1dut: Difference between revisions

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==FIV DUTP PYROPHOSPHATASE==
==FIV DUTP PYROPHOSPHATASE==
<StructureSection load='1dut' size='340' side='right' caption='[[1dut]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
<StructureSection load='1dut' size='340' side='right'caption='[[1dut]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1dut]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Feline_immunodeficiency_virus_(isolate_petaluma) Feline immunodeficiency virus (isolate petaluma)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DUT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1DUT FirstGlance]. <br>
<table><tr><td colspan='2'>[[1dut]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Feline_immunodeficiency_virus_(isolate_Petaluma) Feline immunodeficiency virus (isolate Petaluma)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DUT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DUT FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9&#8491;</td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/dUTP_diphosphatase dUTP diphosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.1.23 3.6.1.23] </span></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1dut FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dut OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1dut RCSB], [http://www.ebi.ac.uk/pdbsum/1dut PDBsum]</span></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=1dut FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dut OCA], [https://pdbe.org/1dut PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dut RCSB], [https://www.ebi.ac.uk/pdbsum/1dut PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dut ProSAT]</span></td></tr>
</table>
</table>
== Function ==
[https://www.uniprot.org/uniprot/POL_FIVPE POL_FIVPE] During replicative cycle of retroviruses, the reverse-transcribed viral DNA is integrated into the host chromosome by the viral integrase enzyme. RNase H activity is associated with the reverse transcriptase.
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
Check<jmol>
   <jmolCheckbox>
   <jmolCheckbox>
     <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/du/1dut_consurf.spt"</scriptWhenChecked>
     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/du/1dut_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
   </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].
</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=1dut ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
We have determined the crystal structure of dUTP pyrophosphatase (dUTPase) from feline immunodeficiency virus (FIV) at 1.9 A resolution. The structure has been solved by the multiple isomorphous replacement (MIR) method using a P6(3) crystal form. The results show that the enzyme is a trimer of 14.3 kDa subunits with marked structural similarity to E. coli dUTPase. In both enzymes the C-terminal strand of an anti-parallel beta-barrel participates in the beta-sheet of an adjacent subunit to form an interdigitated, biologically functional trimer. In the P6(3) crystal form one trimer packs on the 6(3) screw-axis and another on the threefold axis so that there are two independent monomers per asymmetric unit. A Mg2+ ion is coordinated by three asparate residues on the threefold axis of each trimer. Alignment of 17 viral, prokaryotic, and eukaryotic dUTPase sequences reveals five conserved motifs. Four of these map onto the interface between pairs of subunits, defining a putative active site region; the fifth resides in the C-terminal 16 residues, which is disordered in the crystals. Conserved motifs from all three subunits are required to create a given active site. With respect to viral protein expression, it is particularly interesting that the gene for dUTPase (DU) resides in the middle of the Pol gene, the enzyme cassette of the retroviral genome. Other enzymes encoded in the Pol polyprotein, including protease (PR), reverse transcriptase (RT), and most likely integrase (IN), are dimeric enzymes, which implies that the stoichiometry of expression of active trimeric dUTPase is distinct from the other Pol-encoded enzymes. Additionally, due to structural constraints, it is unlikely that dUTPase can attain an active form prior to cleavage from the polyprotein.
Crystal structure of dUTP pyrophosphatase from feline immunodeficiency virus.,Prasad GS, Stura EA, McRee DE, Laco GS, Hasselkus-Light C, Elder JH, Stout CD Protein Sci. 1996 Dec;5(12):2429-37. PMID:8976551<ref>PMID:8976551</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>


==See Also==
==See Also==
*[[Deoxyuridine 5'-triphosphate nucleotidohydrolase|Deoxyuridine 5'-triphosphate nucleotidohydrolase]]
*[[DUTPase 3D structures|DUTPase 3D structures]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: DUTP diphosphatase]]
[[Category: Large Structures]]
[[Category: Elder, J H]]
[[Category: Elder JH]]
[[Category: Hasselkus-Light, C]]
[[Category: Hasselkus-Light C]]
[[Category: Laco, G S]]
[[Category: Laco GS]]
[[Category: Mcree, D E]]
[[Category: Mcree DE]]
[[Category: Prasad, G S]]
[[Category: Prasad GS]]
[[Category: Stout, C D]]
[[Category: Stout CD]]
[[Category: Stura, E A]]
[[Category: Stura EA]]
[[Category: Acid anhydride hydrolase]]
[[Category: Aspartyl protease]]
[[Category: Endonuclease]]
[[Category: Hydrolase]]
[[Category: Nucleotide metabolism]]
[[Category: Polyprotein]]
[[Category: Rna-directed dna polymerase]]

Latest revision as of 09:59, 7 February 2024

FIV DUTP PYROPHOSPHATASEFIV DUTP PYROPHOSPHATASE

Structural highlights

1dut is a 2 chain structure with sequence from Feline immunodeficiency virus (isolate Petaluma). Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.9Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

POL_FIVPE During replicative cycle of retroviruses, the reverse-transcribed viral DNA is integrated into the host chromosome by the viral integrase enzyme. RNase H activity is associated with the reverse transcriptase.

Evolutionary Conservation

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

See Also

1dut, resolution 1.90Å

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