2ihn: Difference between revisions
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[[Image:2ihn.gif|left|200px]] | [[Image:2ihn.gif|left|200px]] | ||
'''Co-crystal of Bacteriophage T4 RNase H with a fork DNA substrate''' | {{Structure | ||
|PDB= 2ihn |SIZE=350|CAPTION= <scene name='initialview01'>2ihn</scene>, resolution 3.00Å | |||
|SITE= | |||
|LIGAND= | |||
|ACTIVITY= [http://en.wikipedia.org/wiki/Ribonuclease_H Ribonuclease H], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.26.4 3.1.26.4] | |||
|GENE= rnh, 33.2, das ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id= Bacteriophage T4]) | |||
}} | |||
'''Co-crystal of Bacteriophage T4 RNase H with a fork DNA substrate''' | |||
==Overview== | ==Overview== | ||
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==About this Structure== | ==About this Structure== | ||
2IHN is a [ | 2IHN is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Bacteriophage_t4 Bacteriophage t4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IHN OCA]. | ||
==Reference== | ==Reference== | ||
Crystal structure of bacteriophage T4 5' nuclease in complex with a branched DNA reveals how flap endonuclease-1 family nucleases bind their substrates., Devos JM, Tomanicek SJ, Jones CE, Nossal NG, Mueser TC, J Biol Chem. 2007 Oct 26;282(43):31713-24. Epub 2007 Aug 9. PMID:[http:// | Crystal structure of bacteriophage T4 5' nuclease in complex with a branched DNA reveals how flap endonuclease-1 family nucleases bind their substrates., Devos JM, Tomanicek SJ, Jones CE, Nossal NG, Mueser TC, J Biol Chem. 2007 Oct 26;282(43):31713-24. Epub 2007 Aug 9. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17693399 17693399] | ||
[[Category: Bacteriophage t4]] | [[Category: Bacteriophage t4]] | ||
[[Category: Ribonuclease H]] | [[Category: Ribonuclease H]] | ||
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[[Category: protein:dna complex]] | [[Category: protein:dna complex]] | ||
''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 17:29:42 2008'' | ||
Revision as of 15:29, 20 March 2008
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| 2ihn, resolution 3.00Å | |||||||||||||
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| Gene: | rnh, 33.2, das (Bacteriophage T4) | ||||||||||||
| Activity: | Ribonuclease H, with EC number 3.1.26.4 | ||||||||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||||||||
Co-crystal of Bacteriophage T4 RNase H with a fork DNA substrate
Overview
Bacteriophage T4 RNase H, a flap endonuclease-1 family nuclease, removes RNA primers from lagging strand fragments. It has both 5' nuclease and flap endonuclease activities. Our previous structure of native T4 RNase H (PDB code 1TFR) revealed an active site composed of highly conserved Asp residues and two bound hydrated magnesium ions. Here, we report the crystal structure of T4 RNase H in complex with a fork DNA substrate bound in its active site. This is the first structure of a flap endonuclease-1 family protein with its complete branched substrate. The fork duplex interacts with an extended loop of the helix-hairpin-helix motif class 2. The 5' arm crosses over the active site, extending below the bridge (helical arch) region. Cleavage assays of this DNA substrate identify a primary cut site 7-bases in from the 5' arm. The scissile phosphate, the first bond in the duplex DNA adjacent to the 5' arm, lies above a magnesium binding site. The less ordered 3' arm reaches toward the C and N termini of the enzyme, which are binding sites for T4 32 protein and T4 45 clamp, respectively. In the crystal structure, the scissile bond is located within the double-stranded DNA, between the first two duplex nucleotides next to the 5' arm, and lies above a magnesium binding site. This complex provides important insight into substrate recognition and specificity of the flap endonuclease-1 enzymes.
About this Structure
2IHN is a Single protein structure of sequence from Bacteriophage t4. Full crystallographic information is available from OCA.
Reference
Crystal structure of bacteriophage T4 5' nuclease in complex with a branched DNA reveals how flap endonuclease-1 family nucleases bind their substrates., Devos JM, Tomanicek SJ, Jones CE, Nossal NG, Mueser TC, J Biol Chem. 2007 Oct 26;282(43):31713-24. Epub 2007 Aug 9. PMID:17693399
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