1ril: Difference between revisions

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[[Image:1ril.jpg|left|200px]]


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==CRYSTAL STRUCTURE OF RIBONUCLEASE H FROM THERMUS THERMOPHILUS HB8 REFINED AT 2.8 ANGSTROMS RESOLUTION==
The line below this paragraph, containing "STRUCTURE_1ril", creates the "Structure Box" on the page.
<StructureSection load='1ril' size='340' side='right'caption='[[1ril]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<table><tr><td colspan='2'>[[1ril]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RIL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RIL FirstGlance]. <br>
or leave the SCENE parameter empty for the default display.
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.8&#8491;</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1ril FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ril OCA], [https://pdbe.org/1ril PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ril RCSB], [https://www.ebi.ac.uk/pdbsum/1ril PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ril ProSAT]</span></td></tr>
{{STRUCTURE_1ril|  PDB=1ril |  SCENE= }}
</table>
== Function ==
[https://www.uniprot.org/uniprot/RNH_THET8 RNH_THET8] Endonuclease that specifically degrades the RNA of RNA-DNA hybrids.
== 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/ri/1ril_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=1ril ConSurf].
<div style="clear:both"></div>


'''CRYSTAL STRUCTURE OF RIBONUCLEASE H FROM THERMUS THERMOPHILUS HB8 REFINED AT 2.8 ANGSTROMS RESOLUTION'''
==See Also==
 
*[[Ribonuclease 3D structures|Ribonuclease 3D structures]]
 
__TOC__
==Overview==
</StructureSection>
The crystal structure of Thermus thermophilus RNase H was determined at 2.8 A resolution. The structure was solved by the molecular replacement method, based on the accurately refined structure of Escherichia coli RNase HI, which shows 52% amino acid sequence identity. Crystallographic refinement led to an R-factor of 0.205, with a 0.019 A root-mean-square deviation from ideal bond lengths and 0.048 A from ideal bond angle distances. Structural comparison shows a striking similarity in the overall folding of the thermophilic and mesophilic enzymes. The root-mean-square displacement is 0.95 A between equivalent alpha-carbon atoms from all elements of secondary structure (five alpha-helices and five beta-strands). However, some notable differences, which account for the enhanced thermostability of T. thermophilus RNase H, are observed in loop structures and side-chain conformations. The substitution of Gly for the left-handed helical residue (Lys95) in the E. coli enzyme is proposed to substantially enhance the thermostability, due to the release of steric hindrance caused by the beta-carbon atom. Furthermore, it is likely that the expansion of an aromatic cluster, arising from the replacement of Ile78 in the mesophilic enzyme by Phe, and the increased number of salt-bridges additively contribute to the stability.
[[Category: Large Structures]]
 
==About this Structure==
1RIL is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RIL OCA].
 
==Reference==
Crystal structure of ribonuclease H from Thermus thermophilus HB8 refined at 2.8 A resolution., Ishikawa K, Okumura M, Katayanagi K, Kimura S, Kanaya S, Nakamura H, Morikawa K, J Mol Biol. 1993 Mar 20;230(2):529-42. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/8385228 8385228]
[[Category: Ribonuclease H]]
[[Category: Single protein]]
[[Category: Thermus thermophilus]]
[[Category: Thermus thermophilus]]
[[Category: Ishikawa, K.]]
[[Category: Ishikawa K]]
[[Category: Kanaya, S.]]
[[Category: Kanaya S]]
[[Category: Katayanagi, K.]]
[[Category: Katayanagi K]]
[[Category: Kimura, S.]]
[[Category: Kimura S]]
[[Category: Morikawa, K.]]
[[Category: Morikawa K]]
[[Category: Nakamura, H.]]
[[Category: Nakamura H]]
[[Category: Okumura, M.]]
[[Category: Okumura M]]
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May  3 07:32:30 2008''

Latest revision as of 11:23, 14 February 2024

CRYSTAL STRUCTURE OF RIBONUCLEASE H FROM THERMUS THERMOPHILUS HB8 REFINED AT 2.8 ANGSTROMS RESOLUTIONCRYSTAL STRUCTURE OF RIBONUCLEASE H FROM THERMUS THERMOPHILUS HB8 REFINED AT 2.8 ANGSTROMS RESOLUTION

Structural highlights

1ril is a 1 chain structure with sequence from Thermus thermophilus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.8Å
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RNH_THET8 Endonuclease that specifically degrades the RNA of RNA-DNA hybrids.

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

1ril, resolution 2.80Å

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