2oig

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of RS21-C6 core segment and dm5CTP complex

Structural highlights

2oig is a 4 chain structure with sequence from Mus musculus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 3.3Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

DCTP1_MOUSE Hydrolyzes deoxynucleoside triphosphates (dNTPs) to the corresponding nucleoside monophosphates. Has a strong preference for modified dCTP. Activity is highest with 5-iodo-dCTP, followed by 5-bromo-dCTP, unmodified dCTP, 5-methyl-dCTP and 5-chloro-dCTP. Hydrolyzes 2-chloro-dATP and 2-hydroxy-dATP with lower efficiency, and has even lower activity with unmodified dATP, dTTP and dUTP (in vitro). Does not hydrolyze ATP, UTP, ITP, GTP, dADP, dCDP or dGTP. May protect DNA or RNA against the incorporation of non-canonical nucleotide triphosphates. May protect cells against inappropriate methylation of CpG islands by DNA methyltransferases.^[1] ^[2]

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

RS21-C6, which is highly expressed in all vertebrate genomes and green plants, is proposed to have nucleoside triphosphate pyrophosphohydrolase activity. Here, we report the crystal structures of the core fragment of RS21-C6, named RSCUT, and the complex with the substrate 5-methyl dCTP. The refined structure of RSCUT consists mainly of alpha-helices and shows formation of a tightly associated tetramer. On the basis of the structure of the RSCUT-m5dCTP complex and the results of pyrophosphatase activity assays, several key residues involved in the substrate binding of RS21-C6 have been identified. Tetramer formation is shown to be required for substrate binding.

Crystal structure of RS21-C6, involved in nucleoside triphosphate pyrophosphohydrolysis.,Wu B, Liu Y, Zhao Q, Liao S, Zhang J, Bartlam M, Chen W, Rao Z J Mol Biol. 2007 Apr 13;367(5):1405-12. Epub 2007 Jan 26. PMID:17320107^[3]

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

References

↑ Wu B, Liu Y, Zhao Q, Liao S, Zhang J, Bartlam M, Chen W, Rao Z. Crystal structure of RS21-C6, involved in nucleoside triphosphate pyrophosphohydrolysis. J Mol Biol. 2007 Apr 13;367(5):1405-12. Epub 2007 Jan 26. PMID:17320107 doi:10.1016/j.jmb.2007.01.057
↑ Nonaka M, Tsuchimoto D, Sakumi K, Nakabeppu Y. Mouse RS21-C6 is a mammalian 2'-deoxycytidine 5'-triphosphate pyrophosphohydrolase that prefers 5-iodocytosine. FEBS J. 2009 Mar;276(6):1654-66. doi: 10.1111/j.1742-4658.2009.06898.x. Epub 2009, Feb 7. PMID:19220460 doi:http://dx.doi.org/10.1111/j.1742-4658.2009.06898.x
↑ Wu B, Liu Y, Zhao Q, Liao S, Zhang J, Bartlam M, Chen W, Rao Z. Crystal structure of RS21-C6, involved in nucleoside triphosphate pyrophosphohydrolysis. J Mol Biol. 2007 Apr 13;367(5):1405-12. Epub 2007 Jan 26. PMID:17320107 doi:10.1016/j.jmb.2007.01.057

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2oig"

@@ Line 1: / Line 1: @@
 ==Crystal structure of RS21-C6 core segment and dm5CTP complex==
-<StructureSection load='2oig' size='340' side='right' caption='[[2oig]], [[Resolution|resolution]] 3.30&Aring;' scene=''>
+<StructureSection load='2oig' size='340' side='right'caption='[[2oig]], [[Resolution|resolution]] 3.30&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2oig]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OIG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2OIG FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2oig]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OIG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2OIG FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=523:2-DEOXY-5-METHYLCYTIDINE+5-(TETRAHYDROGEN+TRIPHOSPHATE)'>523</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]] 3.3&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2oie|2oie]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=523:2-DEOXY-5-METHYLCYTIDINE+5-(TETRAHYDROGEN+TRIPHOSPHATE)'>523</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=2oig FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2oig OCA], [http://pdbe.org/2oig PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2oig RCSB], [http://www.ebi.ac.uk/pdbsum/2oig 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=2oig FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2oig OCA], [https://pdbe.org/2oig PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2oig RCSB], [https://www.ebi.ac.uk/pdbsum/2oig PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2oig ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/DCTP1_MOUSE DCTP1_MOUSE]] Hydrolyzes deoxynucleoside triphosphates (dNTPs) to the corresponding nucleoside monophosphates. Has a strong preference for modified dCTP. Activity is highest with 5-iodo-dCTP, followed by 5-bromo-dCTP, unmodified dCTP, 5-methyl-dCTP and 5-chloro-dCTP. Hydrolyzes 2-chloro-dATP and 2-hydroxy-dATP with lower efficiency, and has even lower activity with unmodified dATP, dTTP and dUTP (in vitro). Does not hydrolyze ATP, UTP, ITP, GTP, dADP, dCDP or dGTP. May protect DNA or RNA against the incorporation of non-canonical nucleotide triphosphates. May protect cells against inappropriate methylation of CpG islands by DNA methyltransferases.<ref>PMID:17320107</ref> <ref>PMID:19220460</ref>
+[https://www.uniprot.org/uniprot/DCTP1_MOUSE DCTP1_MOUSE] Hydrolyzes deoxynucleoside triphosphates (dNTPs) to the corresponding nucleoside monophosphates. Has a strong preference for modified dCTP. Activity is highest with 5-iodo-dCTP, followed by 5-bromo-dCTP, unmodified dCTP, 5-methyl-dCTP and 5-chloro-dCTP. Hydrolyzes 2-chloro-dATP and 2-hydroxy-dATP with lower efficiency, and has even lower activity with unmodified dATP, dTTP and dUTP (in vitro). Does not hydrolyze ATP, UTP, ITP, GTP, dADP, dCDP or dGTP. May protect DNA or RNA against the incorporation of non-canonical nucleotide triphosphates. May protect cells against inappropriate methylation of CpG islands by DNA methyltransferases.<ref>PMID:17320107</ref> <ref>PMID:19220460</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/oi/2oig_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/oi/2oig_consurf.spt"</scriptWhenChecked>
-    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <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/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=2oig ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 32: / Line 33: @@
 __TOC__
 </StructureSection>
-[[Category: Lk3 transgenic mice]]
+[[Category: Large Structures]]
-[[Category: Bartlam, M]]
+[[Category: Mus musculus]]
-[[Category: Chen, W]]
+[[Category: Bartlam M]]
-[[Category: Liao, S]]
+[[Category: Chen W]]
-[[Category: Liu, Y]]
+[[Category: Liao S]]
-[[Category: Rao, Z]]
+[[Category: Liu Y]]
-[[Category: Wu, B]]
+[[Category: Rao Z]]
-[[Category: Zhang, J]]
+[[Category: Wu B]]
-[[Category: Zhao, Q]]
+[[Category: Zhang J]]
-[[Category: Helix]]
+[[Category: Zhao Q]]
-[[Category: Hydrolase]]
-[[Category: Protein-nucleoside triphosphate complex]]
-[[Category: Substrate complex]]

2oig

From Proteopedia

Current revision

Crystal structure of RS21-C6 core segment and dm5CTP complex

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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