1h7f - Revision history

OCA at 08:54, 9 May 2024

OCA — Thu, 09 May 2024 08:54:22 GMT

←Older revision		Revision as of 08:54, 9 May 2024
Line 20:		Line 20:
	</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=1h7f 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=1h7f ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The enzyme CMP-Kdo synthetase (CKS) catalyzes the activation of the sugar Kdo (2-keto-3-deoxy-manno-octonic acid) by forming a monophosphate diester. CKS is a pharmaceutical target because CMP-Kdo is used in the biosynthesis of lipopolysaccharides that are vital for Gram-negative bacteria. We have refined the structure of the unligated capsule-specific CKS from Escherichia coli at 1.8 A resolution (1 A=0.1 nm) and we have established the structures of its complexes with the substrate CTP, with CDP and CMP as well as with the product analog CMP-NeuAc (CMP-sialate) by X-ray diffraction analyses at resolutions between 2.1 A and 2.5 A. The N-terminal domains of the dimeric enzyme bind CTP in a peculiar nucleotide-binding fold, whereas the C-terminal domains form the dimer interface. The observed binding geometries together with the amino acid variabilities during evolution and the locations of a putative Mg(2+) and of a very strongly bound water molecule suggest a pathway for the catalysis. The N-terminal domain shows sequence homology with the CMP-NeuAc synthetases. Moreover, the chain fold and the substrate-binding position of CKS resemble those of other enzymes processing nucleotide-sugars.
		+
		+	The structure of CMP:2-keto-3-deoxy-manno-octonic acid synthetase and of its complexes with substrates and substrate analogs.,Jelakovic S, Schulz GE J Mol Biol. 2001 Sep 7;312(1):143-55. PMID:11545592<ref>PMID:11545592</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 1h7f" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 11:29, 27 March 2024

OCA — Wed, 27 Mar 2024 11:29:01 GMT

←Older revision		Revision as of 11:29, 27 March 2024
Line 3:		Line 3:
	<StructureSection load='1h7f' size='340' side='right'caption='[[1h7f]], [[Resolution\|resolution]] 2.12Å' scene=''>		<StructureSection load='1h7f' size='340' side='right'caption='[[1h7f]], [[Resolution\|resolution]] 2.12Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1h7f]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"bacillus_coli"_migula_1895 "bacillus~~ coli~~" migula 1895~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1H7F OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1H7F FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1h7f]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1H7F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1H7F FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=C5P:CYTIDINE~~-~~5-MONOPHOSPHATE'>C5P</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]] 2.12Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1h6j\|1h6j]]~~, [[~~1h7e~~\|~~1h7e]], [[1h7g\|1h7g]], [[1h7h\|1h7h~~]]</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=C5P:CYTIDINE-5-MONOPHOSPHATE'>C5P</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>KPSU ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~562~~ "~~Bacillus coli~~" ~~Migula 1895])</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=1h7f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1h7f OCA], [https://pdbe.org/1h7f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1h7f RCSB], [https://www.ebi.ac.uk/pdbsum/1h7f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1h7f ProSAT]</span></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>[http://en.wikipedia.org/wiki/3-deoxy-manno-octulosonate_cytidylyltransferase 3-deoxy-manno-octulosonate cytidylyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.38 2.7.7.38] </~~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=1h7f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1h7f OCA], [~~http~~://pdbe.org/1h7f PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1h7f RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1h7f PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1h7f ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/KPSU5_ECOLX KPSU5_ECOLX]] Activates KDO (a required 8-carbon sugar) for incorporation into bacterial lipopolysaccharide in Gram-negative bacteria.	+	[https://www.uniprot.org/uniprot/KPSU5_ECOLX KPSU5_ECOLX] Activates KDO (a required 8-carbon sugar) for incorporation into bacterial lipopolysaccharide in Gram-negative bacteria.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 22:		Line 20:
	</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=1h7f 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=1h7f ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The enzyme CMP-Kdo synthetase (CKS) catalyzes the activation of the sugar Kdo (2-keto-3-deoxy-manno-octonic acid) by forming a monophosphate diester. CKS is a pharmaceutical target because CMP-Kdo is used in the biosynthesis of lipopolysaccharides that are vital for Gram-negative bacteria. We have refined the structure of the unligated capsule-specific CKS from Escherichia coli at 1.8 A resolution (1 A=0.1 nm) and we have established the structures of its complexes with the substrate CTP, with CDP and CMP as well as with the product analog CMP-NeuAc (CMP-sialate) by X-ray diffraction analyses at resolutions between 2.1 A and 2.5 A. The N-terminal domains of the dimeric enzyme bind CTP in a peculiar nucleotide-binding fold, whereas the C-terminal domains form the dimer interface. The observed binding geometries together with the amino acid variabilities during evolution and the locations of a putative Mg(2+) and of a very strongly bound water molecule suggest a pathway for the catalysis. The N-terminal domain shows sequence homology with the CMP-NeuAc synthetases. Moreover, the chain fold and the substrate-binding position of CKS resemble those of other enzymes processing nucleotide-sugars.
-
-	The structure of CMP:2-keto-3-deoxy-manno-octonic acid synthetase and of its complexes with substrates and substrate analogs.,Jelakovic S, Schulz GE J Mol Biol. 2001 Sep 7;312(1):143-55. PMID:11545592<ref>PMID:11545592</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1h7f" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus~~ coli ~~migula 1895]]~~	+	[[Category: Escherichia coli]]
-	~~[[Category: 3-deoxy-manno-octulosonate cytidylyltransferase~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Jelakovic, S]]	+	[[Category: Jelakovic S]]
-	[[Category: Schulz~~, G E]]~~	+	[[Category: Schulz GE]]
-	~~[[Category: Cmp-kdo synthetase]]~~	+
-	~~[[Category: Lipopolysaccharide biosynthesis]]~~	+
-	~~[[Category: Nucleoside monophosphate glycoside]]~~	+
-	~~[[Category: Nucleotidyltransferase]]~~	+
-	~~[[Category: Sugar-activating enzyme~~]]	+

OCA at 10:30, 18 November 2020

OCA — Wed, 18 Nov 2020 10:30:59 GMT

←Older revision		Revision as of 10:30, 18 November 2020
Line 1:		Line 1:

	==The structure of CMP:2-keto-3-deoxy-manno-octonic acid synthetase and of its complexes with substrates and substrate analogues, CMP complex==		==The structure of CMP:2-keto-3-deoxy-manno-octonic acid synthetase and of its complexes with substrates and substrate analogues, CMP complex==
-	<StructureSection load='1h7f' size='340' side='right' caption='[[1h7f]], [[Resolution\|resolution]] 2.12Å' scene=''>	+	<StructureSection load='1h7f' size='340' side='right'caption='[[1h7f]], [[Resolution\|resolution]] 2.12Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1h7f]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1H7F OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1H7F FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1h7f]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1H7F OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1H7F FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=C5P:CYTIDINE-5-MONOPHOSPHATE'>C5P</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=C5P:CYTIDINE-5-MONOPHOSPHATE'>C5P</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1h6j\|1h6j]], [[1h7e\|1h7e]], [[1h7g\|1h7g]], [[1h7h\|1h7h]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1h6j\|1h6j]], [[1h7e\|1h7e]], [[1h7g\|1h7g]], [[1h7h\|1h7h]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">KPSU ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">KPSU ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/3-deoxy-manno-octulosonate_cytidylyltransferase 3-deoxy-manno-octulosonate cytidylyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.38 2.7.7.38] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/3-deoxy-manno-octulosonate_cytidylyltransferase 3-deoxy-manno-octulosonate cytidylyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.38 2.7.7.38] </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=1h7f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1h7f OCA], [http://pdbe.org/1h7f PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1h7f RCSB], [http://www.ebi.ac.uk/pdbsum/1h7f PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1h7f 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=1h7f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1h7f OCA], [http://pdbe.org/1h7f PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1h7f RCSB], [http://www.ebi.ac.uk/pdbsum/1h7f PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1h7f ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 37:		Line 37:
	[[Category: Bacillus coli migula 1895]]		[[Category: Bacillus coli migula 1895]]
	[[Category: 3-deoxy-manno-octulosonate cytidylyltransferase]]		[[Category: 3-deoxy-manno-octulosonate cytidylyltransferase]]
		+	[[Category: Large Structures]]
	[[Category: Jelakovic, S]]		[[Category: Jelakovic, S]]
	[[Category: Schulz, G E]]		[[Category: Schulz, G E]]

OCA at 09:20, 10 January 2018

OCA — Wed, 10 Jan 2018 09:20:52 GMT

←Older revision		Revision as of 09:20, 10 January 2018
Line 1:		Line 1:
-	==~~THE STRUCTURE OF~~ CMP:2-~~KETO~~-3-~~DEOXY~~-~~MANNO~~-~~OCTONIC ACID SYNTHETASE AND OF ITS COMPLEXES WITH SUBSTRATES AND SUBSTRATE ANALOGUES~~, CMP ~~COMPLEX~~==	+
		+	==The structure of CMP:2-keto-3-deoxy-manno-octonic acid synthetase and of its complexes with substrates and substrate analogues, CMP complex==
	<StructureSection load='1h7f' size='340' side='right' caption='[[1h7f]], [[Resolution\|resolution]] 2.12Å' scene=''>		<StructureSection load='1h7f' size='340' side='right' caption='[[1h7f]], [[Resolution\|resolution]] 2.12Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
Line 7:		Line 8:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">KPSU ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">KPSU ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/3-deoxy-manno-octulosonate_cytidylyltransferase 3-deoxy-manno-octulosonate cytidylyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.38 2.7.7.38] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/3-deoxy-manno-octulosonate_cytidylyltransferase 3-deoxy-manno-octulosonate cytidylyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.38 2.7.7.38] </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=1h7f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1h7f OCA], [http://pdbe.org/1h7f PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1h7f RCSB], [http://www.ebi.ac.uk/pdbsum/1h7f 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=1h7f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1h7f OCA], [http://pdbe.org/1h7f PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1h7f RCSB], [http://www.ebi.ac.uk/pdbsum/1h7f PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1h7f ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 15:		Line 16:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/h7/1h7f_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/h7/1h7f_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 08:25, 10 February 2016

OCA — Wed, 10 Feb 2016 08:25:53 GMT

←Older revision		Revision as of 08:25, 10 February 2016
Line 19:		Line 19:
	<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=1h7f ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 07:04, 11 September 2015

OCA — Fri, 11 Sep 2015 07:04:50 GMT

←Older revision		Revision as of 07:04, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='1h7f' size='340' side='right' caption='[[1h7f]], [[Resolution\|resolution]] 2.12Å' scene=''>		<StructureSection load='1h7f' size='340' side='right' caption='[[1h7f]], [[Resolution\|resolution]] 2.12Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1h7f]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Escherichia_coli Escherichia~~ coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1H7F OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1H7F FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1h7f]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1H7F OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1H7F FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=C5P:CYTIDINE-5-MONOPHOSPHATE'>C5P</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=C5P:CYTIDINE-5-MONOPHOSPHATE'>C5P</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1h6j\|1h6j]], [[1h7e\|1h7e]], [[1h7g\|1h7g]], [[1h7h\|1h7h]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1h6j\|1h6j]], [[1h7e\|1h7e]], [[1h7g\|1h7g]], [[1h7h\|1h7h]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">KPSU ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 ~~Escherichia~~ coli])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">KPSU ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/3-deoxy-manno-octulosonate_cytidylyltransferase 3-deoxy-manno-octulosonate cytidylyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.38 2.7.7.38] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/3-deoxy-manno-octulosonate_cytidylyltransferase 3-deoxy-manno-octulosonate cytidylyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.38 2.7.7.38] </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=1h7f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1h7f OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1h7f RCSB], [http://www.ebi.ac.uk/pdbsum/1h7f 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=1h7f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1h7f OCA], [http://pdbe.org/1h7f PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1h7f RCSB], [http://www.ebi.ac.uk/pdbsum/1h7f PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/KPSU5_ECOLX KPSU5_ECOLX]] Activates KDO (a required 8-carbon sugar) for incorporation into bacterial lipopolysaccharide in Gram-negative bacteria.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 27:		Line 29:
	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 1h7f" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacillus coli migula 1895]]
	[[Category: 3-deoxy-manno-octulosonate cytidylyltransferase]]		[[Category: 3-deoxy-manno-octulosonate cytidylyltransferase]]
-	[[Category: Escherichia coli]]
	[[Category: Jelakovic, S]]		[[Category: Jelakovic, S]]
	[[Category: Schulz, G E]]		[[Category: Schulz, G E]]

OCA at 21:26, 22 December 2014

OCA — Mon, 22 Dec 2014 21:26:16 GMT

OCA at 15:38, 29 September 2014

OCA — Mon, 29 Sep 2014 15:38:16 GMT

←Older revision		Revision as of 15:38, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1h7f.~~png~~\|~~left~~\|200px]]	+	==THE STRUCTURE OF CMP:2-KETO-3-DEOXY-MANNO-OCTONIC ACID SYNTHETASE AND OF ITS COMPLEXES WITH SUBSTRATES AND SUBSTRATE ANALOGUES, CMP COMPLEX==
		+	<StructureSection load='1h7f' size='340' side='right' caption='[[1h7f]], [[Resolution\|resolution]] 2.12Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1h7f]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1H7F OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1H7F FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=C5P:CYTIDINE-5-MONOPHOSPHATE'>C5P</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1h6j\|1h6j]], [[1h7e\|1h7e]], [[1h7g\|1h7g]], [[1h7h\|1h7h]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">KPSU ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/3-deoxy-manno-octulosonate_cytidylyltransferase 3-deoxy-manno-octulosonate cytidylyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.38 2.7.7.38] </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=1h7f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1h7f OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1h7f RCSB], [http://www.ebi.ac.uk/pdbsum/1h7f 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/h7/1h7f_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 ==
		+	The enzyme CMP-Kdo synthetase (CKS) catalyzes the activation of the sugar Kdo (2-keto-3-deoxy-manno-octonic acid) by forming a monophosphate diester. CKS is a pharmaceutical target because CMP-Kdo is used in the biosynthesis of lipopolysaccharides that are vital for Gram-negative bacteria. We have refined the structure of the unligated capsule-specific CKS from Escherichia coli at 1.8 A resolution (1 A=0.1 nm) and we have established the structures of its complexes with the substrate CTP, with CDP and CMP as well as with the product analog CMP-NeuAc (CMP-sialate) by X-ray diffraction analyses at resolutions between 2.1 A and 2.5 A. The N-terminal domains of the dimeric enzyme bind CTP in a peculiar nucleotide-binding fold, whereas the C-terminal domains form the dimer interface. The observed binding geometries together with the amino acid variabilities during evolution and the locations of a putative Mg(2+) and of a very strongly bound water molecule suggest a pathway for the catalysis. The N-terminal domain shows sequence homology with the CMP-NeuAc synthetases. Moreover, the chain fold and the substrate-binding position of CKS resemble those of other enzymes processing nucleotide-sugars.

-	~~{{STRUCTURE_1h7f\| PDB=1h7f \| SCENE= }}~~	+	The structure of CMP:2-keto-3-deoxy-manno-octonic acid synthetase and of its complexes with substrates and substrate analogs.,Jelakovic S, Schulz GE J Mol Biol. 2001 Sep 7;312(1):143-55. PMID:11545592<ref>PMID:11545592</ref>

-	~~===THE STRUCTURE OF CMP:2-KETO-3-DEOXY-MANNO-OCTONIC ACID SYNTHETASE AND OF ITS COMPLEXES WITH SUBSTRATES AND SUBSTRATE ANALOGUES~~, ~~CMP COMPLEX===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_11545592}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1h7f]] is~~ a ~~2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Escherichia_coli Escherichia coli]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1H7F OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:011545592<~~/~~ref~~><~~ref group="xtra">PMID:008706906</ref><references group="xtra"~~/>	+
	[[Category: 3-deoxy-manno-octulosonate cytidylyltransferase]]		[[Category: 3-deoxy-manno-octulosonate cytidylyltransferase]]
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]

OCA at 09:31, 16 January 2013

OCA — Wed, 16 Jan 2013 09:31:08 GMT

←Older revision		Revision as of 09:31, 16 January 2013
Line 1:		Line 1:
	[[Image:1h7f.png\|left\|200px]]		[[Image:1h7f.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1h7f", 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_1h7f\| PDB=1h7f \| SCENE= }}		{{STRUCTURE_1h7f\| PDB=1h7f \| SCENE= }}

	===THE STRUCTURE OF CMP:2-KETO-3-DEOXY-MANNO-OCTONIC ACID SYNTHETASE AND OF ITS COMPLEXES WITH SUBSTRATES AND SUBSTRATE ANALOGUES, CMP COMPLEX===		===THE STRUCTURE OF CMP:2-KETO-3-DEOXY-MANNO-OCTONIC ACID SYNTHETASE AND OF ITS COMPLEXES WITH SUBSTRATES AND SUBSTRATE ANALOGUES, CMP COMPLEX===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_11545592}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 11545592 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_11545592}}		{{ABSTRACT_PUBMED_11545592}}

Line 22:		Line 11:

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~11545592~~</ref><ref group="xtra">PMID:~~8706906~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:011545592</ref><ref group="xtra">PMID:008706906</ref><references group="xtra"/>
	[[Category: 3-deoxy-manno-octulosonate cytidylyltransferase]]		[[Category: 3-deoxy-manno-octulosonate cytidylyltransferase]]
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]

OCA: Protected "1h7f" [edit=sysop:move=sysop]

OCA — Tue, 15 Mar 2011 00:02:22 GMT

Protected "1h7f" [edit=sysop:move=sysop]

←Older revision

Revision as of 00:02, 15 March 2011

←Older revision		Revision as of 21:26, 22 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1h7f]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1H7F OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1H7F FirstGlance]. <br>		<table><tr><td colspan='2'>[[1h7f]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1H7F OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1H7F FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=C5P:CYTIDINE-5-MONOPHOSPHATE'>C5P</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=C5P:CYTIDINE-5-MONOPHOSPHATE'>C5P</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1h6j\|1h6j]], [[1h7e\|1h7e]], [[1h7g\|1h7g]], [[1h7h\|1h7h]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1h6j\|1h6j]], [[1h7e\|1h7e]], [[1h7g\|1h7g]], [[1h7h\|1h7h]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">KPSU ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">KPSU ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/3-deoxy-manno-octulosonate_cytidylyltransferase 3-deoxy-manno-octulosonate cytidylyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.38 2.7.7.38] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/3-deoxy-manno-octulosonate_cytidylyltransferase 3-deoxy-manno-octulosonate cytidylyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.38 2.7.7.38] </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=1h7f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1h7f OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1h7f RCSB], [http://www.ebi.ac.uk/pdbsum/1h7f 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=1h7f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1h7f OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1h7f RCSB], [http://www.ebi.ac.uk/pdbsum/1h7f PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 33:		Line 33:
	[[Category: 3-deoxy-manno-octulosonate cytidylyltransferase]]		[[Category: 3-deoxy-manno-octulosonate cytidylyltransferase]]
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
-	[[Category: Jelakovic, S.]]	+	[[Category: Jelakovic, S]]
-	[[Category: Schulz, G E.]]	+	[[Category: Schulz, G E]]
	[[Category: Cmp-kdo synthetase]]		[[Category: Cmp-kdo synthetase]]
	[[Category: Lipopolysaccharide biosynthesis]]		[[Category: Lipopolysaccharide biosynthesis]]