2fkh: Difference between revisions
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[[Image:2fkh.gif|left|200px]] | [[Image:2fkh.gif|left|200px]] | ||
'''Crystal Form II of Pre-Reactive Complex of Restriction Endonuclease HinP1I with Cognate DNA and Calcium Ions''' | {{Structure | ||
|PDB= 2fkh |SIZE=350|CAPTION= <scene name='initialview01'>2fkh</scene>, resolution 3.09Å | |||
|SITE= | |||
|LIGAND= <scene name='pdbligand=CA:CALCIUM ION'>CA</scene> | |||
|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] | |||
|GENE= hinP1IR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=727 Haemophilus influenzae]) | |||
}} | |||
'''Crystal Form II of Pre-Reactive Complex of Restriction Endonuclease HinP1I with Cognate DNA and Calcium Ions''' | |||
==Overview== | ==Overview== | ||
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==About this Structure== | ==About this Structure== | ||
2FKH is a [ | 2FKH 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=2FKH OCA]. | ||
==Reference== | ==Reference== | ||
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:// | 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://www.ncbi.nlm.nih.gov/pubmed/16473850 16473850] | ||
[[Category: Haemophilus influenzae]] | [[Category: Haemophilus influenzae]] | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
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[[Category: restriction endonuclease]] | [[Category: restriction endonuclease]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 16:53:29 2008'' | ||
Revision as of 17:53, 20 March 2008
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| , resolution 3.09Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | |||||||
| Gene: | hinP1IR (Haemophilus influenzae) | ||||||
| Activity: | Type II site-specific deoxyribonuclease, with EC number 3.1.21.4 | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Crystal Form II of Pre-Reactive Complex of Restriction Endonuclease HinP1I with Cognate DNA and Calcium Ions
OverviewOverview
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 StructureAbout this Structure
2FKH is a Single protein structure of sequence from Haemophilus influenzae. Full crystallographic information is available from OCA.
ReferenceReference
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
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