2ihn
From Proteopedia
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==Overview== | ==Overview== | ||
| - | Bacteriophage T4 RNase H, a flap endonuclease-1 family nuclease, removes | + | 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== | ==About this Structure== | ||
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==Reference== | ==Reference== | ||
| - | Crystal structure of bacteriophage T4 5' nuclease in complex with a branched DNA reveals how | + | 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://ispc.weizmann.ac.il//pmbin/getpm?pmid=17693399 17693399] |
[[Category: Bacteriophage t4]] | [[Category: Bacteriophage t4]] | ||
[[Category: Ribonuclease H]] | [[Category: Ribonuclease H]] | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
| - | [[Category: Devos, J | + | [[Category: Devos, J M.]] |
| - | [[Category: Mueser, T | + | [[Category: Mueser, T C.]] |
[[Category: 5'-3' exonuclease]] | [[Category: 5'-3' exonuclease]] | ||
[[Category: bpt4 rnase h]] | [[Category: bpt4 rnase h]] | ||
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[[Category: protein:dna complex]] | [[Category: protein:dna complex]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 17:52:47 2008'' |
Revision as of 15:52, 21 February 2008
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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. Active as Ribonuclease H, with EC number 3.1.26.4 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
Page seeded by OCA on Thu Feb 21 17:52:47 2008
