1q3k - Revision history

OCA at 08:12, 14 February 2024

OCA — Wed, 14 Feb 2024 08:12:47 GMT

←Older revision		Revision as of 08:12, 14 February 2024
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	<StructureSection load='1q3k' size='340' side='right'caption='[[1q3k]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='1q3k' size='340' side='right'caption='[[1q3k]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1q3k]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"bacillus_fluorescens_putidus"_flugge_1886 "bacillus fluorescens putidus" flugge 1886~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Q3K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1Q3K FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1q3k]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_putida Pseudomonas putida]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Q3K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1Q3K FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>~~, ~~<scene name='pdbligand=ZN:ZINC+ION'>ZN</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='~~activity~~'><td class="sblockLbl"><b>~~Activity~~:</b></td><td class="sblockDat"><~~span class~~='~~plainlinks~~'>~~[https:~~/~~/en.wikipedia.org/wiki/Creatininase Creatininase]~~, ~~with EC number [https~~:~~//www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.2.10 3.5.2.10]~~ </~~span~~></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=1q3k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q3k OCA], [https://pdbe.org/1q3k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1q3k RCSB], [https://www.ebi.ac.uk/pdbsum/1q3k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1q3k ProSAT]</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=1q3k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q3k OCA], [https://pdbe.org/1q3k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1q3k RCSB], [https://www.ebi.ac.uk/pdbsum/1q3k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1q3k ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/CRNA_PSEPU CRNA_PSEPU]] Cyclic amidohydrolase that catalyzes the reversible conversion of creatinine to creatine. Is also active toward glycocyamidine, though the reaction rate is very low, but it is completely inert toward hydantoin and its derivatives.<ref>PMID:500580</ref>	+	[https://www.uniprot.org/uniprot/CRNA_PSEPU CRNA_PSEPU] Cyclic amidohydrolase that catalyzes the reversible conversion of creatinine to creatine. Is also active toward glycocyamidine, though the reaction rate is very low, but it is completely inert toward hydantoin and its derivatives.<ref>PMID:500580</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=1q3k 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=1q3k ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Creatinine amidohydrolase (creatininase; EC 3.5.2.10) from Pseudomonas putida, a homohexameric enzyme with a molecular mass of 28.4 kDa per subunit, is a cyclic amidohydrolase catalysing the reversible conversion of creatinine to creatine. The enzyme plays a key role in the bacterial degradation of creatinine. The three-dimensional structure of creatininase from P.putida was determined and refined to 2.1A. The structure shows the six subunits arranged as a trimer of dimers and definitely disproves previous reports that the enzyme has an octameric quaternary structure. Each monomer consists of a central, four-stranded, parallel beta-sheet flanked by two alpha-helices on both sides of the beta-sheet. This topology is unique within the superfamily of amidohydrolases. Moreover, creatininase possesses a novel fold with no close structural relatives within the Protein Data Bank. Each creatininase monomer contains a binuclear zinc centre near the C termini of the beta-strands and the N termini of the main alpha-helices. These zinc ions indicate the location of the active site unambiguously. The active site is entirely buried and is not accessible from the solution without movement of parts of the protein. The two zinc ions are bridged by a water molecule and by an aspartate residue, which acts as a bidentate ligand. They differ from each other in the number and the spatial arrangement of their ligands. One of them is tetrahedrally and the other trigonal-bipyramidally ligated. Using two water molecules of the first coordination sphere as anchor points, a creatinine-water adduct resembling the transition state of the hydrolysation reaction was modelled into the active site. The resulting complex in combination with structural comparisons with other amidohydrolases enabled us to identify the most probable candidate for the catalytic base and to suggest a putative reaction mechanism. Surprisingly these structural comparisons revealed a similarity in the active-site arrangement between creatininase and the hydantoinase-like cyclic amidohydrolases that was unexpected, given the completely unrelated primary and tertiary structures. In particular, the zinc-bridging aspartate residue of creatininase is a spatially and functionally analogue to a carboxylated lysine residue found in dihydroorotase and the hydantoinases. Hence, creatininase and the hydantoinase-like cyclic amidohydrolases represent a further example of convergent evolution within the enzyme class of hydrolases.
-
-	Crystal structure of creatininase from Pseudomonas putida: a novel fold and a case of convergent evolution.,Beuth B, Niefind K, Schomburg D J Mol Biol. 2003 Sep 5;332(1):287-301. PMID:12946365<ref>PMID:12946365</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1q3k" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Bacillus fluorescens putidus flugge 1886]]
-	[[Category: Creatininase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Beuth, B~~]]	+	[[Category: Pseudomonas putida]]
-	[[Category: ~~Niefind, K~~]]	+	[[Category: Beuth B]]
-	[[Category: ~~Schomburg, D~~]]	+	[[Category: Niefind K]]
-	[[Category: ~~Alpha-beta-fold]]~~	+	[[Category: Schomburg D]]
-	~~[[Category: Hydrolase~~]]	+

OCA at 06:02, 28 April 2021

OCA — Wed, 28 Apr 2021 06:02:23 GMT

←Older revision		Revision as of 06:02, 28 April 2021
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	<StructureSection load='1q3k' size='340' side='right'caption='[[1q3k]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='1q3k' size='340' side='right'caption='[[1q3k]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1q3k]] is a 6 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"bacillus_fluorescens_putidus"_flugge_1886 "bacillus fluorescens putidus" flugge 1886]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Q3K OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1Q3K FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1q3k]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_fluorescens_putidus"_flugge_1886 "bacillus fluorescens putidus" flugge 1886]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Q3K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1Q3K FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Creatininase Creatininase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.2.10 3.5.2.10] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Creatininase Creatininase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.2.10 3.5.2.10] </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=1q3k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q3k OCA], [~~http~~://pdbe.org/1q3k PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1q3k RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1q3k PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1q3k ProSAT]</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=1q3k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q3k OCA], [https://pdbe.org/1q3k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1q3k RCSB], [https://www.ebi.ac.uk/pdbsum/1q3k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1q3k ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/CRNA_PSEPU CRNA_PSEPU]] Cyclic amidohydrolase that catalyzes the reversible conversion of creatinine to creatine. Is also active toward glycocyamidine, though the reaction rate is very low, but it is completely inert toward hydantoin and its derivatives.<ref>PMID:500580</ref>	+	[[https://www.uniprot.org/uniprot/CRNA_PSEPU CRNA_PSEPU]] Cyclic amidohydrolase that catalyzes the reversible conversion of creatinine to creatine. Is also active toward glycocyamidine, though the reaction rate is very low, but it is completely inert toward hydantoin and its derivatives.<ref>PMID:500580</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 06:57, 24 July 2019

OCA — Wed, 24 Jul 2019 06:57:55 GMT

←Older revision		Revision as of 06:57, 24 July 2019
Line 1:		Line 1:

	==Crystal structure of creatinine amidohydrolase (creatininase)==		==Crystal structure of creatinine amidohydrolase (creatininase)==
-	<StructureSection load='1q3k' size='340' side='right' caption='[[1q3k]], [[Resolution\|resolution]] 2.10Å' scene=''>	+	<StructureSection load='1q3k' size='340' side='right'caption='[[1q3k]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1q3k]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_fluorescens_putidus"_flugge_1886 "bacillus fluorescens putidus" flugge 1886]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Q3K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Q3K FirstGlance]. <br>		<table><tr><td colspan='2'>[[1q3k]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_fluorescens_putidus"_flugge_1886 "bacillus fluorescens putidus" flugge 1886]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Q3K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Q3K FirstGlance]. <br>
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	[[Category: Bacillus fluorescens putidus flugge 1886]]		[[Category: Bacillus fluorescens putidus flugge 1886]]
	[[Category: Creatininase]]		[[Category: Creatininase]]
		+	[[Category: Large Structures]]
	[[Category: Beuth, B]]		[[Category: Beuth, B]]
	[[Category: Niefind, K]]		[[Category: Niefind, K]]

OCA at 08:29, 24 February 2018

OCA — Sat, 24 Feb 2018 08:29:31 GMT

←Older revision		Revision as of 08:29, 24 February 2018
Line 1:		Line 1:
		+
	==Crystal structure of creatinine amidohydrolase (creatininase)==		==Crystal structure of creatinine amidohydrolase (creatininase)==
	<StructureSection load='1q3k' size='340' side='right' caption='[[1q3k]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='1q3k' size='340' side='right' caption='[[1q3k]], [[Resolution\|resolution]] 2.10Å' scene=''>
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	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Creatininase Creatininase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.2.10 3.5.2.10] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Creatininase Creatininase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.2.10 3.5.2.10] </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=1q3k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q3k OCA], [http://pdbe.org/1q3k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1q3k RCSB], [http://www.ebi.ac.uk/pdbsum/1q3k 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=1q3k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q3k OCA], [http://pdbe.org/1q3k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1q3k RCSB], [http://www.ebi.ac.uk/pdbsum/1q3k PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1q3k ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 13:		Line 14:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/q3/1q3k_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/q3/1q3k_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>

OCA at 03:47, 10 February 2016

OCA — Wed, 10 Feb 2016 03:47:52 GMT

←Older revision		Revision as of 03:47, 10 February 2016
Line 17:		Line 17:
	<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=1q3k ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 05:04, 11 September 2015

OCA — Fri, 11 Sep 2015 05:04:57 GMT

←Older revision		Revision as of 05:04, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='1q3k' size='340' side='right' caption='[[1q3k]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='1q3k' size='340' side='right' caption='[[1q3k]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1q3k]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Pseudomonas_putida Pseudomonas putida~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Q3K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Q3K FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1q3k]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_fluorescens_putidus"_flugge_1886 "bacillus fluorescens putidus" flugge 1886]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Q3K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Q3K FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Creatininase Creatininase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.2.10 3.5.2.10] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Creatininase Creatininase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.2.10 3.5.2.10] </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=1q3k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q3k OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1q3k RCSB], [http://www.ebi.ac.uk/pdbsum/1q3k 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=1q3k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q3k OCA], [http://pdbe.org/1q3k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1q3k RCSB], [http://www.ebi.ac.uk/pdbsum/1q3k PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[http://www.uniprot.org/uniprot/~~P83772_PSEPU P83772_PSEPU~~]] Cyclic amidohydrolase that catalyzes the reversible conversion of creatinine to creatine. Is also active toward glycocyamidine, though the reaction rate is very low, but it is completely inert toward hydantoin and its derivatives.<ref>PMID:500580</ref>	+	[[http://www.uniprot.org/uniprot/CRNA_PSEPU CRNA_PSEPU]] Cyclic amidohydrolase that catalyzes the reversible conversion of creatinine to creatine. Is also active toward glycocyamidine, though the reaction rate is very low, but it is completely inert toward hydantoin and its derivatives.<ref>PMID:500580</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 27:		Line 27:
	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 1q3k" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacillus fluorescens putidus flugge 1886]]
	[[Category: Creatininase]]		[[Category: Creatininase]]
-	[[Category: Pseudomonas putida]]
	[[Category: Beuth, B]]		[[Category: Beuth, B]]
	[[Category: Niefind, K]]		[[Category: Niefind, K]]

OCA at 11:34, 25 December 2014

OCA — Thu, 25 Dec 2014 11:34:49 GMT

←Older revision		Revision as of 11:34, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1q3k]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseudomonas_putida Pseudomonas putida]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Q3K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Q3K FirstGlance]. <br>		<table><tr><td colspan='2'>[[1q3k]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseudomonas_putida Pseudomonas putida]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Q3K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Q3K FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Creatininase Creatininase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.2.10 3.5.2.10] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Creatininase Creatininase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.2.10 3.5.2.10] </span></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=1q3k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q3k OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1q3k RCSB], [http://www.ebi.ac.uk/pdbsum/1q3k 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=1q3k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q3k OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1q3k RCSB], [http://www.ebi.ac.uk/pdbsum/1q3k PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/P83772_PSEPU P83772_PSEPU]] Cyclic amidohydrolase that catalyzes the reversible conversion of creatinine to creatine. Is also active toward glycocyamidine, though the reaction rate is very low, but it is completely inert toward hydantoin and its derivatives.<ref>PMID:500580</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 31:		Line 33:
	[[Category: Creatininase]]		[[Category: Creatininase]]
	[[Category: Pseudomonas putida]]		[[Category: Pseudomonas putida]]
-	[[Category: Beuth, B.]]	+	[[Category: Beuth, B]]
-	[[Category: Niefind, K.]]	+	[[Category: Niefind, K]]
-	[[Category: Schomburg, D.]]	+	[[Category: Schomburg, D]]
	[[Category: Alpha-beta-fold]]		[[Category: Alpha-beta-fold]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]

OCA at 14:17, 29 September 2014

OCA — Mon, 29 Sep 2014 14:17:24 GMT

←Older revision		Revision as of 14:17, 29 September 2014
Line 1:		Line 1:
-	[[~~Image~~:1q3k.~~png\|left~~\|200px]]	+	==Crystal structure of creatinine amidohydrolase (creatininase)==
		+	<StructureSection load='1q3k' size='340' side='right' caption='[[1q3k]], [[Resolution\|resolution]] 2.10Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1q3k]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseudomonas_putida Pseudomonas putida]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Q3K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Q3K FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Creatininase Creatininase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.2.10 3.5.2.10] </span></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=1q3k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q3k OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1q3k RCSB], [http://www.ebi.ac.uk/pdbsum/1q3k 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/q3/1q3k_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 ==
		+	Creatinine amidohydrolase (creatininase; EC 3.5.2.10) from Pseudomonas putida, a homohexameric enzyme with a molecular mass of 28.4 kDa per subunit, is a cyclic amidohydrolase catalysing the reversible conversion of creatinine to creatine. The enzyme plays a key role in the bacterial degradation of creatinine. The three-dimensional structure of creatininase from P.putida was determined and refined to 2.1A. The structure shows the six subunits arranged as a trimer of dimers and definitely disproves previous reports that the enzyme has an octameric quaternary structure. Each monomer consists of a central, four-stranded, parallel beta-sheet flanked by two alpha-helices on both sides of the beta-sheet. This topology is unique within the superfamily of amidohydrolases. Moreover, creatininase possesses a novel fold with no close structural relatives within the Protein Data Bank. Each creatininase monomer contains a binuclear zinc centre near the C termini of the beta-strands and the N termini of the main alpha-helices. These zinc ions indicate the location of the active site unambiguously. The active site is entirely buried and is not accessible from the solution without movement of parts of the protein. The two zinc ions are bridged by a water molecule and by an aspartate residue, which acts as a bidentate ligand. They differ from each other in the number and the spatial arrangement of their ligands. One of them is tetrahedrally and the other trigonal-bipyramidally ligated. Using two water molecules of the first coordination sphere as anchor points, a creatinine-water adduct resembling the transition state of the hydrolysation reaction was modelled into the active site. The resulting complex in combination with structural comparisons with other amidohydrolases enabled us to identify the most probable candidate for the catalytic base and to suggest a putative reaction mechanism. Surprisingly these structural comparisons revealed a similarity in the active-site arrangement between creatininase and the hydantoinase-like cyclic amidohydrolases that was unexpected, given the completely unrelated primary and tertiary structures. In particular, the zinc-bridging aspartate residue of creatininase is a spatially and functionally analogue to a carboxylated lysine residue found in dihydroorotase and the hydantoinases. Hence, creatininase and the hydantoinase-like cyclic amidohydrolases represent a further example of convergent evolution within the enzyme class of hydrolases.

-	~~{{STRUCTURE_1q3k\| PDB=1q3k \| SCENE= }}~~	+	Crystal structure of creatininase from Pseudomonas putida: a novel fold and a case of convergent evolution.,Beuth B, Niefind K, Schomburg D J Mol Biol. 2003 Sep 5;332(1):287-301. PMID:12946365<ref>PMID:12946365</ref>

-	~~===Crystal structure~~ of ~~creatinine amidohydrolase (creatininase)===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_12946365}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1q3k]] is a 6 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Pseudomonas_putida Pseudomonas putida]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1Q3K OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:012946365<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Creatininase]]		[[Category: Creatininase]]
	[[Category: Pseudomonas putida]]		[[Category: Pseudomonas putida]]

OCA: Protected "1q3k" [edit=sysop:move=sysop]

OCA — Wed, 02 Jan 2013 10:06:12 GMT

Protected "1q3k" [edit=sysop:move=sysop]

←Older revision

Revision as of 10:06, 2 January 2013

OCA at 10:06, 2 January 2013

OCA — Wed, 02 Jan 2013 10:06:09 GMT

←Older revision		Revision as of 10:06, 2 January 2013
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-	{{Seed}}
	[[Image:1q3k.png\|left\|200px]]		[[Image:1q3k.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1q3k", 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_1q3k\| PDB=1q3k \| SCENE= }}		{{STRUCTURE_1q3k\| PDB=1q3k \| SCENE= }}

	===Crystal structure of creatinine amidohydrolase (creatininase)===		===Crystal structure of creatinine amidohydrolase (creatininase)===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_12946365}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 12946365 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_12946365}}		{{ABSTRACT_PUBMED_12946365}}

	==About this Structure==		==About this Structure==
-	~~1Q3K~~ is a 6 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Pseudomonas_putida Pseudomonas putida]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Q3K OCA].	+	[[1q3k]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseudomonas_putida Pseudomonas putida]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Q3K OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~12946365~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:012946365</ref><references group="xtra"/>
	[[Category: Creatininase]]		[[Category: Creatininase]]
	[[Category: Pseudomonas putida]]		[[Category: Pseudomonas putida]]
Line 30:		Line 18:
	[[Category: Schomburg, D.]]		[[Category: Schomburg, D.]]
	[[Category: Alpha-beta-fold]]		[[Category: Alpha-beta-fold]]
-		+	[[Category: Hydrolase]]
-	~~''Page seeded by~~ [~~http~~:~~//oca.weizmann.ac.il/oca OCA~~ ] ~~on Tue Feb 17 15:11:27 2009''~~	+