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2ihn
From Proteopedia
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|PDB= 2ihn |SIZE=350|CAPTION= <scene name='initialview01'>2ihn</scene>, resolution 3.00Å | |PDB= 2ihn |SIZE=350|CAPTION= <scene name='initialview01'>2ihn</scene>, resolution 3.00Å | ||
|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/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] | + | |ACTIVITY= <span class='plainlinks'>[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] </span> |
| - | |GENE= rnh, 33.2, das ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id= | + | |GENE= rnh, 33.2, das ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10665 Enterobacteria phage T4]) |
| + | |DOMAIN= | ||
| + | |RELATEDENTRY=[[1tfr|1TFR]] | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ihn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ihn OCA], [http://www.ebi.ac.uk/pdbsum/2ihn PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2ihn RCSB]</span> | ||
}} | }} | ||
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==About this Structure== | ==About this Structure== | ||
| - | 2IHN is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/ | + | 2IHN is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_t4 Enterobacteria phage 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://www.ncbi.nlm.nih.gov/pubmed/17693399 17693399] | 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: | + | [[Category: Enterobacteria phage t4]] |
[[Category: Ribonuclease H]] | [[Category: Ribonuclease H]] | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
| Line 33: | Line 36: | ||
[[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 Mon Mar 31 03:44:29 2008'' |
Revision as of 00:44, 31 March 2008
| |||||||
| , resolution 3.00Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , , | ||||||
| Gene: | rnh, 33.2, das (Enterobacteria phage T4) | ||||||
| Activity: | Ribonuclease H, with EC number 3.1.26.4 | ||||||
| Related: | 1TFR
| ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| 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 Enterobacteria phage 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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