1rnj: Difference between revisions

From Proteopedia
Jump to navigationJump to search
← Older edit
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,330,058 edits
No edit summary
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,330,058 edits
No edit summary
 
(11 intermediate revisions by the same user not shown)
Line 1: Line 1:
{{Seed}}
[[Image:1rnj.png|left|200px]]


<!--
==Crystal structure of inactive mutant dUTPase complexed with substrate analogue imido-dUTP==
The line below this paragraph, containing "STRUCTURE_1rnj", creates the "Structure Box" on the page.
<StructureSection load='1rnj' size='340' side='right'caption='[[1rnj]], [[Resolution|resolution]] 1.70&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'>[[1rnj]] 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=1RNJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RNJ 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]] 1.7&#8491;</td></tr>
-->
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DUP:2-DEOXYURIDINE+5-ALPHA,BETA-IMIDO-TRIPHOSPHATE'>DUP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>
{{STRUCTURE_1rnj|  PDB=1rnj  |  SCENE=  }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1rnj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rnj OCA], [https://pdbe.org/1rnj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1rnj RCSB], [https://www.ebi.ac.uk/pdbsum/1rnj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1rnj ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/DUT_ECOLI DUT_ECOLI] This enzyme is involved in nucleotide metabolism: it produces dUMP, the immediate precursor of thymidine nucleotides and it decreases the intracellular concentration of dUTP so that uracil cannot be incorporated into DNA.[HAMAP-Rule:MF_00116]
== 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/1rnj_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=1rnj ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
dUTPase is essential to keep uracil out of DNA. Crystal structures of substrate (dUTP and alpha,beta-imino-dUTP) and product complexes of wild type and mutant dUTPases were determined to reveal how an enzyme responsible for DNA integrity functions. A kinetic analysis of wild type and mutant dUTPases was performed to obtain relevant mechanistic information in solution. Substrate hydrolysis is shown to be initiated via in-line nucleophile attack of a water molecule oriented by an activating conserved aspartate residue. Substrate binding in a catalytically competent conformation is achieved by (i) multiple interactions of the triphosphate moiety with catalysis-assisting Mg2+, (ii) a concerted motion of residues from three conserved enzyme motifs as compared with the apoenzyme, and (iii) an intricate hydrogen-bonding network that includes several water molecules in the active site. Results provide an understanding for the catalytic role of conserved residues in dUTPases.


===Crystal structure of inactive mutant dUTPase complexed with substrate analogue imido-dUTP===
Structural insights into the catalytic mechanism of phosphate ester hydrolysis by dUTPase.,Barabas O, Pongracz V, Kovari J, Wilmanns M, Vertessy BG J Biol Chem. 2004 Oct 8;279(41):42907-15. Epub 2004 Jun 17. PMID:15208312<ref>PMID:15208312</ref>


From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1rnj" style="background-color:#fffaf0;"></div>


<!--
==See Also==
The line below this paragraph, {{ABSTRACT_PUBMED_15208312}}, adds the Publication Abstract to the page
*[[DUTPase 3D structures|DUTPase 3D structures]]
(as it appears on PubMed at http://www.pubmed.gov), where 15208312 is the PubMed ID number.
== References ==
-->
<references/>
{{ABSTRACT_PUBMED_15208312}}
__TOC__
 
</StructureSection>
==About this Structure==
1RNJ is a [[Single protein]] 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=1RNJ OCA].
 
==Reference==
Structural insights into the catalytic mechanism of phosphate ester hydrolysis by dUTPase., Barabas O, Pongracz V, Kovari J, Wilmanns M, Vertessy BG, J Biol Chem. 2004 Oct 8;279(41):42907-15. Epub 2004 Jun 17. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15208312 15208312]
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
[[Category: Single protein]]
[[Category: Large Structures]]
[[Category: DUTP diphosphatase]]
[[Category: Barabas O]]
[[Category: Barabas, O.]]
[[Category: Kovari J]]
[[Category: Kovari, J.]]
[[Category: Pongracz V]]
[[Category: Pongracz, V.]]
[[Category: Vertessy BG]]
[[Category: Vertessy, B G.]]
[[Category: Wilmanns M]]
[[Category: Wilmanns, M.]]
[[Category: Enzyme-ligand complex]]
[[Category: Jelly roll]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 14:39:48 2008''
Retrieved from "https://proteopedia.org/1rnj"