1p4s - Revision history

OCA at 08:57, 22 May 2024

OCA — Wed, 22 May 2024 08:57:48 GMT

←Older revision		Revision as of 08:57, 22 May 2024
Line 19:		Line 19:
	</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=1p4s 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=1p4s ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Tuberculosis is the leading cause of death worldwide from a single infectious disease. Search of new therapeutic tools requires the discovery and biochemical characterization of new potential targets among the bacterial proteins essential for the survival and virulence. Among them are the nucleoside monophosphate kinases, involved in the nucleotide biosynthesis. In this work, we determined the solution structure of adenylate kinase (AK) from Mycobacterium tuberculosis (AKmt), a protein of 181 residues that was found to be essential for bacterial survival. The structure was calculated by a simulated annealing protocol and energy minimization using experimental restraints, collected by nuclear magnetic resonance spectroscopy. The final, well-defined 20 NMR structures show an average root-mean-square deviation of 0.77 A for the backbone atoms in regular secondary structure segments. The protein has a central CORE domain, composed of a five-stranded parallel beta-sheet surrounded by seven alpha-helices, and two peripheral domains, AMPbd and LID. As compared to other crystallographic structures of free form AKs, AKmt is more compact, with the AMP(bd) domain closer to the CORE of the protein. Analysis of the (15)N relaxation data enabled us to obtain the global rotational correlation time (9.19 ns) and the generalized order parameters (S(2)) of amide vectors along the polypeptide sequence. The protein exhibits restricted movements on a picosecond to nanosecond time scale in the secondary structural regions with amplitudes characterized by an average S(2)() value of 0.87. The loops beta1/alpha1, beta2/alpha2, alpha2/alpha3, alpha3/alpha4, alpha4/beta3, beta3/alpha5, alpha6/alpha7 (LID), alpha7/alpha8, and beta5/alpha9 exhibit rapid fluctuations with enhanced amplitudes. These structural and dynamic features of AKmt may be related to its low catalytic activity that is 10-fold lower than in their eukaryote counterparts.
		+
		+	Structural and dynamic studies on ligand-free adenylate kinase from Mycobacterium tuberculosis revealed a closed conformation that can be related to the reduced catalytic activity.,Miron S, Munier-Lehmann H, Craescu CT Biochemistry. 2004 Jan 13;43(1):67-77. PMID:14705932<ref>PMID:14705932</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 1p4s" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==

OCA at 05:52, 17 April 2024

OCA — Wed, 17 Apr 2024 05:52:46 GMT

←Older revision		Revision as of 05:52, 17 April 2024
Line 1:		Line 1:

	==Solution structure of Mycobacterium tuberculosis adenylate kinase==		==Solution structure of Mycobacterium tuberculosis adenylate kinase==
-	<StructureSection load='1p4s' size='340' side='right'caption='[[1p4s~~]], [[NMR_Ensembles_of_Models \| 20 NMR models~~]]' scene=''>	+	<StructureSection load='1p4s' size='340' side='right'caption='[[1p4s]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1p4s]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"bacillus_tuberculosis"_(zopf_1883)_klein_1884 "bacillus~~ tuberculosis~~" (zopf 1883) klein 1884~~]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1P4S OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1P4S FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1p4s]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1P4S OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1P4S FirstGlance]. <br>
-	</td></tr><tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>ADK OR RV0733 OR MT0757 OR MTV041.07 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~1773~~ "~~Bacillus tuberculosis~~" ~~(Zopf 1883) Klein 1884])</td></tr>~~	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Adenylate_kinase Adenylate kinase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.3 2.7.4.3] </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=1p4s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1p4s OCA], [https://pdbe.org/1p4s PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1p4s RCSB], [https://www.ebi.ac.uk/pdbsum/1p4s PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1p4s 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=1p4s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1p4s OCA], [https://pdbe.org/1p4s PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1p4s RCSB], [https://www.ebi.ac.uk/pdbsum/1p4s PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1p4s ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/KAD_MYCTU KAD_MYCTU]] Catalyzes the reversible transfer of the terminal phosphate group between ATP and AMP. This small ubiquitous enzyme involved in the energy metabolism and nucleotide synthesis, is essential for maintenance and cell growth. Has a broad specificity for nucleoside triphosphates, being highly active with ATP or dATP as phosphate donors, and less active with GTP or UTP.<ref>PMID:10398370</ref>	+	[https://www.uniprot.org/uniprot/KAD_MYCTU KAD_MYCTU] Catalyzes the reversible transfer of the terminal phosphate group between ATP and AMP. This small ubiquitous enzyme involved in the energy metabolism and nucleotide synthesis, is essential for maintenance and cell growth. Has a broad specificity for nucleoside triphosphates, being highly active with ATP or dATP as phosphate donors, and less active with GTP or UTP.<ref>PMID:10398370</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 20:		Line 19:
	</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=1p4s 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=1p4s ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Tuberculosis is the leading cause of death worldwide from a single infectious disease. Search of new therapeutic tools requires the discovery and biochemical characterization of new potential targets among the bacterial proteins essential for the survival and virulence. Among them are the nucleoside monophosphate kinases, involved in the nucleotide biosynthesis. In this work, we determined the solution structure of adenylate kinase (AK) from Mycobacterium tuberculosis (AKmt), a protein of 181 residues that was found to be essential for bacterial survival. The structure was calculated by a simulated annealing protocol and energy minimization using experimental restraints, collected by nuclear magnetic resonance spectroscopy. The final, well-defined 20 NMR structures show an average root-mean-square deviation of 0.77 A for the backbone atoms in regular secondary structure segments. The protein has a central CORE domain, composed of a five-stranded parallel beta-sheet surrounded by seven alpha-helices, and two peripheral domains, AMPbd and LID. As compared to other crystallographic structures of free form AKs, AKmt is more compact, with the AMP(bd) domain closer to the CORE of the protein. Analysis of the (15)N relaxation data enabled us to obtain the global rotational correlation time (9.19 ns) and the generalized order parameters (S(2)) of amide vectors along the polypeptide sequence. The protein exhibits restricted movements on a picosecond to nanosecond time scale in the secondary structural regions with amplitudes characterized by an average S(2)() value of 0.87. The loops beta1/alpha1, beta2/alpha2, alpha2/alpha3, alpha3/alpha4, alpha4/beta3, beta3/alpha5, alpha6/alpha7 (LID), alpha7/alpha8, and beta5/alpha9 exhibit rapid fluctuations with enhanced amplitudes. These structural and dynamic features of AKmt may be related to its low catalytic activity that is 10-fold lower than in their eukaryote counterparts.
-
-	Structural and dynamic studies on ligand-free adenylate kinase from Mycobacterium tuberculosis revealed a closed conformation that can be related to the reduced catalytic activity.,Miron S, Munier-Lehmann H, Craescu CT Biochemistry. 2004 Jan 13;43(1):67-77. PMID:14705932<ref>PMID:14705932</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1p4s" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 36:		Line 26:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Adenylate kinase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Craescu~~, C T~~]]	+	[[Category: Mycobacterium tuberculosis]]
-	[[Category: Miron, S]]	+	[[Category: Craescu CT]]
-	[[Category: Munier-Lehmann, H]]	+	[[Category: Miron S]]
-	~~[[Category: Alpha/beta]]~~	+	[[Category: Munier-Lehmann H]]
-	~~[[Category: Transferase~~]]	+

OCA at 08:27, 23 February 2022

OCA — Wed, 23 Feb 2022 08:27:44 GMT

←Older revision		Revision as of 08:27, 23 February 2022
Line 3:		Line 3:
	<StructureSection load='1p4s' size='340' side='right'caption='[[1p4s]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>		<StructureSection load='1p4s' size='340' side='right'caption='[[1p4s]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1p4s]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"bacillus_tuberculosis"_(zopf_1883)_klein_1884 "bacillus tuberculosis" (zopf 1883) klein 1884]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1P4S OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1P4S FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1p4s]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_tuberculosis"_(zopf_1883)_klein_1884 "bacillus tuberculosis" (zopf 1883) klein 1884]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1P4S OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1P4S FirstGlance]. <br>
-	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ADK OR RV0733 OR MT0757 OR MTV041.07 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 "Bacillus tuberculosis" (Zopf 1883) Klein 1884])</td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ADK OR RV0733 OR MT0757 OR MTV041.07 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 "Bacillus tuberculosis" (Zopf 1883) Klein 1884])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Adenylate_kinase Adenylate kinase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.3 2.7.4.3] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Adenylate_kinase Adenylate kinase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.3 2.7.4.3] </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=1p4s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1p4s OCA], [~~http~~://pdbe.org/1p4s PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1p4s RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1p4s PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1p4s 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=1p4s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1p4s OCA], [https://pdbe.org/1p4s PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1p4s RCSB], [https://www.ebi.ac.uk/pdbsum/1p4s PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1p4s ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/KAD_MYCTU KAD_MYCTU]] Catalyzes the reversible transfer of the terminal phosphate group between ATP and AMP. This small ubiquitous enzyme involved in the energy metabolism and nucleotide synthesis, is essential for maintenance and cell growth. Has a broad specificity for nucleoside triphosphates, being highly active with ATP or dATP as phosphate donors, and less active with GTP or UTP.<ref>PMID:10398370</ref>	+	[[https://www.uniprot.org/uniprot/KAD_MYCTU KAD_MYCTU]] Catalyzes the reversible transfer of the terminal phosphate group between ATP and AMP. This small ubiquitous enzyme involved in the energy metabolism and nucleotide synthesis, is essential for maintenance and cell growth. Has a broad specificity for nucleoside triphosphates, being highly active with ATP or dATP as phosphate donors, and less active with GTP or UTP.<ref>PMID:10398370</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 07:22, 9 December 2020

OCA — Wed, 09 Dec 2020 07:22:50 GMT

←Older revision		Revision as of 07:22, 9 December 2020
Line 1:		Line 1:

	==Solution structure of Mycobacterium tuberculosis adenylate kinase==		==Solution structure of Mycobacterium tuberculosis adenylate kinase==
-	<StructureSection load='1p4s' size='340' side='right' caption='[[1p4s]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>	+	<StructureSection load='1p4s' size='340' side='right'caption='[[1p4s]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1p4s]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_tuberculosis"_(zopf_1883)_klein_1884 "bacillus tuberculosis" (zopf 1883) klein 1884]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1P4S OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1P4S FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1p4s]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_tuberculosis"_(zopf_1883)_klein_1884 "bacillus tuberculosis" (zopf 1883) klein 1884]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1P4S OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1P4S FirstGlance]. <br>
	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ADK OR RV0733 OR MT0757 OR MTV041.07 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 "Bacillus tuberculosis" (Zopf 1883) Klein 1884])</td></tr>		</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ADK OR RV0733 OR MT0757 OR MTV041.07 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 "Bacillus tuberculosis" (Zopf 1883) Klein 1884])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Adenylate_kinase Adenylate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.3 2.7.4.3] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Adenylate_kinase Adenylate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.3 2.7.4.3] </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=1p4s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1p4s OCA], [http://pdbe.org/1p4s PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1p4s RCSB], [http://www.ebi.ac.uk/pdbsum/1p4s PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1p4s 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=1p4s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1p4s OCA], [http://pdbe.org/1p4s PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1p4s RCSB], [http://www.ebi.ac.uk/pdbsum/1p4s PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1p4s ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 29:		Line 29:
	</div>		</div>
	<div class="pdbe-citations 1p4s" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1p4s" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Adenylate kinase 3D structures\|Adenylate kinase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 34:		Line 37:
	</StructureSection>		</StructureSection>
	[[Category: Adenylate kinase]]		[[Category: Adenylate kinase]]
		+	[[Category: Large Structures]]
	[[Category: Craescu, C T]]		[[Category: Craescu, C T]]
	[[Category: Miron, S]]		[[Category: Miron, S]]

OCA at 07:46, 15 February 2018

OCA — Thu, 15 Feb 2018 07:46:08 GMT

←Older revision		Revision as of 07:46, 15 February 2018
Line 1:		Line 1:
		+
	==Solution structure of Mycobacterium tuberculosis adenylate kinase==		==Solution structure of Mycobacterium tuberculosis adenylate kinase==
	<StructureSection load='1p4s' size='340' side='right' caption='[[1p4s]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>		<StructureSection load='1p4s' size='340' side='right' caption='[[1p4s]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ADK OR RV0733 OR MT0757 OR MTV041.07 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 "Bacillus tuberculosis" (Zopf 1883) Klein 1884])</td></tr>		</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ADK OR RV0733 OR MT0757 OR MTV041.07 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 "Bacillus tuberculosis" (Zopf 1883) Klein 1884])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Adenylate_kinase Adenylate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.3 2.7.4.3] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Adenylate_kinase Adenylate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.3 2.7.4.3] </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=1p4s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1p4s OCA], [http://pdbe.org/1p4s PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1p4s RCSB], [http://www.ebi.ac.uk/pdbsum/1p4s 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=1p4s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1p4s OCA], [http://pdbe.org/1p4s PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1p4s RCSB], [http://www.ebi.ac.uk/pdbsum/1p4s PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1p4s 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/p4/1p4s_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/p4/1p4s_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>
Line 28:		Line 29:
	</div>		</div>
	<div class="pdbe-citations 1p4s" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1p4s" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Adenylate kinase\|Adenylate kinase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 20:47, 9 February 2016

OCA — Tue, 09 Feb 2016 20:47:43 GMT

←Older revision		Revision as of 20:47, 9 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=1p4s ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 01:54, 11 September 2015

OCA — Fri, 11 Sep 2015 01:54:07 GMT

←Older revision		Revision as of 01:54, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='1p4s' size='340' side='right' caption='[[1p4s]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>		<StructureSection load='1p4s' size='340' side='right' caption='[[1p4s]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1p4s]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Mycobacterium_tuberculosis Mycobacterium~~ tuberculosis]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1P4S OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1P4S FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1p4s]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_tuberculosis"_(zopf_1883)_klein_1884 "bacillus tuberculosis" (zopf 1883) klein 1884]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1P4S OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1P4S FirstGlance]. <br>
-	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ADK OR RV0733 OR MT0757 OR MTV041.07 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 ~~Mycobacterium~~ tuberculosis])</td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ADK OR RV0733 OR MT0757 OR MTV041.07 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 "Bacillus tuberculosis" (Zopf 1883) Klein 1884])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Adenylate_kinase Adenylate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.3 2.7.4.3] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Adenylate_kinase Adenylate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.3 2.7.4.3] </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=1p4s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1p4s OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1p4s RCSB], [http://www.ebi.ac.uk/pdbsum/1p4s 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=1p4s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1p4s OCA], [http://pdbe.org/1p4s PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1p4s RCSB], [http://www.ebi.ac.uk/pdbsum/1p4s PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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 1p4s" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 35:		Line 36:
	</StructureSection>		</StructureSection>
	[[Category: Adenylate kinase]]		[[Category: Adenylate kinase]]
-	[[Category: Mycobacterium tuberculosis]]
	[[Category: Craescu, C T]]		[[Category: Craescu, C T]]
	[[Category: Miron, S]]		[[Category: Miron, S]]

OCA at 09:26, 25 December 2014

OCA — Thu, 25 Dec 2014 09:26:14 GMT

←Older revision		Revision as of 09:26, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1p4s]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1P4S OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1P4S FirstGlance]. <br>		<table><tr><td colspan='2'>[[1p4s]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1P4S OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1P4S FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ADK OR RV0733 OR MT0757 OR MTV041.07 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 Mycobacterium tuberculosis])</td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ADK OR RV0733 OR MT0757 OR MTV041.07 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 Mycobacterium tuberculosis])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Adenylate_kinase Adenylate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.3 2.7.4.3] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Adenylate_kinase Adenylate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.3 2.7.4.3] </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=1p4s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1p4s OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1p4s RCSB], [http://www.ebi.ac.uk/pdbsum/1p4s 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=1p4s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1p4s OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1p4s RCSB], [http://www.ebi.ac.uk/pdbsum/1p4s PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/KAD_MYCTU KAD_MYCTU]] Catalyzes the reversible transfer of the terminal phosphate group between ATP and AMP. This small ubiquitous enzyme involved in the energy metabolism and nucleotide synthesis, is essential for maintenance and cell growth. Has a broad specificity for nucleoside triphosphates, being highly active with ATP or dATP as phosphate donors, and less active with GTP or UTP.<ref>PMID:10398370</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 34:		Line 36:
	[[Category: Adenylate kinase]]		[[Category: Adenylate kinase]]
	[[Category: Mycobacterium tuberculosis]]		[[Category: Mycobacterium tuberculosis]]
-	[[Category: Craescu, C T.]]	+	[[Category: Craescu, C T]]
-	[[Category: Miron, S.]]	+	[[Category: Miron, S]]
-	[[Category: Munier-Lehmann, H.]]	+	[[Category: Munier-Lehmann, H]]
	[[Category: Alpha/beta]]		[[Category: Alpha/beta]]
	[[Category: Transferase]]		[[Category: Transferase]]

OCA at 22:27, 28 September 2014

OCA — Sun, 28 Sep 2014 22:27:27 GMT

←Older revision		Revision as of 22:27, 28 September 2014
Line 1:		Line 1:
-	[[~~Image~~:1p4s.~~png\|left~~\|200px]]	+	==Solution structure of Mycobacterium tuberculosis adenylate kinase==
		+	<StructureSection load='1p4s' size='340' side='right' caption='[[1p4s]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1p4s]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1P4S OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1P4S FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ADK OR RV0733 OR MT0757 OR MTV041.07 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 Mycobacterium tuberculosis])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Adenylate_kinase Adenylate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.3 2.7.4.3] </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=1p4s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1p4s OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1p4s RCSB], [http://www.ebi.ac.uk/pdbsum/1p4s 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/p4/1p4s_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 ==
		+	Tuberculosis is the leading cause of death worldwide from a single infectious disease. Search of new therapeutic tools requires the discovery and biochemical characterization of new potential targets among the bacterial proteins essential for the survival and virulence. Among them are the nucleoside monophosphate kinases, involved in the nucleotide biosynthesis. In this work, we determined the solution structure of adenylate kinase (AK) from Mycobacterium tuberculosis (AKmt), a protein of 181 residues that was found to be essential for bacterial survival. The structure was calculated by a simulated annealing protocol and energy minimization using experimental restraints, collected by nuclear magnetic resonance spectroscopy. The final, well-defined 20 NMR structures show an average root-mean-square deviation of 0.77 A for the backbone atoms in regular secondary structure segments. The protein has a central CORE domain, composed of a five-stranded parallel beta-sheet surrounded by seven alpha-helices, and two peripheral domains, AMPbd and LID. As compared to other crystallographic structures of free form AKs, AKmt is more compact, with the AMP(bd) domain closer to the CORE of the protein. Analysis of the (15)N relaxation data enabled us to obtain the global rotational correlation time (9.19 ns) and the generalized order parameters (S(2)) of amide vectors along the polypeptide sequence. The protein exhibits restricted movements on a picosecond to nanosecond time scale in the secondary structural regions with amplitudes characterized by an average S(2)() value of 0.87. The loops beta1/alpha1, beta2/alpha2, alpha2/alpha3, alpha3/alpha4, alpha4/beta3, beta3/alpha5, alpha6/alpha7 (LID), alpha7/alpha8, and beta5/alpha9 exhibit rapid fluctuations with enhanced amplitudes. These structural and dynamic features of AKmt may be related to its low catalytic activity that is 10-fold lower than in their eukaryote counterparts.

-	~~{{STRUCTURE_1p4s\| PDB=1p4s \| SCENE= }}~~	+	Structural and dynamic studies on ligand-free adenylate kinase from Mycobacterium tuberculosis revealed a closed conformation that can be related to the reduced catalytic activity.,Miron S, Munier-Lehmann H, Craescu CT Biochemistry. 2004 Jan 13;43(1):67-77. PMID:14705932<ref>PMID:14705932</ref>

-	~~===Solution structure~~ of ~~Mycobacterium tuberculosis adenylate kinase===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_14705932}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1p4s]] is a 1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]~~. ~~Full experimental information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1P4S OCA].~~	+

	==See Also==		==See Also==
	*[[Adenylate kinase\|Adenylate kinase]]		*[[Adenylate kinase\|Adenylate kinase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:014705932<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Adenylate kinase]]		[[Category: Adenylate kinase]]
	[[Category: Mycobacterium tuberculosis]]		[[Category: Mycobacterium tuberculosis]]

OCA at 15:05, 20 October 2012

OCA — Sat, 20 Oct 2012 15:05:32 GMT

←Older revision		Revision as of 15:05, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[1p4s]] is a 1 chain structure ~~of [[Adenylate kinase]]~~ with sequence from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1P4S OCA].	+	[[1p4s]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1P4S OCA].

	==See Also==		==See Also==