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New page: left|200px<br /><applet load="2fkh" size="350" color="white" frame="true" align="right" spinBox="true" caption="2fkh, resolution 3.09Å" /> '''Crystal Form II of P...
 
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[[Image:2fkh.gif|left|200px]]<br /><applet load="2fkh" size="350" color="white" frame="true" align="right" spinBox="true"
caption="2fkh, resolution 3.09&Aring;" />
'''Crystal Form II of Pre-Reactive Complex of Restriction Endonuclease HinP1I with Cognate DNA and Calcium Ions'''<br />


==Overview==
==Crystal Form II of Pre-Reactive Complex of Restriction Endonuclease HinP1I with Cognate DNA and Calcium Ions==
HinP1I recognizes and cleaves the palindromic tetranucleotide sequence G, downward arrowCGC in DNA. We report three structures of HinP1I-DNA, complexes: in the presence of Ca(2+) (pre-reactive complex), in the, absence of metal ion (binary complex) and in the presence of Mg(2+), (post-reactive complex). HinP1I forms a back-to-back dimer with two active, sites and two DNA duplexes bound on the outer surfaces of the dimer facing, away from each other. The 10 bp DNA duplexes undergo protein-induced, distortions exhibiting features of A-, B- and Z-conformations: bending on, one side (by intercalation of a phenylalanine side chain into the major, groove), base flipping on the other side of the recognition site (by, expanding the step rise distance of the local base pair to Z-form) and a, local A-form conformation between the two central C:G base pairs of the, recognition site (by binding of the N-terminal helix in the minor groove)., In the pre- and post-reactive complexes, two metals (Ca(2+) or Mg(2+)) are, found in the active site. The enzyme appears to cleave DNA sequentially, hydrolyzing first one DNA strand, as seen in the post-reactive complex in, the crystalline state, and then the other, as supported by the observation, that, in solution, a nicked DNA intermediate accumulates before, linearization.
<StructureSection load='2fkh' size='340' side='right'caption='[[2fkh]], [[Resolution|resolution]] 3.09&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[2fkh]] is a 3 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=2FKH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2FKH FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.09&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</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=2fkh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fkh OCA], [https://pdbe.org/2fkh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2fkh RCSB], [https://www.ebi.ac.uk/pdbsum/2fkh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2fkh ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/Q5I6E6_HAEIF Q5I6E6_HAEIF]
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
HinP1I recognizes and cleaves the palindromic tetranucleotide sequence G downward arrowCGC in DNA. We report three structures of HinP1I-DNA complexes: in the presence of Ca(2+) (pre-reactive complex), in the absence of metal ion (binary complex) and in the presence of Mg(2+) (post-reactive complex). HinP1I forms a back-to-back dimer with two active sites and two DNA duplexes bound on the outer surfaces of the dimer facing away from each other. The 10 bp DNA duplexes undergo protein-induced distortions exhibiting features of A-, B- and Z-conformations: bending on one side (by intercalation of a phenylalanine side chain into the major groove), base flipping on the other side of the recognition site (by expanding the step rise distance of the local base pair to Z-form) and a local A-form conformation between the two central C:G base pairs of the recognition site (by binding of the N-terminal helix in the minor groove). In the pre- and post-reactive complexes, two metals (Ca(2+) or Mg(2+)) are found in the active site. The enzyme appears to cleave DNA sequentially, hydrolyzing first one DNA strand, as seen in the post-reactive complex in the crystalline state, and then the other, as supported by the observation that, in solution, a nicked DNA intermediate accumulates before linearization.


==About this Structure==
DNA nicking by HinP1I endonuclease: bending, base flipping and minor groove expansion.,Horton JR, Zhang X, Maunus R, Yang Z, Wilson GG, Roberts RJ, Cheng X Nucleic Acids Res. 2006 Feb 9;34(3):939-48. Print 2006. PMID:16473850<ref>PMID:16473850</ref>
2FKH is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Haemophilus_influenzae Haemophilus influenzae] with <scene name='pdbligand=CA:'>CA</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [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] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FKH OCA].


==Reference==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
DNA nicking by HinP1I endonuclease: bending, base flipping and minor groove expansion., Horton JR, Zhang X, Maunus R, Yang Z, Wilson GG, Roberts RJ, Cheng X, Nucleic Acids Res. 2006 Feb 9;34(3):939-48. Print 2006. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16473850 16473850]
</div>
<div class="pdbe-citations 2fkh" style="background-color:#fffaf0;"></div>
 
==See Also==
*[[Endonuclease 3D structures|Endonuclease 3D structures]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Haemophilus influenzae]]
[[Category: Haemophilus influenzae]]
[[Category: Single protein]]
[[Category: Large Structures]]
[[Category: Type II site-specific deoxyribonuclease]]
[[Category: Horton JR]]
[[Category: Horton, J.R.]]
[[Category: CA]]
[[Category: dna superhelix]]
[[Category: protein dimerizaton]]
[[Category: protein-dna-metal ion complex]]
[[Category: restriction endonuclease]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jan 29 19:38:43 2008''

Latest revision as of 12:28, 30 August 2023

Crystal Form II of Pre-Reactive Complex of Restriction Endonuclease HinP1I with Cognate DNA and Calcium IonsCrystal Form II of Pre-Reactive Complex of Restriction Endonuclease HinP1I with Cognate DNA and Calcium Ions

Structural highlights

2fkh is a 3 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 3.09Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

Q5I6E6_HAEIF

Publication Abstract from PubMed

HinP1I recognizes and cleaves the palindromic tetranucleotide sequence G downward arrowCGC in DNA. We report three structures of HinP1I-DNA complexes: in the presence of Ca(2+) (pre-reactive complex), in the absence of metal ion (binary complex) and in the presence of Mg(2+) (post-reactive complex). HinP1I forms a back-to-back dimer with two active sites and two DNA duplexes bound on the outer surfaces of the dimer facing away from each other. The 10 bp DNA duplexes undergo protein-induced distortions exhibiting features of A-, B- and Z-conformations: bending on one side (by intercalation of a phenylalanine side chain into the major groove), base flipping on the other side of the recognition site (by expanding the step rise distance of the local base pair to Z-form) and a local A-form conformation between the two central C:G base pairs of the recognition site (by binding of the N-terminal helix in the minor groove). In the pre- and post-reactive complexes, two metals (Ca(2+) or Mg(2+)) are found in the active site. The enzyme appears to cleave DNA sequentially, hydrolyzing first one DNA strand, as seen in the post-reactive complex in the crystalline state, and then the other, as supported by the observation that, in solution, a nicked DNA intermediate accumulates before linearization.

DNA nicking by HinP1I endonuclease: bending, base flipping and minor groove expansion.,Horton JR, Zhang X, Maunus R, Yang Z, Wilson GG, Roberts RJ, Cheng X Nucleic Acids Res. 2006 Feb 9;34(3):939-48. Print 2006. PMID:16473850[1]

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

See Also

References

  1. ↑ Horton JR, Zhang X, Maunus R, Yang Z, Wilson GG, Roberts RJ, Cheng X. DNA nicking by HinP1I endonuclease: bending, base flipping and minor groove expansion. Nucleic Acids Res. 2006 Feb 9;34(3):939-48. Print 2006. PMID:16473850 doi:34/3/939

2fkh, resolution 3.09Å

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