2kdk - Revision history

OCA at 13:07, 26 July 2023

2023-07-26T13:07:55Z

← Older revision		Revision as of 13:07, 26 July 2023
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	==Structure of human circadian clock protein BMAL2 C-terminal PAS domain==		==Structure of human circadian clock protein BMAL2 C-terminal PAS domain==
	<StructureSection load='2kdk' size='340' side='right'caption='[[2kdk~~]], [[NMR_Ensembles_of_Models \| 10 NMR models~~]]' scene=''>		<StructureSection load='2kdk' size='340' side='right'caption='[[2kdk]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2kdk]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Human Human~~]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KDK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2KDK FirstGlance]. <br>		<table><tr><td colspan='2'>[[2kdk]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KDK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2KDK FirstGlance]. <br>
	</td></tr><tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>ARNTL2, BMAL2, CLIF, MOP9 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~9606 HUMAN])~~</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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2kdk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2kdk OCA], [https://pdbe.org/2kdk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2kdk RCSB], [https://www.ebi.ac.uk/pdbsum/2kdk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2kdk 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=2kdk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2kdk OCA], [https://pdbe.org/2kdk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2kdk RCSB], [https://www.ebi.ac.uk/pdbsum/2kdk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2kdk ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[https://www.uniprot.org/uniprot/BMAL2_HUMAN BMAL2_HUMAN]] Transcriptional activator which forms a core component of the circadian clock. The circadian clock, an internal time-keeping system, regulates various physiological processes through the generation of approximately 24 hour circadian rhythms in gene expression, which are translated into rhythms in metabolism and behavior. It is derived from the Latin roots 'circa' (about) and 'diem' (day) and acts as an important regulator of a wide array of physiological functions including metabolism, sleep, body temperature, blood pressure, endocrine, immune, cardiovascular, and renal function. Consists of two major components: the central clock, residing in the suprachiasmatic nucleus (SCN) of the brain, and the peripheral clocks that are present in nearly every tissue and organ system. Both the central and peripheral clocks can be reset by environmental cues, also known as Zeitgebers (German for 'timegivers'). The predominant Zeitgeber for the central clock is light, which is sensed by retina and signals directly to the SCN. The central clock entrains the peripheral clocks through neuronal and hormonal signals, body temperature and feeding-related cues, aligning all clocks with the external light/dark cycle. Circadian rhythms allow an organism to achieve temporal homeostasis with its environment at the molecular level by regulating gene expression to create a peak of protein expression once every 24 hours to control when a particular physiological process is most active with respect to the solar day. Transcription and translation of core clock components (CLOCK, NPAS2, ARNTL/BMAL1, ARNTL2/BMAL2, PER1, PER2, PER3, CRY1 and CRY2) plays a critical role in rhythm generation, whereas delays imposed by post-translational modifications (PTMs) are important for determining the period (tau) of the rhythms (tau refers to the period of a rhythm and is the length, in time, of one complete cycle). A diurnal rhythm is synchronized with the day/night cycle, while the ultradian and infradian rhythms have a period shorter and longer than 24 hours, respectively. Disruptions in the circadian rhythms contribute to the pathology of cardiovascular diseases, cancer, metabolic syndromes and aging. A transcription/translation feedback loop (TTFL) forms the core of the molecular circadian clock mechanism. Transcription factors, CLOCK or NPAS2 and ARNTL/BMAL1 or ARNTL2/BMAL2, form the positive limb of the feedback loop, act in the form of a heterodimer and activate the transcription of core clock genes and clock-controlled genes (involved in key metabolic processes), harboring E-box elements (5'-CACGTG-3') within their promoters. The core clock genes: PER1/2/3 and CRY1/2 which are transcriptional repressors form the negative limb of the feedback loop and interact with the CLOCK\|NPAS2-ARNTL/BMAL1\|ARNTL2/BMAL2 heterodimer inhibiting its activity and thereby negatively regulating their own expression. This heterodimer also activates nuclear receptors NR1D1/2 and RORA/B/G, which form a second feedback loop and which activate and repress ARNTL/BMAL1 transcription, respectively. The CLOCK-ARNTL2/BMAL2 heterodimer activates the transcription of SERPINE1/PAI1 and BHLHE40/DEC1.<ref>PMID:11018023</ref> <ref>PMID:12738229</ref> <ref>PMID:14672706</ref>		[https://www.uniprot.org/uniprot/BMAL2_HUMAN BMAL2_HUMAN] Transcriptional activator which forms a core component of the circadian clock. The circadian clock, an internal time-keeping system, regulates various physiological processes through the generation of approximately 24 hour circadian rhythms in gene expression, which are translated into rhythms in metabolism and behavior. It is derived from the Latin roots 'circa' (about) and 'diem' (day) and acts as an important regulator of a wide array of physiological functions including metabolism, sleep, body temperature, blood pressure, endocrine, immune, cardiovascular, and renal function. Consists of two major components: the central clock, residing in the suprachiasmatic nucleus (SCN) of the brain, and the peripheral clocks that are present in nearly every tissue and organ system. Both the central and peripheral clocks can be reset by environmental cues, also known as Zeitgebers (German for 'timegivers'). The predominant Zeitgeber for the central clock is light, which is sensed by retina and signals directly to the SCN. The central clock entrains the peripheral clocks through neuronal and hormonal signals, body temperature and feeding-related cues, aligning all clocks with the external light/dark cycle. Circadian rhythms allow an organism to achieve temporal homeostasis with its environment at the molecular level by regulating gene expression to create a peak of protein expression once every 24 hours to control when a particular physiological process is most active with respect to the solar day. Transcription and translation of core clock components (CLOCK, NPAS2, ARNTL/BMAL1, ARNTL2/BMAL2, PER1, PER2, PER3, CRY1 and CRY2) plays a critical role in rhythm generation, whereas delays imposed by post-translational modifications (PTMs) are important for determining the period (tau) of the rhythms (tau refers to the period of a rhythm and is the length, in time, of one complete cycle). A diurnal rhythm is synchronized with the day/night cycle, while the ultradian and infradian rhythms have a period shorter and longer than 24 hours, respectively. Disruptions in the circadian rhythms contribute to the pathology of cardiovascular diseases, cancer, metabolic syndromes and aging. A transcription/translation feedback loop (TTFL) forms the core of the molecular circadian clock mechanism. Transcription factors, CLOCK or NPAS2 and ARNTL/BMAL1 or ARNTL2/BMAL2, form the positive limb of the feedback loop, act in the form of a heterodimer and activate the transcription of core clock genes and clock-controlled genes (involved in key metabolic processes), harboring E-box elements (5'-CACGTG-3') within their promoters. The core clock genes: PER1/2/3 and CRY1/2 which are transcriptional repressors form the negative limb of the feedback loop and interact with the CLOCK\|NPAS2-ARNTL/BMAL1\|ARNTL2/BMAL2 heterodimer inhibiting its activity and thereby negatively regulating their own expression. This heterodimer also activates nuclear receptors NR1D1/2 and RORA/B/G, which form a second feedback loop and which activate and repress ARNTL/BMAL1 transcription, respectively. The CLOCK-ARNTL2/BMAL2 heterodimer activates the transcription of SERPINE1/PAI1 and BHLHE40/DEC1.<ref>PMID:11018023</ref> <ref>PMID:12738229</ref> <ref>PMID:14672706</ref>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Human~~]]		[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Correia, C]]		[[Category: Correia C]]
	[[Category: Mer, G]]		[[Category: Mer G]]
	[[Category: Prendergast~~, F G~~]]		[[Category: Prendergast FG]]
	[[Category: Wasielewski, E]]		[[Category: Wasielewski E]]
	~~[[Category: Activator]]~~
	~~[[Category: Biological rhythm]]~~
	~~[[Category: Circadian clock]]~~
	~~[[Category: Dna-binding]]~~
	~~[[Category: Nucleus]]~~
	~~[[Category: Pas domain]]~~
	~~[[Category: Transcription]]~~
	~~[[Category: Transcription regulation]]~~
	~~[[Category: Transcription regulator~~]]

OCA at 08:18, 7 April 2021

2021-04-07T08:18:10Z

← Older revision		Revision as of 08:18, 7 April 2021
Line 1:		Line 1:

	==Structure of human circadian clock protein BMAL2 C-terminal PAS domain==		==Structure of human circadian clock protein BMAL2 C-terminal PAS domain==
	<StructureSection load='2kdk' size='340' side='right' caption='[[2kdk]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>		<StructureSection load='2kdk' size='340' side='right'caption='[[2kdk]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2kdk]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Human Human]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KDK OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2KDK FirstGlance]. <br>		<table><tr><td colspan='2'>[[2kdk]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KDK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2KDK FirstGlance]. <br>
	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ARNTL2, BMAL2, CLIF, MOP9 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>		</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ARNTL2, BMAL2, CLIF, MOP9 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=2kdk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2kdk OCA], [~~http~~://pdbe.org/2kdk PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2kdk RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2kdk PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2kdk 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=2kdk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2kdk OCA], [https://pdbe.org/2kdk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2kdk RCSB], [https://www.ebi.ac.uk/pdbsum/2kdk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2kdk ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[~~http~~://www.uniprot.org/uniprot/BMAL2_HUMAN BMAL2_HUMAN]] Transcriptional activator which forms a core component of the circadian clock. The circadian clock, an internal time-keeping system, regulates various physiological processes through the generation of approximately 24 hour circadian rhythms in gene expression, which are translated into rhythms in metabolism and behavior. It is derived from the Latin roots 'circa' (about) and 'diem' (day) and acts as an important regulator of a wide array of physiological functions including metabolism, sleep, body temperature, blood pressure, endocrine, immune, cardiovascular, and renal function. Consists of two major components: the central clock, residing in the suprachiasmatic nucleus (SCN) of the brain, and the peripheral clocks that are present in nearly every tissue and organ system. Both the central and peripheral clocks can be reset by environmental cues, also known as Zeitgebers (German for 'timegivers'). The predominant Zeitgeber for the central clock is light, which is sensed by retina and signals directly to the SCN. The central clock entrains the peripheral clocks through neuronal and hormonal signals, body temperature and feeding-related cues, aligning all clocks with the external light/dark cycle. Circadian rhythms allow an organism to achieve temporal homeostasis with its environment at the molecular level by regulating gene expression to create a peak of protein expression once every 24 hours to control when a particular physiological process is most active with respect to the solar day. Transcription and translation of core clock components (CLOCK, NPAS2, ARNTL/BMAL1, ARNTL2/BMAL2, PER1, PER2, PER3, CRY1 and CRY2) plays a critical role in rhythm generation, whereas delays imposed by post-translational modifications (PTMs) are important for determining the period (tau) of the rhythms (tau refers to the period of a rhythm and is the length, in time, of one complete cycle). A diurnal rhythm is synchronized with the day/night cycle, while the ultradian and infradian rhythms have a period shorter and longer than 24 hours, respectively. Disruptions in the circadian rhythms contribute to the pathology of cardiovascular diseases, cancer, metabolic syndromes and aging. A transcription/translation feedback loop (TTFL) forms the core of the molecular circadian clock mechanism. Transcription factors, CLOCK or NPAS2 and ARNTL/BMAL1 or ARNTL2/BMAL2, form the positive limb of the feedback loop, act in the form of a heterodimer and activate the transcription of core clock genes and clock-controlled genes (involved in key metabolic processes), harboring E-box elements (5'-CACGTG-3') within their promoters. The core clock genes: PER1/2/3 and CRY1/2 which are transcriptional repressors form the negative limb of the feedback loop and interact with the CLOCK\|NPAS2-ARNTL/BMAL1\|ARNTL2/BMAL2 heterodimer inhibiting its activity and thereby negatively regulating their own expression. This heterodimer also activates nuclear receptors NR1D1/2 and RORA/B/G, which form a second feedback loop and which activate and repress ARNTL/BMAL1 transcription, respectively. The CLOCK-ARNTL2/BMAL2 heterodimer activates the transcription of SERPINE1/PAI1 and BHLHE40/DEC1.<ref>PMID:11018023</ref> <ref>PMID:12738229</ref> <ref>PMID:14672706</ref>		[[https://www.uniprot.org/uniprot/BMAL2_HUMAN BMAL2_HUMAN]] Transcriptional activator which forms a core component of the circadian clock. The circadian clock, an internal time-keeping system, regulates various physiological processes through the generation of approximately 24 hour circadian rhythms in gene expression, which are translated into rhythms in metabolism and behavior. It is derived from the Latin roots 'circa' (about) and 'diem' (day) and acts as an important regulator of a wide array of physiological functions including metabolism, sleep, body temperature, blood pressure, endocrine, immune, cardiovascular, and renal function. Consists of two major components: the central clock, residing in the suprachiasmatic nucleus (SCN) of the brain, and the peripheral clocks that are present in nearly every tissue and organ system. Both the central and peripheral clocks can be reset by environmental cues, also known as Zeitgebers (German for 'timegivers'). The predominant Zeitgeber for the central clock is light, which is sensed by retina and signals directly to the SCN. The central clock entrains the peripheral clocks through neuronal and hormonal signals, body temperature and feeding-related cues, aligning all clocks with the external light/dark cycle. Circadian rhythms allow an organism to achieve temporal homeostasis with its environment at the molecular level by regulating gene expression to create a peak of protein expression once every 24 hours to control when a particular physiological process is most active with respect to the solar day. Transcription and translation of core clock components (CLOCK, NPAS2, ARNTL/BMAL1, ARNTL2/BMAL2, PER1, PER2, PER3, CRY1 and CRY2) plays a critical role in rhythm generation, whereas delays imposed by post-translational modifications (PTMs) are important for determining the period (tau) of the rhythms (tau refers to the period of a rhythm and is the length, in time, of one complete cycle). A diurnal rhythm is synchronized with the day/night cycle, while the ultradian and infradian rhythms have a period shorter and longer than 24 hours, respectively. Disruptions in the circadian rhythms contribute to the pathology of cardiovascular diseases, cancer, metabolic syndromes and aging. A transcription/translation feedback loop (TTFL) forms the core of the molecular circadian clock mechanism. Transcription factors, CLOCK or NPAS2 and ARNTL/BMAL1 or ARNTL2/BMAL2, form the positive limb of the feedback loop, act in the form of a heterodimer and activate the transcription of core clock genes and clock-controlled genes (involved in key metabolic processes), harboring E-box elements (5'-CACGTG-3') within their promoters. The core clock genes: PER1/2/3 and CRY1/2 which are transcriptional repressors form the negative limb of the feedback loop and interact with the CLOCK\|NPAS2-ARNTL/BMAL1\|ARNTL2/BMAL2 heterodimer inhibiting its activity and thereby negatively regulating their own expression. This heterodimer also activates nuclear receptors NR1D1/2 and RORA/B/G, which form a second feedback loop and which activate and repress ARNTL/BMAL1 transcription, respectively. The CLOCK-ARNTL2/BMAL2 heterodimer activates the transcription of SERPINE1/PAI1 and BHLHE40/DEC1.<ref>PMID:11018023</ref> <ref>PMID:12738229</ref> <ref>PMID:14672706</ref>
	== References ==		== References ==
	<references/>		<references/>
Line 14:		Line 14:
	</StructureSection>		</StructureSection>
	[[Category: Human]]		[[Category: Human]]
			[[Category: Large Structures]]
	[[Category: Correia, C]]		[[Category: Correia, C]]
	[[Category: Mer, G]]		[[Category: Mer, G]]

OCA at 11:11, 18 July 2018

2018-07-18T11:11:54Z

← Older revision		Revision as of 11:11, 18 July 2018
Line 1:		Line 1:

	==Structure of human circadian clock protein BMAL2 C-terminal PAS domain==		==Structure of human circadian clock protein BMAL2 C-terminal PAS domain==
	<StructureSection load='2kdk' size='340' side='right' caption='[[2kdk]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>		<StructureSection load='2kdk' size='340' side='right' caption='[[2kdk]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>
Line 4:		Line 5:
	<table><tr><td colspan='2'>[[2kdk]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KDK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2KDK FirstGlance]. <br>		<table><tr><td colspan='2'>[[2kdk]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KDK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2KDK FirstGlance]. <br>
	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ARNTL2, BMAL2, CLIF, MOP9 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>		</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ARNTL2, BMAL2, CLIF, MOP9 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=2kdk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2kdk OCA], [http://pdbe.org/2kdk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2kdk RCSB], [http://www.ebi.ac.uk/pdbsum/2kdk 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=2kdk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2kdk OCA], [http://pdbe.org/2kdk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2kdk RCSB], [http://www.ebi.ac.uk/pdbsum/2kdk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2kdk ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 00:36, 11 September 2015

2015-09-11T00:36:05Z

← Older revision		Revision as of 00:36, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='2kdk' size='340' side='right' caption='[[2kdk]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>		<StructureSection load='2kdk' size='340' side='right' caption='[[2kdk]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2kdk]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Homo_sapiens Homo sapiens~~]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KDK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2KDK FirstGlance]. <br>		<table><tr><td colspan='2'>[[2kdk]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KDK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2KDK FirstGlance]. <br>
	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ARNTL2, BMAL2, CLIF, MOP9 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 ~~Homo sapiens~~])</td></tr>		</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ARNTL2, BMAL2, CLIF, MOP9 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=2kdk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2kdk OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2kdk RCSB], [http://www.ebi.ac.uk/pdbsum/2kdk 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=2kdk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2kdk OCA], [http://pdbe.org/2kdk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2kdk RCSB], [http://www.ebi.ac.uk/pdbsum/2kdk PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 12:		Line 12:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Homo sapiens~~]]		[[Category: Human]]
	[[Category: Correia, C]]		[[Category: Correia, C]]
	[[Category: Mer, G]]		[[Category: Mer, G]]

OCA at 08:27, 25 December 2014

2014-12-25T08:27:42Z

← Older revision		Revision as of 08:27, 25 December 2014
Line 6:		Line 6:
	<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=2kdk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2kdk OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2kdk RCSB], [http://www.ebi.ac.uk/pdbsum/2kdk 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=2kdk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2kdk OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2kdk RCSB], [http://www.ebi.ac.uk/pdbsum/2kdk PDBsum]</span></td></tr>
	</table>		</table>
			== Function ==
			[[http://www.uniprot.org/uniprot/BMAL2_HUMAN BMAL2_HUMAN]] Transcriptional activator which forms a core component of the circadian clock. The circadian clock, an internal time-keeping system, regulates various physiological processes through the generation of approximately 24 hour circadian rhythms in gene expression, which are translated into rhythms in metabolism and behavior. It is derived from the Latin roots 'circa' (about) and 'diem' (day) and acts as an important regulator of a wide array of physiological functions including metabolism, sleep, body temperature, blood pressure, endocrine, immune, cardiovascular, and renal function. Consists of two major components: the central clock, residing in the suprachiasmatic nucleus (SCN) of the brain, and the peripheral clocks that are present in nearly every tissue and organ system. Both the central and peripheral clocks can be reset by environmental cues, also known as Zeitgebers (German for 'timegivers'). The predominant Zeitgeber for the central clock is light, which is sensed by retina and signals directly to the SCN. The central clock entrains the peripheral clocks through neuronal and hormonal signals, body temperature and feeding-related cues, aligning all clocks with the external light/dark cycle. Circadian rhythms allow an organism to achieve temporal homeostasis with its environment at the molecular level by regulating gene expression to create a peak of protein expression once every 24 hours to control when a particular physiological process is most active with respect to the solar day. Transcription and translation of core clock components (CLOCK, NPAS2, ARNTL/BMAL1, ARNTL2/BMAL2, PER1, PER2, PER3, CRY1 and CRY2) plays a critical role in rhythm generation, whereas delays imposed by post-translational modifications (PTMs) are important for determining the period (tau) of the rhythms (tau refers to the period of a rhythm and is the length, in time, of one complete cycle). A diurnal rhythm is synchronized with the day/night cycle, while the ultradian and infradian rhythms have a period shorter and longer than 24 hours, respectively. Disruptions in the circadian rhythms contribute to the pathology of cardiovascular diseases, cancer, metabolic syndromes and aging. A transcription/translation feedback loop (TTFL) forms the core of the molecular circadian clock mechanism. Transcription factors, CLOCK or NPAS2 and ARNTL/BMAL1 or ARNTL2/BMAL2, form the positive limb of the feedback loop, act in the form of a heterodimer and activate the transcription of core clock genes and clock-controlled genes (involved in key metabolic processes), harboring E-box elements (5'-CACGTG-3') within their promoters. The core clock genes: PER1/2/3 and CRY1/2 which are transcriptional repressors form the negative limb of the feedback loop and interact with the CLOCK\|NPAS2-ARNTL/BMAL1\|ARNTL2/BMAL2 heterodimer inhibiting its activity and thereby negatively regulating their own expression. This heterodimer also activates nuclear receptors NR1D1/2 and RORA/B/G, which form a second feedback loop and which activate and repress ARNTL/BMAL1 transcription, respectively. The CLOCK-ARNTL2/BMAL2 heterodimer activates the transcription of SERPINE1/PAI1 and BHLHE40/DEC1.<ref>PMID:11018023</ref> <ref>PMID:12738229</ref> <ref>PMID:14672706</ref>
			== References ==
			<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 17:28, 21 December 2014

2014-12-21T17:28:08Z

← Older revision		Revision as of 17:28, 21 December 2014
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	~~[[Image:2kdk.png\|left\|200px]]~~		==Structure of human circadian clock protein BMAL2 C-terminal PAS domain==
			<StructureSection load='2kdk' size='340' side='right' caption='[[2kdk]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>
	~~<!--~~		== Structural highlights ==
	~~The line below this paragraph, containing "STRUCTURE_2kdk", creates the "Structure Box" on the page.~~		<table><tr><td colspan='2'>[[2kdk]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KDK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2KDK FirstGlance]. <br>
	~~You may change the PDB parameter (which sets the PDB file loaded into the applet)~~		</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ARNTL2, BMAL2, CLIF, MOP9 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</td></tr>
	~~or the SCENE parameter (which sets the initial scene displayed when the page is loaded),~~		<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=2kdk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2kdk OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2kdk RCSB], [http://www.ebi.ac.uk/pdbsum/2kdk PDBsum]</span></td></tr>
	~~or leave the SCENE parameter empty for the default display.~~		</table>
	~~-->~~		__TOC__
	~~{{STRUCTURE_2kdk\| PDB=2kdk \| SCENE= }}~~		</StructureSection>

	===Structure of human circadian clock protein BMAL2 C-terminal PAS domain===


	==~~About this Structure~~==
	[[2kdk]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KDK OCA].

	==~~See Also~~==
	*[[~~Test page~~]]
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Correia, C.]]		[[Category: Correia, C]]
	[[Category: Mer, G.]]		[[Category: Mer, G]]
	[[Category: Prendergast, F G.]]		[[Category: Prendergast, F G]]
	[[Category: Wasielewski, E.]]		[[Category: Wasielewski, E]]
	[[Category: Activator]]		[[Category: Activator]]
	[[Category: Biological rhythm]]		[[Category: Biological rhythm]]

OCA at 08:01, 30 October 2011

2011-10-30T08:01:34Z

← Older revision		Revision as of 08:01, 30 October 2011
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	[[Image:2kdk.~~jpg~~\|left\|200px]]		[[Image:2kdk.png\|left\|200px]]

	<!--		<!--
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	==About this Structure==		==About this Structure==
	[[2kdk]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KDK OCA].		[[2kdk]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KDK OCA].

			==See Also==
			*[[Test page]]
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Correia, C.]]		[[Category: Correia, C.]]
	[[Category: Mer, G.]]		[[Category: Mer, G.]]
			[[Category: Prendergast, F G.]]
	[[Category: Wasielewski, E.]]		[[Category: Wasielewski, E.]]
			[[Category: Activator]]
			[[Category: Biological rhythm]]
			[[Category: Circadian clock]]
			[[Category: Dna-binding]]
			[[Category: Nucleus]]
			[[Category: Pas domain]]
			[[Category: Transcription]]
			[[Category: Transcription regulation]]
			[[Category: Transcription regulator]]

OCA: Protected "2kdk" [edit=sysop:move=sysop]

2011-04-13T05:18:30Z

Protected "2kdk" [edit=sysop:move=sysop]

← Older revision	Revision as of 05:18, 13 April 2011
(No difference)

OCA at 05:18, 13 April 2011

2011-04-13T05:18:26Z

← Older revision		Revision as of 05:18, 13 April 2011
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	~~'''Unreleased structure'''~~		[[Image:2kdk.jpg\|left\|200px]]

	The ~~entry~~ 2kdk ~~is ON HOLD~~ ~~until Paper Publication~~		<!--
			The line below this paragraph, containing "STRUCTURE_2kdk", 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_2kdk\| PDB=2kdk \| SCENE= }}

	~~Authors: Wasielewski, E., Correia,~~ C~~., Mer, G.~~		===Structure of human circadian clock protein BMAL2 C-terminal PAS domain===

	~~Description: N/A~~

	~~''Page seeded by~~ [http://oca.weizmann.ac.il/oca OCA ] ~~on Wed Jun 17 09~~:32:~~11 2009''~~		==About this Structure==
			[[2kdk]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KDK OCA].
			[[Category: Homo sapiens]]
			[[Category: Correia, C.]]
			[[Category: Mer, G.]]
			[[Category: Wasielewski, E.]]

OCA at 06:32, 17 June 2009

2009-06-17T06:32:11Z

← Older revision		Revision as of 06:32, 17 June 2009
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

	The entry 2kdk is ON HOLD		The entry 2kdk is ON HOLD until Paper Publication

	Authors: Wasielewski, E., Correia, C., Mer, G.		Authors: Wasielewski, E., Correia, C., Mer, G.
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	Description: N/A		Description: N/A

	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~Jan 21 10~~:33:39 2009''		''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jun 17 09:32:11 2009''