1p8k

From Proteopedia

(Difference between revisions)

Revision as of 09:18, 25 December 2014

The structure and DNA recognition of a bifunctional homing endonuclease and group I intron splicing factor

Structural highlights

1p8k is a 5 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:
Gene:	Aspergillus nidulans (Emericella nidulans)
Resources:	FirstGlance, OCA, RCSB, PDBsum

Function

[ANI1_EMENI] 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 determined the crystal structure of a bifunctional group I intron splicing factor and homing endonuclease, termed the I-AniI maturase, in complex with its DNA target at 2.6 A resolution. The structure demonstrates the remarkable structural conservation of the beta-sheet DNA-binding motif between highly divergent enzyme subfamilies. DNA recognition by I-AniI was further studied using nucleoside deletion and DMS modification interference analyses. Correlation of these results with the crystal structure provides information on the relative importance of individual nucleotide contacts for DNA recognition. Alignment and modeling of two homologous maturases reveals conserved basic surface residues, distant from the DNA-binding surface, that might be involved in RNA binding. A point mutation that introduces a single negative charge in this region uncouples the maturase and endonuclease functions of the protein, inhibiting RNA binding and splicing while maintaining DNA binding and cleavage.

Structural and biochemical analyses of DNA and RNA binding by a bifunctional homing endonuclease and group I intron splicing factor.,Bolduc JM, Spiegel PC, Chatterjee P, Brady KL, Downing ME, Caprara MG, Waring RB, Stoddard BL Genes Dev. 2003 Dec 1;17(23):2875-88. Epub 2003 Nov 21. PMID:14633971^[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
↑ Bolduc JM, Spiegel PC, Chatterjee P, Brady KL, Downing ME, Caprara MG, Waring RB, Stoddard BL. Structural and biochemical analyses of DNA and RNA binding by a bifunctional homing endonuclease and group I intron splicing factor. Genes Dev. 2003 Dec 1;17(23):2875-88. Epub 2003 Nov 21. PMID:14633971 doi:http://dx.doi.org/10.1101/gad.1109003

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/1p8k"

Categories: Emericella nidulans | Bolduc, J M | Stoddard, B L | Hydrolase-dna complex | Hydrolase/dna

@@ Line 3: / Line 3: @@
 == Structural highlights ==
 <table><tr><td colspan='2'>[[1p8k]] is a 5 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=1P8K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1P8K FirstGlance]. <br>
-</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene><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><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='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><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Aspergillus nidulans ([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">Aspergillus nidulans ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=162425 Emericella nidulans])</td></tr>
-<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1p8k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1p8k OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1p8k RCSB], [http://www.ebi.ac.uk/pdbsum/1p8k 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=1p8k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1p8k OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1p8k RCSB], [http://www.ebi.ac.uk/pdbsum/1p8k PDBsum]</span></td></tr>
-<table>
+</table>
+== Function ==
+[[http://www.uniprot.org/uniprot/ANI1_EMENI ANI1_EMENI]] 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.<ref>PMID:9256423</ref> <ref>PMID:10512698</ref> <ref>PMID:12758073</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 34: / Line 36: @@
 </StructureSection>
 [[Category: Emericella nidulans]]
-[[Category: Bolduc, J M.]]
+[[Category: Bolduc, J M]]
-[[Category: Stoddard, B L.]]
+[[Category: Stoddard, B L]]
 [[Category: Hydrolase-dna complex]]
 [[Category: Hydrolase/dna]]

1p8k

From Proteopedia

Revision as of 09:18, 25 December 2014

The structure and DNA recognition of a bifunctional homing endonuclease and group I intron splicing factor

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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