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| {{STRUCTURE_2ihn| PDB=2ihn | SCENE= }} | | {{STRUCTURE_2ihn| PDB=2ihn | SCENE= }} |
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| '''Co-crystal of Bacteriophage T4 RNase H with a fork DNA substrate'''
| | ===Co-crystal of Bacteriophage T4 RNase H with a fork DNA substrate=== |
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| ==Overview==
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| 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.
| | The line below this paragraph, {{ABSTRACT_PUBMED_17693399}}, adds the Publication Abstract to the page |
| | (as it appears on PubMed at http://www.pubmed.gov), where 17693399 is the PubMed ID number. |
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| | {{ABSTRACT_PUBMED_17693399}} |
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| ==About this Structure== | | ==About this Structure== |
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| [[Category: Hydrolase/dna complex]] | | [[Category: Hydrolase/dna complex]] |
| [[Category: Protein:dna complex]] | | [[Category: Protein:dna complex]] |
| ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May 4 07:30:58 2008'' | | |
| | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 11:30:32 2008'' |
