2qlp: Difference between revisions

From Proteopedia
Jump to navigation Jump to search
← Older edit
No edit summary
No edit summary
 
(12 intermediate revisions by the same user not shown)
Line 1: Line 1:
[[Image:2qlp.jpg|left|200px]]


{{Structure
==Bifunctional dCTP deaminase:dUTPase from Mycobacterium tuberculosis, apo form==
|PDB= 2qlp |SIZE=350|CAPTION= <scene name='initialview01'>2qlp</scene>, resolution 2.47&Aring;
<StructureSection load='2qlp' size='340' side='right'caption='[[2qlp]], [[Resolution|resolution]] 2.47&Aring;' scene=''>
|SITE= <scene name='pdbsite=AC1:1pe+Binding+Site+For+Residue+E+162'>AC1</scene>, <scene name='pdbsite=AC2:1pe+Binding+Site+For+Residue+A+162'>AC2</scene>, <scene name='pdbsite=AC3:1pe+Binding+Site+For+Residue+C+162'>AC3</scene>, <scene name='pdbsite=AC4:1pe+Binding+Site+For+Residue+D+162'>AC4</scene>, <scene name='pdbsite=AC5:1pe+Binding+Site+For+Residue+B+162'>AC5</scene> and <scene name='pdbsite=AC6:1pe+Binding+Site+For+Residue+F+162'>AC6</scene>
== Structural highlights ==
|LIGAND= <scene name='pdbligand=1PE:PENTAETHYLENE GLYCOL'>1PE</scene>
<table><tr><td colspan='2'>[[2qlp]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis_H37Rv Mycobacterium tuberculosis H37Rv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QLP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2QLP FirstGlance]. <br>
|ACTIVITY= [http://en.wikipedia.org/wiki/dCTP_deaminase dCTP deaminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.4.13 3.5.4.13]  
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.47&#8491;</td></tr>
|GENE= dcd ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 Mycobacterium tuberculosis])
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</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=2qlp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qlp OCA], [https://pdbe.org/2qlp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2qlp RCSB], [https://www.ebi.ac.uk/pdbsum/2qlp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2qlp ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/DCDB_MYCTU DCDB_MYCTU] Bifunctional enzyme that catalyzes both the deamination of dCTP to dUTP and the hydrolysis of dUTP to dUMP without releasing the toxic dUTP intermediate. It also acts as a dUTP diphosphatase. Affinity for dCTP and dUTP are very similar.<ref>PMID:18164314</ref>
== 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/ql/2qlp_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=2qlp ConSurf].
<div style="clear:both"></div>


'''Bifunctional dCTP deaminase:dUTPase from Mycobacterium tuberculosis, apo form'''
==See Also==
 
*[[Deaminase 3D structures|Deaminase 3D structures]]
 
== References ==
==Overview==
<references/>
Recombinant deoxycytidine triphosphate (dCTP) deaminase from Mycobacterium tuberculosis was produced in Escherichia coli and purified. The enzyme proved to be a bifunctional dCTP deaminase:deoxyuridine triphosphatase. As such, the M. tuberculosis enzyme is the second bifunctional enzyme to be characterised and provides evidence for bifunctionality of dCTP deaminase occurring outside the Archaea kingdom. A steady-state kinetic analysis revealed that the affinity for dCTP and deoxyuridine triphosphate as substrates for the synthesis of deoxyuridine monophosphate were very similar, a result that contrasts that obtained previously for the archaean Methanocaldococcus jannaschii enzyme, which showed approximately 10-fold lower affinity for deoxyuridine triphosphate than for dCTP. The crystal structures of the enzyme in complex with the inhibitor, thymidine triphosphate, and the apo form have been solved. Comparison of the two shows that upon binding of thymidine triphosphate, the disordered C-terminal arranges as a lid covering the active site, and the enzyme adapts an inactive conformation as a result of structural changes in the active site. In the inactive conformation dephosphorylation cannot take place due to the absence of a water molecule otherwise hydrogen-bonded to O2 of the alpha-phosphate.
__TOC__
 
</StructureSection>
==About this Structure==
[[Category: Large Structures]]
2QLP is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QLP OCA].
[[Category: Mycobacterium tuberculosis H37Rv]]
 
[[Category: Christophersen S]]
==Reference==
[[Category: Harris P]]
Mechanism of dTTP inhibition of the bifunctional dCTP deaminase:dUTPase encoded by Mycobacterium tuberculosis., Helt SS, Thymark M, Harris P, Aagaard C, Dietrich J, Larsen S, Willemoes M, J Mol Biol. 2008 Feb 15;376(2):554-69. Epub 2007 Dec 5. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18164314 18164314]
[[Category: Willemoes M]]
[[Category: Mycobacterium tuberculosis]]
[[Category: Single protein]]
[[Category: dCTP deaminase]]
[[Category: Christophersen, S.]]
[[Category: Harris, P.]]
[[Category: Willemoes, M.]]
[[Category: 1PE]]
[[Category: distorted beta barrel]]
[[Category: hydrolase]]
[[Category: nucleotide metabolism]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 18:27:05 2008''

Latest revision as of 12:16, 21 February 2024

Bifunctional dCTP deaminase:dUTPase from Mycobacterium tuberculosis, apo formBifunctional dCTP deaminase:dUTPase from Mycobacterium tuberculosis, apo form

Structural highlights

2qlp is a 6 chain structure with sequence from Mycobacterium tuberculosis H37Rv. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.47Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

DCDB_MYCTU Bifunctional enzyme that catalyzes both the deamination of dCTP to dUTP and the hydrolysis of dUTP to dUMP without releasing the toxic dUTP intermediate. It also acts as a dUTP diphosphatase. Affinity for dCTP and dUTP are very similar.[1]

Evolutionary Conservation

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

See Also

References

  1. ↑ Helt SS, Thymark M, Harris P, Aagaard C, Dietrich J, Larsen S, Willemoes M. Mechanism of dTTP inhibition of the bifunctional dCTP deaminase:dUTPase encoded by Mycobacterium tuberculosis. J Mol Biol. 2008 Feb 15;376(2):554-69. Epub 2007 Dec 5. PMID:18164314 doi:http://dx.doi.org/10.1016/j.jmb.2007.11.099

2qlp, resolution 2.47Å

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA
Retrieved from "https://proteopedia.openfox.io/wiki/index.php?title=2qlp&oldid=4062844"