2rn2 - Revision history

OCA at 09:23, 21 February 2024

2024-02-21T09:23:16Z

← Older revision		Revision as of 09:23, 21 February 2024
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	<StructureSection load='2rn2' size='340' side='right'caption='[[2rn2]], [[Resolution\|resolution]] 1.48Å' scene=''>		<StructureSection load='2rn2' size='340' side='right'caption='[[2rn2]], [[Resolution\|resolution]] 1.48Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2rn2]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"bacillus_coli"_migula_1895 "bacillus~~ coli~~" migula 1895~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RN2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2RN2 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2rn2]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RN2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2RN2 FirstGlance]. <br>
	</td></tr><tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat">~~<div style='overflow: auto; max~~-~~height: 3em;'>~~[[~~1rnh~~\|~~1rnh~~]]~~</div></td></tr>~~		</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 1.48Å</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Ribonuclease_H Ribonuclease H], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.~~26.4 3.1.26.4] </span>~~</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=2rn2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rn2 OCA], [https://pdbe.org/2rn2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2rn2 RCSB], [https://www.ebi.ac.uk/pdbsum/2rn2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2rn2 ProSAT]</span></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=2rn2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rn2 OCA], [https://pdbe.org/2rn2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2rn2 RCSB], [https://www.ebi.ac.uk/pdbsum/2rn2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2rn2 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[https://www.uniprot.org/uniprot/RNH_ECOLI RNH_ECOLI]] Endonuclease that specifically degrades the RNA of RNA-DNA hybrids. RNase H participates in DNA replication; it helps to specify the origin of genomic replication by suppressing initiation at origins other than the oriC locus; along with the 5'-3' exonuclease of pol1, it removes RNA primers from the Okazaki fragments of lagging strand synthesis; and it defines the origin of replication for ColE1-type plasmids by specific cleavage of an RNA preprimer.[HAMAP-Rule:MF_00042]		[https://www.uniprot.org/uniprot/RNH_ECOLI RNH_ECOLI] Endonuclease that specifically degrades the RNA of RNA-DNA hybrids. RNase H participates in DNA replication; it helps to specify the origin of genomic replication by suppressing initiation at origins other than the oriC locus; along with the 5'-3' exonuclease of pol1, it removes RNA primers from the Okazaki fragments of lagging strand synthesis; and it defines the origin of replication for ColE1-type plasmids by specific cleavage of an RNA preprimer.[HAMAP-Rule:MF_00042]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</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=2rn2 ConSurf].		</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=2rn2 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	~~<div style="background-color:#fffaf0;">~~
	~~== Publication Abstract from PubMed ==~~
	The crystal structure of RNase H from Escherichia coli has been determined by the multiple isomorphous replacement method, and refined by the stereochemically restrained least-squares procedure to a crystallographic R-factor of 0.196 at 1.48 A resolution. In the final structure, the root-mean-square (r.m.s.) deviation for bond lengths is 0.017 A, and for angle distances 0.036 A. The structure is composed of a five-stranded beta-sheet and five alpha-helices, and reveals the details of hydrogen bonding, electrostatic and hydrophobic interactions between intra- and intermolecular residues. The refined structure allows an explanation of the particular interactions between the basic protrusion, consisting of helix alpha III and the following loop, and the remaining major domain. The beta-sheet, alpha II, alpha III and alpha IV form a central hydrophobic cleft that contains all six tryptophan residues, and presumably serves to fix the orientation of the basic protrusion. Two parallel adjacent helices, alpha I and alpha IV, are associated with a few triads of hydrophobic interactions, including many leucine residues, that are similar to the repeated leucine motif. The well-defined electron density map allows detailed discussion of amino acid residues likely to be involved in binding a DNA/RNA hybrid, and construction of a putative model of the enzyme complexed with a DNA/RNA hybrid oligomer. In this model, a protein region, from the Mg(2+)-binding site to the basic protrusion, covers roughly two turns of a DNA/RNA hybrid double helix. A segment (11-23) containing six glycine residues forms a long loop between the beta A and beta B strands. This loop, which protrudes into the solvent region, lies on the interface between the enzyme and a DNA/RNA hybrid in the model of the complex. The mean temperature factors of main-chain atoms show remarkably high values in helix alpha III that constitutes the basic protrusion, suggesting some correlation between its flexibility and the nucleic acid binding function. The Mg(2+)-binding site, surrounded by four invariant acidic residues, can now be described more precisely in conjunction with the catalytic activity. The arrangement of molecules within the crystal appears to be dominated by the cancelling out of a remarkably biased charge distribution on the molecular surface, which is derived in particular from the separation between the acidic Mg(2+)-binding site and the basic protrusion.

	Structural details of ribonuclease H from Escherichia coli as refined to an atomic resolution.,Katayanagi K, Miyagawa M, Matsushima M, Ishikawa M, Kanaya S, Nakamura H, Ikehara M, Matsuzaki T, Morikawa K J Mol Biol. 1992 Feb 20;223(4):1029-52. PMID:1311386<ref>PMID:1311386</ref>

	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~
	~~</div>~~
	~~<div class="pdbe-citations 2rn2" style="background-color:#fffaf0;"></div>~~

	==See Also==		==See Also==
	*[[Ribonuclease 3D structures\|Ribonuclease 3D structures]]		*[[Ribonuclease 3D structures\|Ribonuclease 3D structures]]
	~~== References ==~~
	~~<references/>~~
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Bacillus~~ coli ~~migula 1895~~]]		[[Category: Escherichia coli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	~~[[Category: Ribonuclease H]]~~		[[Category: Ikehara M]]
	[[Category: Ikehara, M]]		[[Category: Ishikawa M]]
	[[Category: Ishikawa, M]]		[[Category: Kanaya S]]
	[[Category: Kanaya, S]]		[[Category: Katayanagi K]]
	[[Category: Katayanagi, K]]		[[Category: Matsushima M]]
	[[Category: Matsushima, M]]		[[Category: Matsuzaki T]]
	[[Category: Matsuzaki, T]]		[[Category: Miyagawa M]]
	[[Category: Miyagawa, M]]		[[Category: Morikawa K]]
	[[Category: Morikawa, K]]		[[Category: Nakamura H]]
	[[Category: Nakamura, H]]

OCA at 20:54, 20 October 2021

2021-10-20T20:54:24Z

← Older revision		Revision as of 20:54, 20 October 2021
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	<StructureSection load='2rn2' size='340' side='right'caption='[[2rn2]], [[Resolution\|resolution]] 1.48Å' scene=''>		<StructureSection load='2rn2' size='340' side='right'caption='[[2rn2]], [[Resolution\|resolution]] 1.48Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2rn2]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RN2 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2RN2 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2rn2]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RN2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2RN2 FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1rnh\|1rnh]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1rnh\|1rnh]]</div></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><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></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Ribonuclease_H Ribonuclease H], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.26.4 3.1.26.4] </span></td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2rn2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rn2 OCA], [~~http~~://pdbe.org/2rn2 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2rn2 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2rn2 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2rn2 ProSAT]</span></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=2rn2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rn2 OCA], [https://pdbe.org/2rn2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2rn2 RCSB], [https://www.ebi.ac.uk/pdbsum/2rn2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2rn2 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[~~http~~://www.uniprot.org/uniprot/RNH_ECOLI RNH_ECOLI]] Endonuclease that specifically degrades the RNA of RNA-DNA hybrids. RNase H participates in DNA replication; it helps to specify the origin of genomic replication by suppressing initiation at origins other than the oriC locus; along with the 5'-3' exonuclease of pol1, it removes RNA primers from the Okazaki fragments of lagging strand synthesis; and it defines the origin of replication for ColE1-type plasmids by specific cleavage of an RNA preprimer.[HAMAP-Rule:MF_00042]		[[https://www.uniprot.org/uniprot/RNH_ECOLI RNH_ECOLI]] Endonuclease that specifically degrades the RNA of RNA-DNA hybrids. RNase H participates in DNA replication; it helps to specify the origin of genomic replication by suppressing initiation at origins other than the oriC locus; along with the 5'-3' exonuclease of pol1, it removes RNA primers from the Okazaki fragments of lagging strand synthesis; and it defines the origin of replication for ColE1-type plasmids by specific cleavage of an RNA preprimer.[HAMAP-Rule:MF_00042]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	==See Also==		==See Also==
	*[[Ribonuclease 3D structures\|Ribonuclease 3D structures]]		*[[Ribonuclease 3D structures\|Ribonuclease 3D structures]]
	*[[Temp\|Temp]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 14:24, 18 December 2019

2019-12-18T14:24:34Z

← Older revision		Revision as of 14:24, 18 December 2019
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	==STRUCTURAL DETAILS OF RIBONUCLEASE H FROM ESCHERICHIA COLI AS REFINED TO AN ATOMIC RESOLUTION==		==STRUCTURAL DETAILS OF RIBONUCLEASE H FROM ESCHERICHIA COLI AS REFINED TO AN ATOMIC RESOLUTION==
	<StructureSection load='2rn2' size='340' side='right' caption='[[2rn2]], [[Resolution\|resolution]] 1.48Å' scene=''>		<StructureSection load='2rn2' size='340' side='right'caption='[[2rn2]], [[Resolution\|resolution]] 1.48Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2rn2]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RN2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2RN2 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2rn2]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RN2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2RN2 FirstGlance]. <br>
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	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/rn/2rn2_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/rn/2rn2_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
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	==See Also==		==See Also==
			*[[Ribonuclease 3D structures\|Ribonuclease 3D structures]]
	*[[Temp\|Temp]]		*[[Temp\|Temp]]
	== References ==		== References ==
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	</StructureSection>		</StructureSection>
	[[Category: Bacillus coli migula 1895]]		[[Category: Bacillus coli migula 1895]]
			[[Category: Large Structures]]
	[[Category: Ribonuclease H]]		[[Category: Ribonuclease H]]
	[[Category: Ikehara, M]]		[[Category: Ikehara, M]]

OCA at 07:11, 29 November 2017

2017-11-29T07:11:28Z

← Older revision		Revision as of 07:11, 29 November 2017
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	==STRUCTURAL DETAILS OF RIBONUCLEASE H FROM ESCHERICHIA COLI AS REFINED TO AN ATOMIC RESOLUTION==		==STRUCTURAL DETAILS OF RIBONUCLEASE H FROM ESCHERICHIA COLI AS REFINED TO AN ATOMIC RESOLUTION==
	<StructureSection load='2rn2' size='340' side='right' caption='[[2rn2]], [[Resolution\|resolution]] 1.48Å' scene=''>		<StructureSection load='2rn2' size='340' side='right' caption='[[2rn2]], [[Resolution\|resolution]] 1.48Å' scene=''>
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	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1rnh\|1rnh]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1rnh\|1rnh]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><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></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><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></td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2rn2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rn2 OCA], [http://pdbe.org/2rn2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2rn2 RCSB], [http://www.ebi.ac.uk/pdbsum/2rn2 PDBsum]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2rn2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rn2 OCA], [http://pdbe.org/2rn2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2rn2 RCSB], [http://www.ebi.ac.uk/pdbsum/2rn2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2rn2 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	==See Also==		==See Also==
	*[[Ribonuclease\|Ribonuclease]]
	*[[Temp\|Temp]]		*[[Temp\|Temp]]
	== References ==		== References ==

OCA at 22:34, 8 February 2016

2016-02-08T22:34:24Z

← Older revision		Revision as of 22:34, 8 February 2016
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	<StructureSection load='2rn2' size='340' side='right' caption='[[2rn2]], [[Resolution\|resolution]] 1.48Å' scene=''>		<StructureSection load='2rn2' size='340' side='right' caption='[[2rn2]], [[Resolution\|resolution]] 1.48Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2rn2]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Escherichia_coli Escherichia~~ coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RN2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2RN2 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2rn2]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RN2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2RN2 FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1rnh\|1rnh]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1rnh\|1rnh]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><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></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><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></td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2rn2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rn2 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2rn2 RCSB], [http://www.ebi.ac.uk/pdbsum/2rn2 PDBsum]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2rn2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rn2 OCA], [http://pdbe.org/2rn2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2rn2 RCSB], [http://www.ebi.ac.uk/pdbsum/2rn2 PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</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/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].		</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=2rn2 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
			<div class="pdbe-citations 2rn2" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Ribonuclease\|Ribonuclease]]		*[[Ribonuclease\|Ribonuclease]]
	*[[Temp\|Temp]]		*[[Temp\|Temp]]
	*[[User:Jaime.Prilusky/Test/tree\|User:Jaime.Prilusky/Test/tree]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Escherichia~~ coli]]		[[Category: Bacillus coli migula 1895]]
	[[Category: Ribonuclease H]]		[[Category: Ribonuclease H]]
	[[Category: Ikehara, M]]		[[Category: Ikehara, M]]

OCA at 02:35, 25 December 2014

2014-12-25T02:35:46Z

← Older revision		Revision as of 02:35, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2rn2]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RN2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2RN2 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2rn2]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RN2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2RN2 FirstGlance]. <br>
	</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1rnh\|1rnh]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1rnh\|1rnh]]</td></tr>
	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><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></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><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></td></tr>
	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2rn2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rn2 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2rn2 RCSB], [http://www.ebi.ac.uk/pdbsum/2rn2 PDBsum]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2rn2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rn2 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2rn2 RCSB], [http://www.ebi.ac.uk/pdbsum/2rn2 PDBsum]</span></td></tr>
	<table>		</table>
			== Function ==
			[[http://www.uniprot.org/uniprot/RNH_ECOLI RNH_ECOLI]] Endonuclease that specifically degrades the RNA of RNA-DNA hybrids. RNase H participates in DNA replication; it helps to specify the origin of genomic replication by suppressing initiation at origins other than the oriC locus; along with the 5'-3' exonuclease of pol1, it removes RNA primers from the Okazaki fragments of lagging strand synthesis; and it defines the origin of replication for ColE1-type plasmids by specific cleavage of an RNA preprimer.[HAMAP-Rule:MF_00042]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 28:		Line 30:
	==See Also==		==See Also==
	*[[Ribonuclease\|Ribonuclease]]		*[[Ribonuclease\|Ribonuclease]]
			*[[Temp\|Temp]]
			*[[User:Jaime.Prilusky/Test/tree\|User:Jaime.Prilusky/Test/tree]]
	== References ==		== References ==
	<references/>		<references/>
Line 34:		Line 38:
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Ribonuclease H]]		[[Category: Ribonuclease H]]
	[[Category: Ikehara, M.]]		[[Category: Ikehara, M]]
	[[Category: Ishikawa, M.]]		[[Category: Ishikawa, M]]
	[[Category: Kanaya, S.]]		[[Category: Kanaya, S]]
	[[Category: Katayanagi, K.]]		[[Category: Katayanagi, K]]
	[[Category: Matsushima, M.]]		[[Category: Matsushima, M]]
	[[Category: Matsuzaki, T.]]		[[Category: Matsuzaki, T]]
	[[Category: Miyagawa, M.]]		[[Category: Miyagawa, M]]
	[[Category: Morikawa, K.]]		[[Category: Morikawa, K]]
	[[Category: Nakamura, H.]]		[[Category: Nakamura, H]]

OCA at 10:28, 29 September 2014

2014-09-29T10:28:44Z

← Older revision		Revision as of 10:28, 29 September 2014
Line 1:		Line 1:
	[[Image:~~2rn2~~.~~png~~\|~~left~~\|~~200px~~]]		==STRUCTURAL DETAILS OF RIBONUCLEASE H FROM ESCHERICHIA COLI AS REFINED TO AN ATOMIC RESOLUTION==
			<StructureSection load='2rn2' size='340' side='right' caption='[[2rn2]], [[Resolution\|resolution]] 1.48Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[2rn2]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RN2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2RN2 FirstGlance]. <br>
			</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1rnh\|1rnh]]</td></tr>
			<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><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></td></tr>
			<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2rn2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rn2 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2rn2 RCSB], [http://www.ebi.ac.uk/pdbsum/2rn2 PDBsum]</span></td></tr>
			<table>
			== 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/rn/2rn2_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/chain_selection.php?pdb_ID=2ata ConSurf].
			<div style="clear:both"></div>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			The crystal structure of RNase H from Escherichia coli has been determined by the multiple isomorphous replacement method, and refined by the stereochemically restrained least-squares procedure to a crystallographic R-factor of 0.196 at 1.48 A resolution. In the final structure, the root-mean-square (r.m.s.) deviation for bond lengths is 0.017 A, and for angle distances 0.036 A. The structure is composed of a five-stranded beta-sheet and five alpha-helices, and reveals the details of hydrogen bonding, electrostatic and hydrophobic interactions between intra- and intermolecular residues. The refined structure allows an explanation of the particular interactions between the basic protrusion, consisting of helix alpha III and the following loop, and the remaining major domain. The beta-sheet, alpha II, alpha III and alpha IV form a central hydrophobic cleft that contains all six tryptophan residues, and presumably serves to fix the orientation of the basic protrusion. Two parallel adjacent helices, alpha I and alpha IV, are associated with a few triads of hydrophobic interactions, including many leucine residues, that are similar to the repeated leucine motif. The well-defined electron density map allows detailed discussion of amino acid residues likely to be involved in binding a DNA/RNA hybrid, and construction of a putative model of the enzyme complexed with a DNA/RNA hybrid oligomer. In this model, a protein region, from the Mg(2+)-binding site to the basic protrusion, covers roughly two turns of a DNA/RNA hybrid double helix. A segment (11-23) containing six glycine residues forms a long loop between the beta A and beta B strands. This loop, which protrudes into the solvent region, lies on the interface between the enzyme and a DNA/RNA hybrid in the model of the complex. The mean temperature factors of main-chain atoms show remarkably high values in helix alpha III that constitutes the basic protrusion, suggesting some correlation between its flexibility and the nucleic acid binding function. The Mg(2+)-binding site, surrounded by four invariant acidic residues, can now be described more precisely in conjunction with the catalytic activity. The arrangement of molecules within the crystal appears to be dominated by the cancelling out of a remarkably biased charge distribution on the molecular surface, which is derived in particular from the separation between the acidic Mg(2+)-binding site and the basic protrusion.

	~~{{STRUCTURE_2rn2\| PDB=2rn2 \| SCENE= }}~~		Structural details of ribonuclease H from Escherichia coli as refined to an atomic resolution.,Katayanagi K, Miyagawa M, Matsushima M, Ishikawa M, Kanaya S, Nakamura H, Ikehara M, Matsuzaki T, Morikawa K J Mol Biol. 1992 Feb 20;223(4):1029-52. PMID:1311386<ref>PMID:1311386</ref>

	~~===STRUCTURAL DETAILS OF RIBONUCLEASE H FROM ESCHERICHIA COLI AS REFINED TO AN ATOMIC RESOLUTION===~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
	~~{{ABSTRACT_PUBMED_1311386}}~~

	~~==About this Structure==~~
	~~[[2rn2]] is~~ a ~~1 chain structure with sequence from [http://en.wikipedia~~.~~org/wiki/Escherichia_coli Escherichia coli]~~. ~~Full crystallographic information is available from [http://oca~~.~~weizmann.ac.il/oca-bin~~/~~ocashort?id=2RN2 OCA].~~

	==See Also==		==See Also==
	*[[Ribonuclease\|Ribonuclease]]		*[[Ribonuclease\|Ribonuclease]]
			== References ==
	==~~Reference~~==		<references/>
	<~~ref group="xtra">PMID:001311386<~~/~~ref~~><~~ref group="xtra">PMID:014695246</ref><ref group="xtra">PMID:017277445</ref><references group="xtra"~~/>		__TOC__
			</StructureSection>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Ribonuclease H]]		[[Category: Ribonuclease H]]

OCA at 11:42, 20 October 2012

2012-10-20T11:42:14Z

← Older revision		Revision as of 11:42, 20 October 2012
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	==About this Structure==		==About this Structure==
	[[2rn2]] is a 1 chain structure ~~of [[Ribonuclease]]~~ with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RN2 OCA].		[[2rn2]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RN2 OCA].

	==See Also==		==See Also==
Line 14:		Line 14:

	==Reference==		==Reference==
	<ref group="xtra">PMID:001311386</ref><ref group="xtra">PMID:008955106</ref><ref group="xtra">PMID:011041241</ref><ref group="xtra">PMID:011106164</ref><ref group="xtra">PMID:011170211</ref><ref group="xtra">PMID:011734033</ref><ref group="xtra">PMID:011917145</ref><ref group="xtra">PMID:014695246</ref><ref group="xtra">PMID:017277445</ref><references group="xtra"/>		<ref group="xtra">PMID:001311386</ref><ref group="xtra">PMID:014695246</ref><ref group="xtra">PMID:017277445</ref><references group="xtra"/>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Ribonuclease H]]		[[Category: Ribonuclease H]]

OCA: Protected "2rn2" [edit=sysop:move=sysop]

2012-07-26T06:18:50Z

Protected "2rn2" [edit=sysop:move=sysop]

← Older revision	Revision as of 06:18, 26 July 2012
(No difference)

OCA at 06:18, 26 July 2012

2012-07-26T06:18:49Z

← Older revision		Revision as of 06:18, 26 July 2012
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	~~{{Seed}}~~
	[[Image:2rn2.png\|left\|200px]]		[[Image:2rn2.png\|left\|200px]]

	~~<!--~~
	~~The line below this paragraph, containing "STRUCTURE_2rn2", creates the "Structure Box" on the page.~~
	~~You may change the PDB parameter (which sets the PDB file loaded into the applet)~~
	~~or the SCENE parameter (which sets the initial scene displayed when the page is loaded),~~
	~~or leave the SCENE parameter empty for the default display.~~
	~~-->~~
	{{STRUCTURE_2rn2\| PDB=2rn2 \| SCENE= }}		{{STRUCTURE_2rn2\| PDB=2rn2 \| SCENE= }}

	===STRUCTURAL DETAILS OF RIBONUCLEASE H FROM ESCHERICHIA COLI AS REFINED TO AN ATOMIC RESOLUTION===		===STRUCTURAL DETAILS OF RIBONUCLEASE H FROM ESCHERICHIA COLI AS REFINED TO AN ATOMIC RESOLUTION===


	~~<!--~~
	~~The line below this paragraph, {{ABSTRACT_PUBMED_1311386}}, adds the Publication Abstract to the page~~
	~~(as it appears on PubMed at http://www.pubmed.gov), where 1311386 is the PubMed ID number.~~
	~~-->~~
	{{ABSTRACT_PUBMED_1311386}}		{{ABSTRACT_PUBMED_1311386}}

	==About this Structure==		==About this Structure==
	~~2RN2~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RN2 OCA].		[[2rn2]] is a 1 chain structure of [[Ribonuclease]] with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RN2 OCA].

			==See Also==
			*[[Ribonuclease\|Ribonuclease]]

	==Reference==		==Reference==
	<ref group="xtra">PMID:~~1311386~~</ref><references group="xtra"/>		<ref group="xtra">PMID:001311386</ref><ref group="xtra">PMID:008955106</ref><ref group="xtra">PMID:011041241</ref><ref group="xtra">PMID:011106164</ref><ref group="xtra">PMID:011170211</ref><ref group="xtra">PMID:011734033</ref><ref group="xtra">PMID:011917145</ref><ref group="xtra">PMID:014695246</ref><ref group="xtra">PMID:017277445</ref><references group="xtra"/>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Ribonuclease H]]		[[Category: Ribonuclease H]]
Line 35:		Line 26:
	[[Category: Morikawa, K.]]		[[Category: Morikawa, K.]]
	[[Category: Nakamura, H.]]		[[Category: Nakamura, H.]]

	~~''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 04:03:40 2009''~~