2gig: Difference between revisions

From Proteopedia
Jump to navigation Jump to search
← Older edit
No edit summary
No edit summary
 
(12 intermediate revisions by the same user not shown)
Line 1: Line 1:
[[Image:2gig.gif|left|200px]]


{{Structure
==Alteration of sequence specificity of the type II restriction endonuclease HINCII through an indirect readout mechanism==
|PDB= 2gig |SIZE=350|CAPTION= <scene name='initialview01'>2gig</scene>, resolution 1.83&Aring;
<StructureSection load='2gig' size='340' side='right'caption='[[2gig]], [[Resolution|resolution]] 1.83&Aring;' scene=''>
|SITE=  
== Structural highlights ==
|LIGAND= <scene name='pdbligand=NA:SODIUM ION'>NA</scene>
<table><tr><td colspan='2'>[[2gig]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Haemophilus_influenzae Haemophilus influenzae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GIG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2GIG FirstGlance]. <br>
|ACTIVITY= [http://en.wikipedia.org/wiki/Type_II_site-specific_deoxyribonuclease Type II site-specific deoxyribonuclease], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.21.4 3.1.21.4]  
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.83&#8491;</td></tr>
|GENE= hincIIR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=727 Haemophilus influenzae])
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene></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=2gig FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gig OCA], [https://pdbe.org/2gig PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2gig RCSB], [https://www.ebi.ac.uk/pdbsum/2gig PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2gig ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/T2C2_HAEIF T2C2_HAEIF] Recognizes the double-stranded sequence GTYRAC and cleaves after Y-3.
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The functional and structural consequences of a mutation of the DNA intercalating residue of HincII, Q138F, are presented. Modeling has suggested that the DNA intercalation by Gln-138 results in DNA distortions potentially used by HincII in indirect readout of its cognate DNA, GTYRAC (Y = C or T, R = A or G) (Horton, N. C., Dorner, L. F., and Perona, J. J. (2002) Nat. Struct. Biol. 9, 42-47). Kinetic data presented here indicate that the mutation of glutamine 138 to phenylalanine (Q138F) results in a change in sequence specificity at the center two base pairs of the cognate recognition site. We show that the preference of HincII for cutting, but not binding, the three cognate sites differing in the center two base pairs has been altered by the mutation Q138F. Five new crystal structures are presented including Q138F HincII bound to GTTAAC and GTCGAC both with and without Ca2+ as well as the structure of wild type HincII bound to GTTAAC. The Q138F HincII/DNA structures show conformational changes in the protein, bound DNA, and at the protein-DNA interface, consistent with the formation of adaptive complexes. Analysis of these structures and the effect of Ca2+ binding on the protein-DNA interface illuminates the origin of the altered specificity by the mutation Q138F in the HincII enzyme.


'''Alteration of sequence specificity of the type II restriction endonuclease HINCII through an indirect readout mechanism'''
Alteration of sequence specificity of the type II restriction endonuclease HincII through an indirect readout mechanism.,Joshi HK, Etzkorn C, Chatwell L, Bitinaite J, Horton NC J Biol Chem. 2006 Aug 18;281(33):23852-69. Epub 2006 May 4. PMID:16675462<ref>PMID:16675462</ref>


From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 2gig" style="background-color:#fffaf0;"></div>


==Overview==
==See Also==
The functional and structural consequences of a mutation of the DNA intercalating residue of HincII, Q138F, are presented. Modeling has suggested that the DNA intercalation by Gln-138 results in DNA distortions potentially used by HincII in indirect readout of its cognate DNA, GTYRAC (Y = C or T, R = A or G) (Horton, N. C., Dorner, L. F., and Perona, J. J. (2002) Nat. Struct. Biol. 9, 42-47). Kinetic data presented here indicate that the mutation of glutamine 138 to phenylalanine (Q138F) results in a change in sequence specificity at the center two base pairs of the cognate recognition site. We show that the preference of HincII for cutting, but not binding, the three cognate sites differing in the center two base pairs has been altered by the mutation Q138F. Five new crystal structures are presented including Q138F HincII bound to GTTAAC and GTCGAC both with and without Ca2+ as well as the structure of wild type HincII bound to GTTAAC. The Q138F HincII/DNA structures show conformational changes in the protein, bound DNA, and at the protein-DNA interface, consistent with the formation of adaptive complexes. Analysis of these structures and the effect of Ca2+ binding on the protein-DNA interface illuminates the origin of the altered specificity by the mutation Q138F in the HincII enzyme.
*[[Endonuclease 3D structures|Endonuclease 3D structures]]
 
== References ==
==About this Structure==
<references/>
2GIG is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Haemophilus_influenzae Haemophilus influenzae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GIG OCA].
__TOC__
 
</StructureSection>
==Reference==
Alteration of sequence specificity of the type II restriction endonuclease HincII through an indirect readout mechanism., Joshi HK, Etzkorn C, Chatwell L, Bitinaite J, Horton NC, J Biol Chem. 2006 Aug 18;281(33):23852-69. Epub 2006 May 4. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16675462 16675462]
[[Category: Haemophilus influenzae]]
[[Category: Haemophilus influenzae]]
[[Category: Single protein]]
[[Category: Large Structures]]
[[Category: Type II site-specific deoxyribonuclease]]
[[Category: Bitinaite J]]
[[Category: Bitinaite, J.]]
[[Category: Chatwell L]]
[[Category: Chatwell, L.]]
[[Category: Etzkorn C]]
[[Category: Etzkorn, C.]]
[[Category: Horton NC]]
[[Category: Horton, N C.]]
[[Category: Joshi HK]]
[[Category: Joshi, H K.]]
[[Category: NA]]
[[Category: dna intercalation]]
[[Category: endonuclease]]
[[Category: indirect readout]]
[[Category: protein dna complex]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 17:05:03 2008''

Latest revision as of 16:05, 26 July 2023

Alteration of sequence specificity of the type II restriction endonuclease HINCII through an indirect readout mechanismAlteration of sequence specificity of the type II restriction endonuclease HINCII through an indirect readout mechanism

Structural highlights

2gig is a 4 chain structure with sequence from Haemophilus influenzae. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.83Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

T2C2_HAEIF Recognizes the double-stranded sequence GTYRAC and cleaves after Y-3.

Publication Abstract from PubMed

The functional and structural consequences of a mutation of the DNA intercalating residue of HincII, Q138F, are presented. Modeling has suggested that the DNA intercalation by Gln-138 results in DNA distortions potentially used by HincII in indirect readout of its cognate DNA, GTYRAC (Y = C or T, R = A or G) (Horton, N. C., Dorner, L. F., and Perona, J. J. (2002) Nat. Struct. Biol. 9, 42-47). Kinetic data presented here indicate that the mutation of glutamine 138 to phenylalanine (Q138F) results in a change in sequence specificity at the center two base pairs of the cognate recognition site. We show that the preference of HincII for cutting, but not binding, the three cognate sites differing in the center two base pairs has been altered by the mutation Q138F. Five new crystal structures are presented including Q138F HincII bound to GTTAAC and GTCGAC both with and without Ca2+ as well as the structure of wild type HincII bound to GTTAAC. The Q138F HincII/DNA structures show conformational changes in the protein, bound DNA, and at the protein-DNA interface, consistent with the formation of adaptive complexes. Analysis of these structures and the effect of Ca2+ binding on the protein-DNA interface illuminates the origin of the altered specificity by the mutation Q138F in the HincII enzyme.

Alteration of sequence specificity of the type II restriction endonuclease HincII through an indirect readout mechanism.,Joshi HK, Etzkorn C, Chatwell L, Bitinaite J, Horton NC J Biol Chem. 2006 Aug 18;281(33):23852-69. Epub 2006 May 4. PMID:16675462[1]

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

See Also

References

  1. ↑ Joshi HK, Etzkorn C, Chatwell L, Bitinaite J, Horton NC. Alteration of sequence specificity of the type II restriction endonuclease HincII through an indirect readout mechanism. J Biol Chem. 2006 Aug 18;281(33):23852-69. Epub 2006 May 4. PMID:16675462 doi:M512339200

2gig, resolution 1.83Å

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA
Retrieved from "https://proteopedia.openfox.io/wiki/index.php?title=2gig&oldid=3810947"