1pkj - Revision history

OCA at 08:08, 14 February 2024

OCA — Wed, 14 Feb 2024 08:08:46 GMT

←Older revision		Revision as of 08:08, 14 February 2024
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	<StructureSection load='1pkj' size='340' side='right'caption='[[1pkj]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='1pkj' size='340' side='right'caption='[[1pkj]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1pkj]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Atcc_43067 Atcc 43067~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PKJ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1PKJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1pkj]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii Methanocaldococcus jannaschii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PKJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1PKJ FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=DUT:DEOXYURIDINE~~-~~5-TRIPHOSPHATE'>DUT</scene>~~, ~~<scene name='pdbligand=EDO:~~1~~,2-ETHANEDIOL'>EDO</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]] 2.1Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max~~-~~height: 3em;~~'>~~[[1pkh\|1pkh]], [[1pkk\|1pkk]]~~</~~div~~><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DUT:DEOXYURIDINE-5-TRIPHOSPHATE'>DUT</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">MJ0430 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2190 ATCC 43067])~~</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=1pkj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pkj OCA], [https://pdbe.org/1pkj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1pkj RCSB], [https://www.ebi.ac.uk/pdbsum/1pkj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1pkj ProSAT]</span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=1pkj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pkj OCA], [~~http~~://pdbe.org/1pkj PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1pkj RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1pkj PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1pkj ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/~~DCD_METJA DCD_METJA~~]~~] Catalyzes two consecutive reactions~~ to ~~form~~ dUMP ~~using dCTP~~ as ~~substrate~~.~~[HAMAP-Rule~~:~~MF_00146]~~	+	[https://www.uniprot.org/uniprot/DCDB_METJA DCDB_METJA] 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 with a lower affinity for dUTP than for dCTP.<ref>PMID:12538648</ref> <ref>PMID:12670946</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</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=1pkj 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=1pkj ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Potentially mutagenic uracil-containing nucleotide intermediates are generated by deamination of dCTP, either spontaneously or enzymatically as the first step in the conversion of dCTP to dTTP. dUTPases convert dUTP to dUMP, thus avoiding the misincorporation of dUTP into DNA and creating the substrate for the next enzyme in the dTTP synthetic pathway, thymidylate synthase. Although dCTP deaminase and dUTPase activities are usually found in separate but homologous enzymes, the hyperthermophile Methanococcus jannaschii has an enzyme, DCD-DUT, that harbors both dCTP deaminase and dUTP pyrophosphatase activities. DCD-DUT has highest activity on dCTP, followed by dUTP, and dTTP inhibits both the deaminase and pyrophosphatase activities. To help clarify structure-function relationships for DCD-DUT, we have determined the crystal structure of the wild-type DCD-DUT protein in its apo form to 1.42A and structures of DCD-DUT in complex with dCTP and dUTP to resolutions of 1.77A and 2.10A, respectively. To gain insights into substrate interactions, we complemented analyses of the experimentally defined weak density for nucleotides with automated docking experiments using dCTP, dUTP, and dTTP. DCD-DUT is a hexamer, unlike the homologous dUTPases, and its subunits contain several insertions and substitutions different from the dUTPase beta barrel core that likely contribute to dCTP specificity and deamination. These first structures of a dCTP deaminase reveal a probable role for an unstructured C-terminal region different from that of the dUTPases and possible mechanisms for both bifunctional enzyme activity and feedback inhibition by dTTP.
-
-	Structural basis for recognition and catalysis by the bifunctional dCTP deaminase and dUTPase from Methanococcus jannaschii.,Huffman JL, Li H, White RH, Tainer JA J Mol Biol. 2003 Aug 22;331(4):885-96. PMID:12909016<ref>PMID:12909016</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1pkj" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 37:		Line 27:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Atcc 43067]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Huffman, J L~~]]	+	[[Category: Methanocaldococcus jannaschii]]
-	[[Category: ~~Li, H~~]]	+	[[Category: Huffman JL]]
-	[[Category: ~~Tainer, J A]]~~	+	[[Category: Li H]]
-	~~[[Category: White, R~~ H]]	+	[[Category: Tainer JA]]
-	[[Category: ~~Dcd-dut~~]]	+	[[Category: White RH]]
-	[[Category: ~~Dctp]]~~	+
-	~~[[Category: Dctp deaminase]]~~	+
-	~~[[Category: Dutp]]~~	+
-	~~[[Category: Dutpase]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Mj0430~~]]	+

OCA at 07:31, 9 December 2020

OCA — Wed, 09 Dec 2020 07:31:38 GMT

←Older revision		Revision as of 07:31, 9 December 2020
Line 1:		Line 1:

	==Structural basis for recognition and catalysis by the bifunctional dCTP deaminase and dUTPase from Methanococcus jannaschii==		==Structural basis for recognition and catalysis by the bifunctional dCTP deaminase and dUTPase from Methanococcus jannaschii==
-	<StructureSection load='1pkj' size='340' side='right' caption='[[1pkj]], [[Resolution\|resolution]] 2.10Å' scene=''>	+	<StructureSection load='1pkj' size='340' side='right'caption='[[1pkj]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1pkj]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_43067 Atcc 43067]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PKJ OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1PKJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1pkj]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_43067 Atcc 43067]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PKJ OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1PKJ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DUT:DEOXYURIDINE-5-TRIPHOSPHATE'>DUT</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DUT:DEOXYURIDINE-5-TRIPHOSPHATE'>DUT</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1pkh\|1pkh]], [[1pkk\|1pkk]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1pkh\|1pkh]], [[1pkk\|1pkk]]</div></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MJ0430 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2190 ATCC 43067])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MJ0430 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2190 ATCC 43067])</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=1pkj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pkj OCA], [http://pdbe.org/1pkj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1pkj RCSB], [http://www.ebi.ac.uk/pdbsum/1pkj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1pkj ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1pkj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pkj OCA], [http://pdbe.org/1pkj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1pkj RCSB], [http://www.ebi.ac.uk/pdbsum/1pkj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1pkj ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 30:		Line 30:
	</div>		</div>
	<div class="pdbe-citations 1pkj" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1pkj" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Deaminase 3D structures\|Deaminase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 35:		Line 38:
	</StructureSection>		</StructureSection>
	[[Category: Atcc 43067]]		[[Category: Atcc 43067]]
		+	[[Category: Large Structures]]
	[[Category: Huffman, J L]]		[[Category: Huffman, J L]]
	[[Category: Li, H]]		[[Category: Li, H]]

OCA at 07:27, 15 February 2018

OCA — Thu, 15 Feb 2018 07:27:04 GMT

←Older revision		Revision as of 07:27, 15 February 2018
Line 1:		Line 1:
		+
	==Structural basis for recognition and catalysis by the bifunctional dCTP deaminase and dUTPase from Methanococcus jannaschii==		==Structural basis for recognition and catalysis by the bifunctional dCTP deaminase and dUTPase from Methanococcus jannaschii==
	<StructureSection load='1pkj' size='340' side='right' caption='[[1pkj]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='1pkj' size='340' side='right' caption='[[1pkj]], [[Resolution\|resolution]] 2.10Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1pkh\|1pkh]], [[1pkk\|1pkk]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1pkh\|1pkh]], [[1pkk\|1pkk]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MJ0430 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2190 ATCC 43067])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MJ0430 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2190 ATCC 43067])</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=1pkj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pkj OCA], [http://pdbe.org/1pkj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1pkj RCSB], [http://www.ebi.ac.uk/pdbsum/1pkj PDBsum]</span></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=1pkj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pkj OCA], [http://pdbe.org/1pkj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1pkj RCSB], [http://www.ebi.ac.uk/pdbsum/1pkj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1pkj ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pk/1pkj_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pk/1pkj_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=1pkj ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 29:		Line 30:
	</div>		</div>
	<div class="pdbe-citations 1pkj" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1pkj" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Deaminase\|Deaminase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 10:28, 11 September 2015

OCA — Fri, 11 Sep 2015 10:28:32 GMT

←Older revision		Revision as of 10:28, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='1pkj' size='340' side='right' caption='[[1pkj]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='1pkj' size='340' side='right' caption='[[1pkj]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1pkj]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Methanocaldococcus_jannaschii Methanocaldococcus jannaschii~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PKJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PKJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1pkj]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_43067 Atcc 43067]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PKJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PKJ FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DUT:DEOXYURIDINE-5-TRIPHOSPHATE'>DUT</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DUT:DEOXYURIDINE-5-TRIPHOSPHATE'>DUT</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1pkh\|1pkh]], [[1pkk\|1pkk]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1pkh\|1pkh]], [[1pkk\|1pkk]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MJ0430 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2190 ~~Methanocaldococcus jannaschii~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MJ0430 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2190 ATCC 43067])</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=1pkj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pkj OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1pkj RCSB], [http://www.ebi.ac.uk/pdbsum/1pkj PDBsum]</span></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=1pkj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pkj OCA], [http://pdbe.org/1pkj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1pkj RCSB], [http://www.ebi.ac.uk/pdbsum/1pkj PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 28:		Line 28:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 1pkj" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 35:		Line 36:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Methanocaldococcus jannaschii~~]]	+	[[Category: Atcc 43067]]
	[[Category: Huffman, J L]]		[[Category: Huffman, J L]]
	[[Category: Li, H]]		[[Category: Li, H]]

OCA at 15:12, 25 December 2014

OCA — Thu, 25 Dec 2014 15:12:10 GMT

←Older revision		Revision as of 15:12, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1pkj]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii Methanocaldococcus jannaschii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PKJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PKJ FirstGlance]. <br>		<table><tr><td colspan='2'>[[1pkj]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii Methanocaldococcus jannaschii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PKJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PKJ FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DUT:DEOXYURIDINE-5-TRIPHOSPHATE'>DUT</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DUT:DEOXYURIDINE-5-TRIPHOSPHATE'>DUT</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1pkh\|1pkh]], [[1pkk\|1pkk]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1pkh\|1pkh]], [[1pkk\|1pkk]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MJ0430 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2190 Methanocaldococcus jannaschii])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MJ0430 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2190 Methanocaldococcus jannaschii])</td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1pkj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pkj OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1pkj RCSB], [http://www.ebi.ac.uk/pdbsum/1pkj PDBsum]</span></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=1pkj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pkj OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1pkj RCSB], [http://www.ebi.ac.uk/pdbsum/1pkj PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/DCD_METJA DCD_METJA]] Catalyzes two consecutive reactions to form dUMP using dCTP as substrate.[HAMAP-Rule:MF_00146]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 34:		Line 36:
	</StructureSection>		</StructureSection>
	[[Category: Methanocaldococcus jannaschii]]		[[Category: Methanocaldococcus jannaschii]]
-	[[Category: Huffman, J L.]]	+	[[Category: Huffman, J L]]
-	[[Category: Li, H.]]	+	[[Category: Li, H]]
-	[[Category: Tainer, J A.]]	+	[[Category: Tainer, J A]]
-	[[Category: White, R H.]]	+	[[Category: White, R H]]
	[[Category: Dcd-dut]]		[[Category: Dcd-dut]]
	[[Category: Dctp]]		[[Category: Dctp]]

OCA at 08:22, 3 October 2014

OCA — Fri, 03 Oct 2014 08:22:04 GMT

←Older revision		Revision as of 08:22, 3 October 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_1pkj\| PDB=1pkj \| SCENE= }}~~	+	==Structural basis for recognition and catalysis by the bifunctional dCTP deaminase and dUTPase from Methanococcus jannaschii==
-	===Structural basis for recognition and catalysis by the bifunctional dCTP deaminase and dUTPase from Methanococcus jannaschii===	+	<StructureSection load='1pkj' size='340' side='right' caption='[[1pkj]], [[Resolution\|resolution]] 2.10Å' scene=''>
-	~~{{ABSTRACT_PUBMED_12909016}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1pkj]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii Methanocaldococcus jannaschii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PKJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PKJ FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DUT:DEOXYURIDINE-5-TRIPHOSPHATE'>DUT</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1pkh\|1pkh]], [[1pkk\|1pkk]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MJ0430 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2190 Methanocaldococcus jannaschii])</td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1pkj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pkj OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1pkj RCSB], [http://www.ebi.ac.uk/pdbsum/1pkj PDBsum]</span></td></tr>
		+	<table>
		+	== 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/pk/1pkj_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/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Potentially mutagenic uracil-containing nucleotide intermediates are generated by deamination of dCTP, either spontaneously or enzymatically as the first step in the conversion of dCTP to dTTP. dUTPases convert dUTP to dUMP, thus avoiding the misincorporation of dUTP into DNA and creating the substrate for the next enzyme in the dTTP synthetic pathway, thymidylate synthase. Although dCTP deaminase and dUTPase activities are usually found in separate but homologous enzymes, the hyperthermophile Methanococcus jannaschii has an enzyme, DCD-DUT, that harbors both dCTP deaminase and dUTP pyrophosphatase activities. DCD-DUT has highest activity on dCTP, followed by dUTP, and dTTP inhibits both the deaminase and pyrophosphatase activities. To help clarify structure-function relationships for DCD-DUT, we have determined the crystal structure of the wild-type DCD-DUT protein in its apo form to 1.42A and structures of DCD-DUT in complex with dCTP and dUTP to resolutions of 1.77A and 2.10A, respectively. To gain insights into substrate interactions, we complemented analyses of the experimentally defined weak density for nucleotides with automated docking experiments using dCTP, dUTP, and dTTP. DCD-DUT is a hexamer, unlike the homologous dUTPases, and its subunits contain several insertions and substitutions different from the dUTPase beta barrel core that likely contribute to dCTP specificity and deamination. These first structures of a dCTP deaminase reveal a probable role for an unstructured C-terminal region different from that of the dUTPases and possible mechanisms for both bifunctional enzyme activity and feedback inhibition by dTTP.

-	~~==Function==~~	+	Structural basis for recognition and catalysis by the bifunctional dCTP deaminase and dUTPase from Methanococcus jannaschii.,Huffman JL, Li H, White RH, Tainer JA J Mol Biol. 2003 Aug 22;331(4):885-96. PMID:12909016<ref>PMID:12909016</ref>
-	~~[[http://www~~.~~uniprot~~.~~org/uniprot/DCD_METJA DCD_METJA]] Catalyzes two consecutive reactions to form dUMP using dCTP as substrate~~.~~[HAMAP-Rule~~:~~MF_00146]~~	+

-	~~==About this Structure==~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[1pkj]] is~~ a ~~2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Methanocaldococcus_jannaschii Methanocaldococcus jannaschii]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1PKJ OCA].~~	+	</div>

-	==~~Reference~~==	+	==See Also==
-	~~<ref group~~=~~"xtra">PMID:012909016</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	*[[Deaminase\|Deaminase]]
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Methanocaldococcus jannaschii]]		[[Category: Methanocaldococcus jannaschii]]
	[[Category: Huffman, J L.]]		[[Category: Huffman, J L.]]

OCA at 10:37, 16 April 2014

OCA — Wed, 16 Apr 2014 10:37:36 GMT

←Older revision		Revision as of 10:37, 16 April 2014
Line 1:		Line 1:
-	[[Image:1pkj.png\|left\|200px]]
-
-	<!--
-	The line below this paragraph, containing "STRUCTURE_1pkj", 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_1pkj\| PDB=1pkj \| SCENE= }}		{{STRUCTURE_1pkj\| PDB=1pkj \| SCENE= }}
-
	===Structural basis for recognition and catalysis by the bifunctional dCTP deaminase and dUTPase from Methanococcus jannaschii===		===Structural basis for recognition and catalysis by the bifunctional dCTP deaminase and dUTPase from Methanococcus jannaschii===
		+	{{ABSTRACT_PUBMED_12909016}}

-		+	==Function==
-	~~<!--~~	+	[[http://www.uniprot.org/uniprot/DCD_METJA DCD_METJA]] Catalyzes two consecutive reactions to form dUMP using dCTP as substrate.[HAMAP-Rule:MF_00146]
-	~~The line below this paragraph, {{ABSTRACT_PUBMED_12909016}}, adds the Publication Abstract to the page~~	+
-	~~(as it appears on PubMed at~~ http://www.~~pubmed~~.~~gov), where 12909016 is the PubMed ID number~~.	+
-	-->	+
-	~~{{ABSTRACT_PUBMED_12909016}}~~	+

	==About this Structure==		==About this Structure==
Line 22:		Line 10:

	==Reference==		==Reference==
-	<ref group="xtra">PMID:012909016</ref><references group="xtra"/>	+	<ref group="xtra">PMID:012909016</ref><references group="xtra"/><references/>
	[[Category: Methanocaldococcus jannaschii]]		[[Category: Methanocaldococcus jannaschii]]
	[[Category: Huffman, J L.]]		[[Category: Huffman, J L.]]

OCA: Protected "1pkj" [edit=sysop:move=sysop]

OCA — Wed, 16 Nov 2011 09:52:38 GMT

Protected "1pkj" [edit=sysop:move=sysop]

←Older revision

Revision as of 09:52, 16 November 2011

OCA at 09:52, 16 November 2011

OCA — Wed, 16 Nov 2011 09:52:37 GMT

←Older revision		Revision as of 09:52, 16 November 2011
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1pkj.png\|left\|200px]]		[[Image:1pkj.png\|left\|200px]]

Line 20:		Line 19:

	==About this Structure==		==About this Structure==
-	~~1PKJ~~ is a 2 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii Methanocaldococcus jannaschii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PKJ OCA].	+	[[1pkj]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii Methanocaldococcus jannaschii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PKJ OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~12909016~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:012909016</ref><references group="xtra"/>
	[[Category: Methanocaldococcus jannaschii]]		[[Category: Methanocaldococcus jannaschii]]
	[[Category: Huffman, J L.]]		[[Category: Huffman, J L.]]
Line 34:		Line 33:
	[[Category: Dutp]]		[[Category: Dutp]]
	[[Category: Dutpase]]		[[Category: Dutpase]]
		+	[[Category: Hydrolase]]
	[[Category: Mj0430]]		[[Category: Mj0430]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 19:53:58 2009''

OCA at 17:53, 17 February 2009

OCA — Tue, 17 Feb 2009 17:53:59 GMT

←Older revision		Revision as of 17:53, 17 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	1PKJ is a ~~[[Single protein]]~~ structure of ~~sequence~~ from [http://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii Methanocaldococcus jannaschii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PKJ OCA].	+	1PKJ is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii Methanocaldococcus jannaschii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PKJ OCA].

	==Reference==		==Reference==
-	Structural basis for recognition and catalysis by the bifunctional dCTP deaminase and dUTPase from Methanococcus jannaschii., Huffman JL, Li H, White RH, Tainer JA, J Mol Biol. 2003 Aug 22;331(4):885-96. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/12909016 12909016]~~	+	<ref group="xtra">PMID:12909016</ref><references group="xtra"/>
	[[Category: Methanocaldococcus jannaschii]]		[[Category: Methanocaldococcus jannaschii]]
-	[[Category: Single protein]]
	[[Category: Huffman, J L.]]		[[Category: Huffman, J L.]]
	[[Category: Li, H.]]		[[Category: Li, H.]]
Line 37:		Line 36:
	[[Category: Mj0430]]		[[Category: Mj0430]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue ~~Jul 29 03~~:49:~~02 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 19:53:58 2009''