4e22 - Revision history

OCA at 11:01, 1 March 2024

2024-03-01T11:01:25Z

← Older revision		Revision as of 11:01, 1 March 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4e22]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Yersinia_pseudotuberculosis_YPIII Yersinia pseudotuberculosis YPIII]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4E22 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4E22 FirstGlance]. <br>		<table><tr><td colspan='2'>[[4e22]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Yersinia_pseudotuberculosis_YPIII Yersinia pseudotuberculosis YPIII]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4E22 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4E22 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.323Å</td></tr>
			<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=4e22 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e22 OCA], [https://pdbe.org/4e22 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4e22 RCSB], [https://www.ebi.ac.uk/pdbsum/4e22 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4e22 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=4e22 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e22 OCA], [https://pdbe.org/4e22 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4e22 RCSB], [https://www.ebi.ac.uk/pdbsum/4e22 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4e22 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[https://www.uniprot.org/uniprot/KCY_YERPY KCY_YERPY]]		[https://www.uniprot.org/uniprot/KCY_YERPY KCY_YERPY]
	~~<div style="background-color:#fffaf0;">~~
	~~== Publication Abstract from PubMed ==~~
	The need for new antibiotics has become pressing in light of the emergence of antibiotic-resistant strains of human pathogens. Yersinia pestis, the causative agent of plague, is a public health threat and also an agent of concern in biodefence. It is a recently emerged clonal derivative of the enteric pathogen Yersinia pseudotuberculosis. Previously, we developed a bioinformatic approach to identify proteins that may be suitable targets for antimicrobial therapy and in particular for the treatment of plague. One such target was cytidine monophosphate (CMP) kinase, which is an essential gene in some organisms. Previously, we had thought CMP kinase was essential for Y. pseudotuberculosis, but by modification of the mutagenesis approach, we report here the production and characterization of a Deltacmk mutant. The isogenic mutant had a growth defect relative to the parental strain, and was highly attenuated in mice. We have also elucidated the structure of the CMP kinase to 2.32 A, and identified three key residues in the active site that are essential for activity of the enzyme. These findings will have implications for the development of novel CMP kinase inhibitors for therapeutic use.

	Structure and function of cytidine monophosphate kinase from Yersinia pseudotuberculosis, essential for virulence but not for survival.,Walker NJ, Clark EA, Ford DC, Bullifent HL, McAlister EV, Duffield ML, Acharya KR, Oyston PC Open Biol. 2012 Dec 5;2(12):120142. doi: 10.1098/rsob.120142. Print 2012. PMID:23271832<ref>PMID:23271832</ref>

	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~
	~~</div>~~
	~~<div class="pdbe-citations 4e22" style="background-color:#fffaf0;"></div>~~

	==See Also==		==See Also==
	*[[Cytidine monophosphate kinase\|Cytidine monophosphate kinase]]		*[[Cytidine monophosphate kinase\|Cytidine monophosphate kinase]]
	~~== References ==~~
	~~<references/>~~
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 06:45, 28 September 2022

2022-09-28T06:45:45Z

← Older revision		Revision as of 06:45, 28 September 2022
Line 1:		Line 1:

	==Structure of cytidine monophosphate kinase from Yersinia pseudotuberculosis==		==Structure of cytidine monophosphate kinase from Yersinia pseudotuberculosis==
	<StructureSection load='4e22' size='340' side='right' caption='[[4e22]], [[Resolution\|resolution]] 2.32Å' scene=''>		<StructureSection load='4e22' size='340' side='right'caption='[[4e22]], [[Resolution\|resolution]] 2.32Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4e22]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Yerpy Yerpy~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4E22 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4E22 FirstGlance]. <br>		<table><tr><td colspan='2'>[[4e22]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Yersinia_pseudotuberculosis_YPIII Yersinia pseudotuberculosis YPIII]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4E22 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4E22 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene~~></td></tr>~~		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">cmk, YPK_2669 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=502800 YERPY])</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=4e22 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e22 OCA], [https://pdbe.org/4e22 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4e22 RCSB], [https://www.ebi.ac.uk/pdbsum/4e22 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4e22 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/(d)CMP_kinase (d)CMP kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.25 2.7.4.25] </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=4e22 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e22 OCA], [~~http~~://pdbe.org/4e22 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4e22 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4e22 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4e22 ProSAT]</span></td></tr>
	</table>		</table>
			== Function ==
			[[https://www.uniprot.org/uniprot/KCY_YERPY KCY_YERPY]]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 25:		Line 25:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Yerpy~~]]		[[Category: Large Structures]]
	[[Category: ~~Acharya, K R~~]]		[[Category: Yersinia pseudotuberculosis YPIII]]
	[[Category: ~~Clark, E A~~]]		[[Category: Acharya KR]]
	[[Category: ~~Cmp/atp binding]]~~		[[Category: Clark EA]]
	~~[[Category: P-loop]]~~
	~~[[Category: Transferase~~]]

OCA at 02:40, 11 December 2016

2016-12-11T02:40:34Z

← Older revision		Revision as of 02:40, 11 December 2016
Line 1:		Line 1:

	==Structure of cytidine monophosphate kinase from Yersinia pseudotuberculosis==		==Structure of cytidine monophosphate kinase from Yersinia pseudotuberculosis==
	<StructureSection load='4e22' size='340' side='right' caption='[[4e22]], [[Resolution\|resolution]] 2.32Å' scene=''>		<StructureSection load='4e22' size='340' side='right' caption='[[4e22]], [[Resolution\|resolution]] 2.32Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4e22]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Yersinia_pseudotuberculosis_ypiii Yersinia pseudotuberculosis ypiii~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4E22 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4E22 FirstGlance]. <br>		<table><tr><td colspan='2'>[[4e22]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Yerpy Yerpy]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4E22 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4E22 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">cmk, YPK_2669 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=502800 ~~Yersinia pseudotuberculosis YPIII~~])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">cmk, YPK_2669 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=502800 YERPY])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/(d)CMP_kinase (d)CMP kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.25 2.7.4.25] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/(d)CMP_kinase (d)CMP kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.25 2.7.4.25] </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=4e22 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e22 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4e22 RCSB], [http://www.ebi.ac.uk/pdbsum/4e22 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=4e22 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e22 OCA], [http://pdbe.org/4e22 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4e22 RCSB], [http://www.ebi.ac.uk/pdbsum/4e22 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4e22 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 16:		Line 17:
	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 4e22" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 23:		Line 25:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Yersinia pseudotuberculosis ypiii~~]]		[[Category: Yerpy]]
	[[Category: Acharya, K R]]		[[Category: Acharya, K R]]
	[[Category: Clark, E A]]		[[Category: Clark, E A]]

OCA at 14:28, 9 December 2014

2014-12-09T14:28:34Z

← Older revision		Revision as of 14:28, 9 December 2014
Line 1:		Line 1:
	[[~~Image~~:~~4e22~~.~~png~~\|~~left~~\|~~200px~~]]		==Structure of cytidine monophosphate kinase from Yersinia pseudotuberculosis==
			<StructureSection load='4e22' size='340' side='right' caption='[[4e22]], [[Resolution\|resolution]] 2.32Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[4e22]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Yersinia_pseudotuberculosis_ypiii Yersinia pseudotuberculosis ypiii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4E22 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4E22 FirstGlance]. <br>
			</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
			<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">cmk, YPK_2669 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=502800 Yersinia pseudotuberculosis YPIII])</td></tr>
			<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/(d)CMP_kinase (d)CMP kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.25 2.7.4.25] </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=4e22 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e22 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4e22 RCSB], [http://www.ebi.ac.uk/pdbsum/4e22 PDBsum]</span></td></tr>
			</table>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			The need for new antibiotics has become pressing in light of the emergence of antibiotic-resistant strains of human pathogens. Yersinia pestis, the causative agent of plague, is a public health threat and also an agent of concern in biodefence. It is a recently emerged clonal derivative of the enteric pathogen Yersinia pseudotuberculosis. Previously, we developed a bioinformatic approach to identify proteins that may be suitable targets for antimicrobial therapy and in particular for the treatment of plague. One such target was cytidine monophosphate (CMP) kinase, which is an essential gene in some organisms. Previously, we had thought CMP kinase was essential for Y. pseudotuberculosis, but by modification of the mutagenesis approach, we report here the production and characterization of a Deltacmk mutant. The isogenic mutant had a growth defect relative to the parental strain, and was highly attenuated in mice. We have also elucidated the structure of the CMP kinase to 2.32 A, and identified three key residues in the active site that are essential for activity of the enzyme. These findings will have implications for the development of novel CMP kinase inhibitors for therapeutic use.

	~~{{STRUCTURE_4e22\| PDB=4e22 \| SCENE= }}~~		Structure and function of cytidine monophosphate kinase from Yersinia pseudotuberculosis, essential for virulence but not for survival.,Walker NJ, Clark EA, Ford DC, Bullifent HL, McAlister EV, Duffield ML, Acharya KR, Oyston PC Open Biol. 2012 Dec 5;2(12):120142. doi: 10.1098/rsob.120142. Print 2012. PMID:23271832<ref>PMID:23271832</ref>

	~~===Structure~~ of ~~cytidine monophosphate kinase from Yersinia pseudotuberculosis===~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>

	~~{{ABSTRACT_PUBMED_23271832}}~~		==See Also==
			*[[Cytidine monophosphate kinase\|Cytidine monophosphate kinase]]
	==~~About this Structure~~==		== References ==
	[[~~4e22~~]] ~~is a 1 chain structure with sequence from [http:~~//en.wikipedia.org/wiki/Yersinia_pseudotuberculosis_ypiii Yersinia pseudotuberculosis ypiii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4E22 OCA].		<references/>
			__TOC__
			</StructureSection>
	[[Category: Yersinia pseudotuberculosis ypiii]]		[[Category: Yersinia pseudotuberculosis ypiii]]
	[[Category: Acharya, K R.]]		[[Category: Acharya, K R]]
	[[Category: Clark, E A.]]		[[Category: Clark, E A]]
	[[Category: Cmp/atp binding]]		[[Category: Cmp/atp binding]]
	[[Category: P-loop]]		[[Category: P-loop]]
	[[Category: Transferase]]		[[Category: Transferase]]

OCA at 08:47, 16 January 2013

2013-01-16T08:47:42Z

← Older revision		Revision as of 08:47, 16 January 2013
Line 1:		Line 1:
	[[Image:4e22.~~jpg~~\|left\|200px]]		[[Image:4e22.png\|left\|200px]]

	{{STRUCTURE_4e22\| PDB=4e22 \| SCENE= }}		{{STRUCTURE_4e22\| PDB=4e22 \| SCENE= }}
Line 5:		Line 5:
	===Structure of cytidine monophosphate kinase from Yersinia pseudotuberculosis===		===Structure of cytidine monophosphate kinase from Yersinia pseudotuberculosis===

			{{ABSTRACT_PUBMED_23271832}}

	==About this Structure==		==About this Structure==

OCA at 11:35, 19 December 2012

2012-12-19T11:35:28Z

← Older revision		Revision as of 11:35, 19 December 2012
Line 1:		Line 1:
	~~'''Unreleased structure'''~~		[[Image:4e22.jpg\|left\|200px]]

	~~The entry~~ 4e22 ~~is ON HOLD~~ ~~until Paper Publication~~		{{STRUCTURE_4e22\| PDB=4e22 \| SCENE= }}

	~~Authors: Clark, E.A., Acharya, K.R.~~		===Structure of cytidine monophosphate kinase from Yersinia pseudotuberculosis===

	~~Description~~: ~~Structure of cytidine monophosphate kinase~~ from Yersinia pseudotuberculosis
			==About this Structure==
			[[4e22]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Yersinia_pseudotuberculosis_ypiii Yersinia pseudotuberculosis ypiii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4E22 OCA].
			[[Category: Yersinia pseudotuberculosis ypiii]]
			[[Category: Acharya, K R.]]
			[[Category: Clark, E A.]]
			[[Category: Cmp/atp binding]]
			[[Category: P-loop]]
			[[Category: Transferase]]

OCA at 07:14, 21 March 2012

2012-03-21T07:14:47Z

← Older revision		Revision as of 07:14, 21 March 2012
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

	The entry 4e22 is ON HOLD		The entry 4e22 is ON HOLD until Paper Publication

	Authors: Clark, E.A., Acharya, K.R.		Authors: Clark, E.A., Acharya, K.R.

	Description: Structure of cytidine monophosphate kinase from Yersinia pseudotuberculosis		Description: Structure of cytidine monophosphate kinase from Yersinia pseudotuberculosis

OCA: Protected "4e22" [edit=sysop:move=sysop]

2012-03-14T06:16:39Z

Protected "4e22" [edit=sysop:move=sysop]

← Older revision	Revision as of 06:16, 14 March 2012
(No difference)

OCA: New page: '''Unreleased structure''' The entry 4e22 is ON HOLD Authors: Clark, E.A., Acharya, K.R. Description: Structure of cytidine monophosphate kinase from Yersinia pseudotuberculosis

2012-03-14T06:16:38Z

New page: '''Unreleased structure''' The entry 4e22 is ON HOLD Authors: Clark, E.A., Acharya, K.R. Description: Structure of cytidine monophosphate kinase from Yersinia pseudotuberculosis

New page

'''Unreleased structure'''

The entry 4e22 is ON HOLD

Authors: Clark, E.A., Acharya, K.R.

Description: Structure of cytidine monophosphate kinase from Yersinia pseudotuberculosis