3v31 - Revision history

OCA at 14:15, 14 March 2024

2024-03-14T14:15:53Z

←Older revision		Revision as of 14:15, 14 March 2024
Line 3:		Line 3:
	<StructureSection load='3v31' size='340' side='right'caption='[[3v31]], [[Resolution\|resolution]] 1.57Å' scene=''>		<StructureSection load='3v31' size='340' side='right'caption='[[3v31]], [[Resolution\|resolution]] 1.57Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3v31]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3V31 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3V31 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3v31]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3V31 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3V31 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>~~, ~~<scene name='pdbligand=NA:SODIUM+ION'>NA</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]] 1.57Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-	~~<tr id~~='~~related'><td class~~=~~"sblockLbl"><b>[[Related_structure\|Related~~:~~]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;~~'>~~[[3so8\|3so8]], [[3v2o\|3v2o]], [[3v2x\|3v2x]]~~</~~div~~>~~</td></tr>~~	+
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ANKRA~~, ~~ANKRA2 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])~~<~~/td></tr>~~	+
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>~~[https://en.wikipedia.org/wiki/Histone_deacetylase Histone deacetylase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.98 3.5.1.98]~~ </~~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=3v31 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3v31 OCA], [https://pdbe.org/3v31 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3v31 RCSB], [https://www.ebi.ac.uk/pdbsum/3v31 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3v31 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=3v31 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3v31 OCA], [https://pdbe.org/3v31 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3v31 RCSB], [https://www.ebi.ac.uk/pdbsum/3v31 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3v31 ProSAT]</span></td></tr>
	</table>		</table>
-	== Disease ==
-	[[https://www.uniprot.org/uniprot/HDAC4_HUMAN HDAC4_HUMAN]] Defects in HDAC4 are the cause of brachydactyly-mental retardation syndrome (BDMR) [MIM:[https://omim.org/entry/600430 600430]]. A syndrome resembling the physical anomalies found in Albright hereditary osteodystrophy. Common features are mild facial dysmorphism, congenital heart defects, distinct brachydactyly type E, mental retardation, developmental delay, seizures, autism spectrum disorder, and stocky build. Soft tissue ossification is absent, and there are no abnormalities in parathyroid hormone or calcium metabolism.<ref>PMID:20691407</ref>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/ANRA2_HUMAN ANRA2_HUMAN]] May facilitate endocytosis by linking megalin to components of the cytoskeleton or endocytic machinery. [[https://www.uniprot.org/uniprot/HDAC4_HUMAN HDAC4_HUMAN]] Responsible for the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4). Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events. Histone deacetylases act via the formation of large multiprotein complexes. Involved in muscle maturation via its interaction with the myocyte enhancer factors such as MEF2A, MEF2C and MEF2D.<ref>PMID:10523670</ref>	+	[https://www.uniprot.org/uniprot/ANRA2_HUMAN ANRA2_HUMAN] May facilitate endocytosis by linking megalin to components of the cytoskeleton or endocytic machinery.
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	Ankyrin repeat family A protein 2 (ANKRA2) interacts with the plasma membrane receptor megalin and the class IIa histone deacetylases HDAC4 and HDAC5. We report that the ankyrin repeat domains of ANKRA2 and its close paralog regulatory factor X-associated ankyrin-containing protein (RFXANK) recognize a PxLPxI/L motif found in diverse binding proteins, including HDAC4, HDAC5, HDAC9, megalin, and regulatory factor X, 5 (RFX5). Crystal structures of the ankyrin repeat domain of ANKRA2 in complex with its binding peptides revealed that each of the middle three ankyrin repeats of ANKRA2 recognizes a residue from the PxLPxI/L motif in a tumbler-lock binding mode, with ANKRA2 acting as the lock and the linear binding motif serving as the key. Structural analysis showed that three disease-causing mutations in RFXANK affect residues that are critical for binding to RFX5. These results suggest a fundamental principle of longitudinal recognition of linear sequences by a repeat-type domain. In addition, phosphorylation of serine 350, a residue embedded within the PxLPxI/L motif of HDAC4, impaired the binding of ANKRA2 but generated a high-affinity docking site for 14-3-3 proteins, which may help sequester this HDAC in the cytoplasm. Thus, the binding preference of the PxLPxI/L motif is signal-dependent. Furthermore, proteome-wide screening suggested that a similar phosphorylation-dependent switch may operate in other pathways. Together, our findings uncover a previously uncharacterized sequence- and signal-dependent peptide recognition mode for a repeat-type protein domain.	+
-		+
-	Sequence-Specific Recognition of a PxLPxI/L Motif by an Ankyrin Repeat Tumbler Lock.,Xu C, Jin J, Bian C, Lam R, Tian R, Weist R, You L, Nie J, Bochkarev A, Tempel W, Tan CS, Wasney GA, Vedadi M, Gish GD, Arrowsmith CH, Pawson T, Yang XJ, Min J Sci Signal. 2012 May 29;5(226):ra39. PMID:22649097<ref>PMID:22649097</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 3v31" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Histone deacetylase]]~~	+	[[Category: Homo sapiens]]
-	~~[[Category: Human~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Arrowsmith~~, C H~~]]	+	[[Category: Arrowsmith CH]]
-	[[Category: Bian~~, C B~~]]	+	[[Category: Bian CB]]
-	[[Category: Bochkarev, A]]	+	[[Category: Bochkarev A]]
-	[[Category: Bountra, C]]	+	[[Category: Bountra C]]
-	[[Category: Edwards~~, A M~~]]	+	[[Category: Edwards AM]]
-	[[Category: Kania, J]]	+	[[Category: Kania J]]
-	[[Category: Lam, R]]	+	[[Category: Lam R]]
-	[[Category: Min, J]]	+	[[Category: Min J]]
-	~~[[Category: Structural genomic~~]]	+	[[Category: Weigelt J]]
-	[[Category: Weigelt, J]]	+	[[Category: Xu C]]
-	[[Category: Xu, C]]	+
-	~~[[Category: Ank repeat]]~~	+
-	~~[[Category: Ankra2]]~~	+
-	~~[[Category: Hdac4]]~~	+
-	~~[[Category: Protein binding]]~~	+
-	~~[[Category: Sgc~~]]	+

OCA at 08:26, 20 July 2022

2022-07-20T08:26:29Z

←Older revision		Revision as of 08:26, 20 July 2022
Line 1:		Line 1:

	==Crystal Structure of the Peptide Bound Complex of the Ankyrin Repeat Domains of Human ANKRA2==		==Crystal Structure of the Peptide Bound Complex of the Ankyrin Repeat Domains of Human ANKRA2==
-	<StructureSection load='3v31' size='340' side='right' caption='[[3v31]], [[Resolution\|resolution]] 1.57Å' scene=''>	+	<StructureSection load='3v31' size='340' side='right'caption='[[3v31]], [[Resolution\|resolution]] 1.57Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3v31]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3V31 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3V31 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3v31]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3V31 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3V31 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3so8\|3so8]], [[3v2o\|3v2o]], [[3v2x\|3v2x]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3so8\|3so8]], [[3v2o\|3v2o]], [[3v2x\|3v2x]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ANKRA, ANKRA2 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ANKRA, ANKRA2 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Histone_deacetylase Histone deacetylase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.98 3.5.1.98] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Histone_deacetylase Histone deacetylase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.98 3.5.1.98] </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=3v31 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3v31 OCA], [~~http~~://pdbe.org/3v31 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3v31 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3v31 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3v31 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=3v31 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3v31 OCA], [https://pdbe.org/3v31 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3v31 RCSB], [https://www.ebi.ac.uk/pdbsum/3v31 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3v31 ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
-	[[~~http~~://www.uniprot.org/uniprot/HDAC4_HUMAN HDAC4_HUMAN]] Defects in HDAC4 are the cause of brachydactyly-mental retardation syndrome (BDMR) [MIM:[~~http~~://omim.org/entry/600430 600430]]. A syndrome resembling the physical anomalies found in Albright hereditary osteodystrophy. Common features are mild facial dysmorphism, congenital heart defects, distinct brachydactyly type E, mental retardation, developmental delay, seizures, autism spectrum disorder, and stocky build. Soft tissue ossification is absent, and there are no abnormalities in parathyroid hormone or calcium metabolism.<ref>PMID:20691407</ref>	+	[[https://www.uniprot.org/uniprot/HDAC4_HUMAN HDAC4_HUMAN]] Defects in HDAC4 are the cause of brachydactyly-mental retardation syndrome (BDMR) [MIM:[https://omim.org/entry/600430 600430]]. A syndrome resembling the physical anomalies found in Albright hereditary osteodystrophy. Common features are mild facial dysmorphism, congenital heart defects, distinct brachydactyly type E, mental retardation, developmental delay, seizures, autism spectrum disorder, and stocky build. Soft tissue ossification is absent, and there are no abnormalities in parathyroid hormone or calcium metabolism.<ref>PMID:20691407</ref>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/ANRA2_HUMAN ANRA2_HUMAN]] May facilitate endocytosis by linking megalin to components of the cytoskeleton or endocytic machinery. [[~~http~~://www.uniprot.org/uniprot/HDAC4_HUMAN HDAC4_HUMAN]] Responsible for the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4). Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events. Histone deacetylases act via the formation of large multiprotein complexes. Involved in muscle maturation via its interaction with the myocyte enhancer factors such as MEF2A, MEF2C and MEF2D.<ref>PMID:10523670</ref>	+	[[https://www.uniprot.org/uniprot/ANRA2_HUMAN ANRA2_HUMAN]] May facilitate endocytosis by linking megalin to components of the cytoskeleton or endocytic machinery. [[https://www.uniprot.org/uniprot/HDAC4_HUMAN HDAC4_HUMAN]] Responsible for the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4). Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events. Histone deacetylases act via the formation of large multiprotein complexes. Involved in muscle maturation via its interaction with the myocyte enhancer factors such as MEF2A, MEF2C and MEF2D.<ref>PMID:10523670</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 30:		Line 30:
	[[Category: Histone deacetylase]]		[[Category: Histone deacetylase]]
	[[Category: Human]]		[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Arrowsmith, C H]]		[[Category: Arrowsmith, C H]]
	[[Category: Bian, C B]]		[[Category: Bian, C B]]

OCA at 17:02, 11 August 2016

2016-08-11T17:02:15Z

←Older revision		Revision as of 17:02, 11 August 2016
Line 1:		Line 1:
		+
	==Crystal Structure of the Peptide Bound Complex of the Ankyrin Repeat Domains of Human ANKRA2==		==Crystal Structure of the Peptide Bound Complex of the Ankyrin Repeat Domains of Human ANKRA2==
	<StructureSection load='3v31' size='340' side='right' caption='[[3v31]], [[Resolution\|resolution]] 1.57Å' scene=''>		<StructureSection load='3v31' size='340' side='right' caption='[[3v31]], [[Resolution\|resolution]] 1.57Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3v31]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Homo_sapiens Homo sapiens~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3V31 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3V31 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3v31]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3V31 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3V31 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3so8\|3so8]], [[3v2o\|3v2o]], [[3v2x\|3v2x]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3so8\|3so8]], [[3v2o\|3v2o]], [[3v2x\|3v2x]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ANKRA, ANKRA2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 ~~Homo sapiens~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ANKRA, ANKRA2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Histone_deacetylase Histone deacetylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.98 3.5.1.98] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Histone_deacetylase Histone deacetylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.98 3.5.1.98] </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=3v31 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3v31 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3v31 RCSB], [http://www.ebi.ac.uk/pdbsum/3v31 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=3v31 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3v31 OCA], [http://pdbe.org/3v31 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3v31 RCSB], [http://www.ebi.ac.uk/pdbsum/3v31 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3v31 ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
Line 22:		Line 23:
	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 3v31" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
Line 27:		Line 29:
	</StructureSection>		</StructureSection>
	[[Category: Histone deacetylase]]		[[Category: Histone deacetylase]]
-	[[Category: ~~Homo sapiens~~]]	+	[[Category: Human]]
	[[Category: Arrowsmith, C H]]		[[Category: Arrowsmith, C H]]
	[[Category: Bian, C B]]		[[Category: Bian, C B]]

OCA at 10:29, 4 January 2015

2015-01-04T10:29:50Z

←Older revision		Revision as of 10:29, 4 January 2015
Line 1:		Line 1:
-	~~{{STRUCTURE_3v31\| PDB=3v31 \| SCENE= }}~~	+	==Crystal Structure of the Peptide Bound Complex of the Ankyrin Repeat Domains of Human ANKRA2==
-	===Crystal Structure of the Peptide Bound Complex of the Ankyrin Repeat Domains of Human ANKRA2===	+	<StructureSection load='3v31' size='340' side='right' caption='[[3v31]], [[Resolution\|resolution]] 1.57Å' scene=''>
-	~~{{ABSTRACT_PUBMED_22649097}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3v31]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3V31 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3V31 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3so8\|3so8]], [[3v2o\|3v2o]], [[3v2x\|3v2x]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ANKRA, ANKRA2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Histone_deacetylase Histone deacetylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.98 3.5.1.98] </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=3v31 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3v31 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3v31 RCSB], [http://www.ebi.ac.uk/pdbsum/3v31 PDBsum]</span></td></tr>
		+	</table>
		+	== Disease ==
		+	[[http://www.uniprot.org/uniprot/HDAC4_HUMAN HDAC4_HUMAN]] Defects in HDAC4 are the cause of brachydactyly-mental retardation syndrome (BDMR) [MIM:[http://omim.org/entry/600430 600430]]. A syndrome resembling the physical anomalies found in Albright hereditary osteodystrophy. Common features are mild facial dysmorphism, congenital heart defects, distinct brachydactyly type E, mental retardation, developmental delay, seizures, autism spectrum disorder, and stocky build. Soft tissue ossification is absent, and there are no abnormalities in parathyroid hormone or calcium metabolism.<ref>PMID:20691407</ref>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/ANRA2_HUMAN ANRA2_HUMAN]] May facilitate endocytosis by linking megalin to components of the cytoskeleton or endocytic machinery. [[http://www.uniprot.org/uniprot/HDAC4_HUMAN HDAC4_HUMAN]] Responsible for the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4). Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events. Histone deacetylases act via the formation of large multiprotein complexes. Involved in muscle maturation via its interaction with the myocyte enhancer factors such as MEF2A, MEF2C and MEF2D.<ref>PMID:10523670</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Ankyrin repeat family A protein 2 (ANKRA2) interacts with the plasma membrane receptor megalin and the class IIa histone deacetylases HDAC4 and HDAC5. We report that the ankyrin repeat domains of ANKRA2 and its close paralog regulatory factor X-associated ankyrin-containing protein (RFXANK) recognize a PxLPxI/L motif found in diverse binding proteins, including HDAC4, HDAC5, HDAC9, megalin, and regulatory factor X, 5 (RFX5). Crystal structures of the ankyrin repeat domain of ANKRA2 in complex with its binding peptides revealed that each of the middle three ankyrin repeats of ANKRA2 recognizes a residue from the PxLPxI/L motif in a tumbler-lock binding mode, with ANKRA2 acting as the lock and the linear binding motif serving as the key. Structural analysis showed that three disease-causing mutations in RFXANK affect residues that are critical for binding to RFX5. These results suggest a fundamental principle of longitudinal recognition of linear sequences by a repeat-type domain. In addition, phosphorylation of serine 350, a residue embedded within the PxLPxI/L motif of HDAC4, impaired the binding of ANKRA2 but generated a high-affinity docking site for 14-3-3 proteins, which may help sequester this HDAC in the cytoplasm. Thus, the binding preference of the PxLPxI/L motif is signal-dependent. Furthermore, proteome-wide screening suggested that a similar phosphorylation-dependent switch may operate in other pathways. Together, our findings uncover a previously uncharacterized sequence- and signal-dependent peptide recognition mode for a repeat-type protein domain.

-	~~==Disease==~~	+	Sequence-Specific Recognition of a PxLPxI/L Motif by an Ankyrin Repeat Tumbler Lock.,Xu C, Jin J, Bian C, Lam R, Tian R, Weist R, You L, Nie J, Bochkarev A, Tempel W, Tan CS, Wasney GA, Vedadi M, Gish GD, Arrowsmith CH, Pawson T, Yang XJ, Min J Sci Signal. 2012 May 29;5(226):ra39. PMID:22649097<ref>PMID:22649097</ref>
-	~~[[http://www.uniprot.org/uniprot/HDAC4_HUMAN HDAC4_HUMAN]] Defects in HDAC4 are the cause~~ of ~~brachydactyly-mental retardation syndrome (BDMR) [MIM:[http:/~~/~~omim.org/entry/600430 600430]]~~. A ~~syndrome resembling the physical anomalies found in Albright hereditary osteodystrophy. Common features are mild facial dysmorphism~~, ~~congenital heart defects~~, ~~distinct brachydactyly type E~~, ~~mental retardation~~, ~~developmental delay~~, ~~seizures~~, ~~autism spectrum disorder~~, ~~and stocky build. Soft tissue ossification is absent~~, ~~and there are no abnormalities in parathyroid hormone or calcium metabolism~~.<ref>PMID:~~20691407~~</ref>	+

-	~~==Function==~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[http:~~/~~/www.uniprot.org/uniprot/ANRA2_HUMAN ANRA2_HUMAN]] May facilitate endocytosis by linking megalin to components~~ of the ~~cytoskeleton or endocytic machinery~~. ~~[[http://www~~.~~uniprot.org/uniprot/HDAC4_HUMAN HDAC4_HUMAN]] Responsible for the deacetylation~~ of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4). Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events. Histone deacetylases act via the formation of large multiprotein complexes. Involved in muscle maturation via its interaction with the myocyte enhancer factors such as MEF2A, MEF2C and MEF2D.<~~ref~~>~~PMID:10523670~~</~~ref~~>	+	</div>
-		+	== References ==
-	==~~About this Structure==~~	+	<references/>
-	[[3v31]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3V31 OCA].	+	__TOC__
-		+	</StructureSection>
-	~~==Reference~~==	+
-	~~<ref group="xtra">PMID:022649097</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+
	[[Category: Histone deacetylase]]		[[Category: Histone deacetylase]]
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
-	[[Category: Arrowsmith, C H.]]	+	[[Category: Arrowsmith, C H]]
-	[[Category: Bian, C B.]]	+	[[Category: Bian, C B]]
-	[[Category: Bochkarev, A.]]	+	[[Category: Bochkarev, A]]
-	[[Category: Bountra, C.]]	+	[[Category: Bountra, C]]
-	[[Category: Edwards, A M.]]	+	[[Category: Edwards, A M]]
-	[[Category: Kania, J.]]	+	[[Category: Kania, J]]
-	[[Category: Lam, R.]]	+	[[Category: Lam, R]]
-	[[Category: Min, J.]]	+	[[Category: Min, J]]
-	[[Category: ~~SGC,~~ Structural ~~Genomics Consortium.~~]]	+	[[Category: Structural genomic]]
-	[[Category: Weigelt, J.]]	+	[[Category: Weigelt, J]]
-	[[Category: Xu, C.]]	+	[[Category: Xu, C]]
	[[Category: Ank repeat]]		[[Category: Ank repeat]]
	[[Category: Ankra2]]		[[Category: Ankra2]]
Line 32:		Line 44:
	[[Category: Protein binding]]		[[Category: Protein binding]]
	[[Category: Sgc]]		[[Category: Sgc]]
-	[[Category: Structural genomics consortium]]

OCA at 02:19, 25 March 2013

2013-03-25T02:19:45Z

←Older revision		Revision as of 02:19, 25 March 2013
Line 1:		Line 1:
-	[[Image:3v31.png\|left\|200px]]
-
-	<!--
-	The line below this paragraph, containing "STRUCTURE_3v31", 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_3v31\| PDB=3v31 \| SCENE= }}		{{STRUCTURE_3v31\| PDB=3v31 \| SCENE= }}
-
	===Crystal Structure of the Peptide Bound Complex of the Ankyrin Repeat Domains of Human ANKRA2===		===Crystal Structure of the Peptide Bound Complex of the Ankyrin Repeat Domains of Human ANKRA2===
		+	{{ABSTRACT_PUBMED_22649097}}

		+	==Disease==
		+	[[http://www.uniprot.org/uniprot/HDAC4_HUMAN HDAC4_HUMAN]] Defects in HDAC4 are the cause of brachydactyly-mental retardation syndrome (BDMR) [MIM:[http://omim.org/entry/600430 600430]]. A syndrome resembling the physical anomalies found in Albright hereditary osteodystrophy. Common features are mild facial dysmorphism, congenital heart defects, distinct brachydactyly type E, mental retardation, developmental delay, seizures, autism spectrum disorder, and stocky build. Soft tissue ossification is absent, and there are no abnormalities in parathyroid hormone or calcium metabolism.<ref>PMID:20691407</ref>

-	~~<!--~~	+	==Function==
-	~~The line below this paragraph, {{ABSTRACT_PUBMED_22649097}}, adds the Publication Abstract~~ to the ~~page~~	+	[[http://www.uniprot.org/uniprot/ANRA2_HUMAN ANRA2_HUMAN]] May facilitate endocytosis by linking megalin to components of the cytoskeleton or endocytic machinery. [[http://www.uniprot.org/uniprot/HDAC4_HUMAN HDAC4_HUMAN]] Responsible for the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4). Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events. Histone deacetylases act via the formation of large multiprotein complexes. Involved in muscle maturation via its interaction with the myocyte enhancer factors such as MEF2A, MEF2C and MEF2D.<ref>PMID:10523670</ref>
-	~~(as it appears on PubMed at~~ http://www.~~pubmed~~.~~gov~~), ~~where 22649097 is~~ the ~~PubMed ID number~~.	+
-	-->	+
-	~~{{ABSTRACT_PUBMED_22649097}}~~	+

	==About this Structure==		==About this Structure==
Line 22:		Line 13:

	==Reference==		==Reference==
-	<ref group="xtra">PMID:022649097</ref><references group="xtra"/>	+	<ref group="xtra">PMID:022649097</ref><references group="xtra"/><references/>
	[[Category: Histone deacetylase]]		[[Category: Histone deacetylase]]
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]

OCA at 05:09, 13 June 2012

2012-06-13T05:09:50Z

←Older revision		Revision as of 05:09, 13 June 2012
Line 1:		Line 1:
-	[[Image:3v31.~~jpg~~\|left\|200px]]	+	[[Image:3v31.png\|left\|200px]]

	<!--		<!--
Line 11:		Line 11:
	===Crystal Structure of the Peptide Bound Complex of the Ankyrin Repeat Domains of Human ANKRA2===		===Crystal Structure of the Peptide Bound Complex of the Ankyrin Repeat Domains of Human ANKRA2===

		+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_22649097}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 22649097 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_22649097}}

	==About this Structure==		==About this Structure==
	[[3v31]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3V31 OCA].		[[3v31]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3V31 OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:022649097</ref><references group="xtra"/>
	[[Category: Histone deacetylase]]		[[Category: Histone deacetylase]]
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]

OCA at 06:18, 4 April 2012

2012-04-04T06:18:08Z

←Older revision		Revision as of 06:18, 4 April 2012
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:3v31.jpg\|left\|200px]]

-	The ~~entry 3v31~~ is ~~ON HOLD~~ ~~until Apr 02 2013~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3v31", 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_3v31\| PDB=3v31 \| SCENE= }}

-	~~Authors: Lam, R., Xu, C., Bian, C.B., Kania, J., Bountra, C., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Min, J., Structural Genomics Consortium (SGC)~~	+	===Crystal Structure of the Peptide Bound Complex of the Ankyrin Repeat Domains of Human ANKRA2===

-	~~Description: Crystal~~ Structure ~~of the Peptide Bound Complex of the Ankyrin Repeat Domains of Human ANKRA2~~	+
		+	==About this Structure==
		+	[[3v31]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3V31 OCA].
		+	[[Category: Histone deacetylase]]
		+	[[Category: Homo sapiens]]
		+	[[Category: Arrowsmith, C H.]]
		+	[[Category: Bian, C B.]]
		+	[[Category: Bochkarev, A.]]
		+	[[Category: Bountra, C.]]
		+	[[Category: Edwards, A M.]]
		+	[[Category: Kania, J.]]
		+	[[Category: Lam, R.]]
		+	[[Category: Min, J.]]
		+	[[Category: SGC, Structural Genomics Consortium.]]
		+	[[Category: Weigelt, J.]]
		+	[[Category: Xu, C.]]
		+	[[Category: Ank repeat]]
		+	[[Category: Ankra2]]
		+	[[Category: Hdac4]]
		+	[[Category: Protein binding]]
		+	[[Category: Sgc]]
		+	[[Category: Structural genomics consortium]]

OCA at 06:02, 8 February 2012

2012-02-08T06:02:38Z

←Older revision		Revision as of 06:02, 8 February 2012
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 3v31 is ON HOLD until ~~Feb 06~~ 2013	+	The entry 3v31 is ON HOLD until Apr 02 2013

	Authors: Lam, R., Xu, C., Bian, C.B., Kania, J., Bountra, C., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Min, J., Structural Genomics Consortium (SGC)		Authors: Lam, R., Xu, C., Bian, C.B., Kania, J., Bountra, C., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Min, J., Structural Genomics Consortium (SGC)

	Description: Crystal Structure of the Peptide Bound Complex of the Ankyrin Repeat Domains of Human ANKRA2		Description: Crystal Structure of the Peptide Bound Complex of the Ankyrin Repeat Domains of Human ANKRA2

OCA at 05:58, 11 January 2012

2012-01-11T05:58:07Z

←Older revision		Revision as of 05:58, 11 January 2012
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 3v31 is ON HOLD	+	The entry 3v31 is ON HOLD until Feb 06 2013

-	Authors: Lam, R., Xu, C., Bian, C. B., Kania, J., Bountra, C., Weigelt, J., Arrowsmith, C. H., Edwards, A. M., Bochkarev, A., Min, J., Structural Genomics Consortium (SGC)	+	Authors: Lam, R., Xu, C., Bian, C.B., Kania, J., Bountra, C., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Min, J., Structural Genomics Consortium (SGC)

	Description: Crystal Structure of the Peptide Bound Complex of the Ankyrin Repeat Domains of Human ANKRA2		Description: Crystal Structure of the Peptide Bound Complex of the Ankyrin Repeat Domains of Human ANKRA2

OCA: Protected "3v31" [edit=sysop:move=sysop]

2011-12-28T06:48:41Z

Protected "3v31" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:48, 28 December 2011