2fl3: Difference between revisions
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|PDB= 2fl3 |SIZE=350|CAPTION= <scene name='initialview01'>2fl3</scene>, resolution 2.39Å | |PDB= 2fl3 |SIZE=350|CAPTION= <scene name='initialview01'>2fl3</scene>, resolution 2.39Å | ||
|SITE= | |SITE= | ||
|LIGAND= | |LIGAND= <scene name='pdbligand=DA:2'-DEOXYADENOSINE-5'-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5'-MONOPHOSPHATE'>DT</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] | |ACTIVITY= <span class='plainlinks'>[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] </span> | ||
|GENE= hinP1IR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=727 Haemophilus influenzae]) | |GENE= hinP1IR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=727 Haemophilus influenzae]) | ||
|DOMAIN= | |||
|RELATEDENTRY=[[1ynm|1YNM]] | |||
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2fl3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fl3 OCA], [http://www.ebi.ac.uk/pdbsum/2fl3 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2fl3 RCSB]</span> | |||
}} | }} | ||
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[[Category: restriction endonuclease]] | [[Category: restriction endonuclease]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 03:04:12 2008'' | ||
Revision as of 03:04, 31 March 2008
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| , resolution 2.39Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , , | ||||||
| Gene: | hinP1IR (Haemophilus influenzae) | ||||||
| Activity: | Type II site-specific deoxyribonuclease, with EC number 3.1.21.4 | ||||||
| Related: | 1YNM
| ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Binary Complex of Restriction Endonuclease HinP1I with Cognate DNA
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
2FL3 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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