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[[Image:2ihn.gif|left|200px]]
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{{STRUCTURE_2ihn|  PDB=2ihn  |  SCENE=  }}
'''Co-crystal of Bacteriophage T4 RNase H with a fork DNA substrate'''


==Co-crystal of Bacteriophage T4 RNase H with a fork DNA substrate==
<StructureSection load='2ihn' size='340' side='right'caption='[[2ihn]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[2ihn]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_virus_T4 Escherichia virus T4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IHN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2IHN FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3&#8491;</td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2ihn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ihn OCA], [https://pdbe.org/2ihn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ihn RCSB], [https://www.ebi.ac.uk/pdbsum/2ihn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ihn ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/RNH_BPT4 RNH_BPT4] 5' to 3' exonuclease that removes the pentamer RNA primers from DNA chains initiated by the T4 primase-helicase.
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ih/2ihn_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2ihn ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
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.


==Overview==
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<ref>PMID:17693399</ref>
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==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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].
</div>
<div class="pdbe-citations 2ihn" style="background-color:#fffaf0;"></div>


==Reference==
==See Also==
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]
*[[Ribonuclease 3D structures|Ribonuclease 3D structures]]
[[Category: Enterobacteria phage t4]]
== References ==
[[Category: Ribonuclease H]]
<references/>
[[Category: Single protein]]
__TOC__
[[Category: Devos, J M.]]
</StructureSection>
[[Category: Mueser, T C.]]
[[Category: Escherichia virus T4]]
[[Category: 5'-3' exonuclease]]
[[Category: Large Structures]]
[[Category: Bpt4 rnase h]]
[[Category: Devos JM]]
[[Category: Fork dna]]
[[Category: Mueser TC]]
[[Category: Hydrolase/dna complex]]
[[Category: Protein:dna complex]]
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May  4 07:30:58 2008''
Retrieved from "https://proteopedia.org/2ihn"