1xjf: Difference between revisions

From Proteopedia
Jump to navigationJump to search
← Older edit
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,331,613 edits
No edit summary
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,331,613 edits
No edit summary
 
(12 intermediate revisions by the same user not shown)
Line 1: Line 1:
[[Image:1xjf.gif|left|200px]]
<!--
The line below this paragraph, containing "STRUCTURE_1xjf", 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_1xjf|  PDB=1xjf  |  SCENE=  }}
'''Structural mechanism of allosteric substrate specificity in a ribonucleotide reductase: dATP complex'''


==Structural mechanism of allosteric substrate specificity in a ribonucleotide reductase: dATP complex==
<StructureSection load='1xjf' size='340' side='right'caption='[[1xjf]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1xjf]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XJF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1XJF 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]] 2.4&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DTP:2-DEOXYADENOSINE+5-TRIPHOSPHATE'>DTP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></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=1xjf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xjf OCA], [https://pdbe.org/1xjf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1xjf RCSB], [https://www.ebi.ac.uk/pdbsum/1xjf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1xjf ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/O33839_THEMT O33839_THEMT]
== 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/xj/1xjf_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=1xjf ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Ribonucleotide reductases (RNRs) catalyze the reduction of ribonucleotides into deoxyribonucleotides, which constitute the precursor pools used for DNA synthesis and repair. Imbalances in these pools increase mutational rates and are detrimental to the cell. Balanced precursor pools are maintained primarily through the regulation of the RNR substrate specificity. Here, the molecular mechanism of the allosteric substrate specificity regulation is revealed through the structures of a dimeric coenzyme B12-dependent RNR from Thermotoga maritima, both in complexes with four effector-substrate nucleotide pairs and in three complexes with only effector. The mechanism is based on the flexibility of loop 2, a key structural element, which forms a bridge between the specificity effector and substrate nucleotides. Substrate specificity is achieved as different effectors and their cognate substrates stabilize specific discrete loop 2 conformations. The mechanism of substrate specificity regulation is probably general for most class I and class II RNRs.


==Overview==
Structural mechanism of allosteric substrate specificity regulation in a ribonucleotide reductase.,Larsson KM, Jordan A, Eliasson R, Reichard P, Logan DT, Nordlund P Nat Struct Mol Biol. 2004 Nov;11(11):1142-9. Epub 2004 Oct 10. PMID:15475969<ref>PMID:15475969</ref>
Ribonucleotide reductases (RNRs) catalyze the reduction of ribonucleotides into deoxyribonucleotides, which constitute the precursor pools used for DNA synthesis and repair. Imbalances in these pools increase mutational rates and are detrimental to the cell. Balanced precursor pools are maintained primarily through the regulation of the RNR substrate specificity. Here, the molecular mechanism of the allosteric substrate specificity regulation is revealed through the structures of a dimeric coenzyme B12-dependent RNR from Thermotoga maritima, both in complexes with four effector-substrate nucleotide pairs and in three complexes with only effector. The mechanism is based on the flexibility of loop 2, a key structural element, which forms a bridge between the specificity effector and substrate nucleotides. Substrate specificity is achieved as different effectors and their cognate substrates stabilize specific discrete loop 2 conformations. The mechanism of substrate specificity regulation is probably general for most class I and class II RNRs.


==About this Structure==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
1XJF is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XJF OCA].
</div>
<div class="pdbe-citations 1xjf" style="background-color:#fffaf0;"></div>


==Reference==
==See Also==
Structural mechanism of allosteric substrate specificity regulation in a ribonucleotide reductase., Larsson KM, Jordan A, Eliasson R, Reichard P, Logan DT, Nordlund P, Nat Struct Mol Biol. 2004 Nov;11(11):1142-9. Epub 2004 Oct 10. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15475969 15475969]
*[[Ribonucleotide reductase 3D structures|Ribonucleotide reductase 3D structures]]
[[Category: Ribonucleoside-diphosphate reductase]]
== References ==
[[Category: Single protein]]
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Thermotoga maritima]]
[[Category: Thermotoga maritima]]
[[Category: Eliasson, R.]]
[[Category: Eliasson R]]
[[Category: Jordan, A.]]
[[Category: Jordan A]]
[[Category: Larsson, K M.]]
[[Category: Larsson K-M]]
[[Category: Logan, D T.]]
[[Category: Logan DT]]
[[Category: Nordlund, P.]]
[[Category: Nordlund P]]
[[Category: Reichard, P.]]
[[Category: Reichard P]]
[[Category: 10 alpha-beta barrel]]
[[Category: Allosteric regulation]]
[[Category: Protein-nucleotide complex]]
[[Category: Ribonucleotide reductase]]
[[Category: Substrate specificity]]
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May  3 15:06:27 2008''
Retrieved from "https://proteopedia.org/1xjf"