1ipa: Difference between revisions

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[[Image:1ipa.png|left|200px]]
==CRYSTAL STRUCTURE OF RNA 2'-O RIBOSE METHYLTRANSFERASE==
<StructureSection load='1ipa' size='340' side='right' caption='[[1ipa]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1ipa]] is a 1 chain structure with 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=1IPA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1IPA FirstGlance]. <br>
</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=1ipa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ipa OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ipa RCSB], [http://www.ebi.ac.uk/pdbsum/1ipa PDBsum], [http://www.topsan.org/Proteins/RSGI/1ipa TOPSAN]</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/ip/1ipa_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 ==
Knots in polypeptide chains have been found in very few proteins. Only two proteins are considered to have a shallow 'trefoil' knot, which tucks a few residues at one end of the chain through a loop exposed on the protein surface. Recently, another protein was found by a mathematical algorithm to have a deep 'figure-of-eight' knot which had not been visually identified. In the present study, the crystal structure of a hypothetical RNA 2'-O-ribose methyltransferase from Thermus thermophilus (RrmA) was determined at 2.4 A resolution and a deep trefoil knot was found for the first time. The present knot is formed by the threading of a 44-residue polypeptide chain through a 41-residue loop and is better defined than the previously reported knots. Two of the three catalytic residues conserved in the 2'-O-ribose methyltransferase family are located in the knotting loop and in the knotted carboxy-terminal chain, which is the first observation that the enzyme active site is constructed right on the knot. On the other hand, the amino-terminal domain exhibits a geometrical similarity to the ribosomal proteins which recognize an internal loop of RNA.


{{STRUCTURE_1ipa|  PDB=1ipa  |  SCENE=  }}
An enzyme with a deep trefoil knot for the active-site architecture.,Nureki O, Shirouzu M, Hashimoto K, Ishitani R, Terada T, Tamakoshi M, Oshima T, Chijimatsu M, Takio K, Vassylyev DG, Shibata T, Inoue Y, Kuramitsu S, Yokoyama S Acta Crystallogr D Biol Crystallogr. 2002 Jul;58(Pt 7):1129-37. Epub 2002, Jun 20. PMID:12077432<ref>PMID:12077432</ref>


===CRYSTAL STRUCTURE OF RNA 2'-O RIBOSE METHYLTRANSFERASE===
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 
</div>
{{ABSTRACT_PUBMED_12077432}}
== References ==
 
<references/>
==About this Structure==
__TOC__
[[1ipa]] is a 1 chain structure with 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=1IPA OCA].
</StructureSection>
 
==Reference==
<ref group="xtra">PMID:012077432</ref><ref group="xtra">PMID:012486711</ref><references group="xtra"/>
[[Category: Thermus thermophilus]]
[[Category: Thermus thermophilus]]
[[Category: Chijimatsu, M.]]
[[Category: Chijimatsu, M.]]

Revision as of 14:45, 28 September 2014

CRYSTAL STRUCTURE OF RNA 2'-O RIBOSE METHYLTRANSFERASECRYSTAL STRUCTURE OF RNA 2'-O RIBOSE METHYLTRANSFERASE

Structural highlights

1ipa 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.
Resources:FirstGlance, OCA, RCSB, PDBsum, TOPSAN

Evolutionary Conservation

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

Publication Abstract from PubMed

Knots in polypeptide chains have been found in very few proteins. Only two proteins are considered to have a shallow 'trefoil' knot, which tucks a few residues at one end of the chain through a loop exposed on the protein surface. Recently, another protein was found by a mathematical algorithm to have a deep 'figure-of-eight' knot which had not been visually identified. In the present study, the crystal structure of a hypothetical RNA 2'-O-ribose methyltransferase from Thermus thermophilus (RrmA) was determined at 2.4 A resolution and a deep trefoil knot was found for the first time. The present knot is formed by the threading of a 44-residue polypeptide chain through a 41-residue loop and is better defined than the previously reported knots. Two of the three catalytic residues conserved in the 2'-O-ribose methyltransferase family are located in the knotting loop and in the knotted carboxy-terminal chain, which is the first observation that the enzyme active site is constructed right on the knot. On the other hand, the amino-terminal domain exhibits a geometrical similarity to the ribosomal proteins which recognize an internal loop of RNA.

An enzyme with a deep trefoil knot for the active-site architecture.,Nureki O, Shirouzu M, Hashimoto K, Ishitani R, Terada T, Tamakoshi M, Oshima T, Chijimatsu M, Takio K, Vassylyev DG, Shibata T, Inoue Y, Kuramitsu S, Yokoyama S Acta Crystallogr D Biol Crystallogr. 2002 Jul;58(Pt 7):1129-37. Epub 2002, Jun 20. PMID:12077432[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

  1. ↑ Nureki O, Shirouzu M, Hashimoto K, Ishitani R, Terada T, Tamakoshi M, Oshima T, Chijimatsu M, Takio K, Vassylyev DG, Shibata T, Inoue Y, Kuramitsu S, Yokoyama S. An enzyme with a deep trefoil knot for the active-site architecture. Acta Crystallogr D Biol Crystallogr. 2002 Jul;58(Pt 7):1129-37. Epub 2002, Jun 20. PMID:12077432

1ipa, resolution 2.40Å

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