2lrr - Revision history

OCA at 05:50, 15 May 2024

OCA — Wed, 15 May 2024 05:50:21 GMT

←Older revision		Revision as of 05:50, 15 May 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2lrr]] 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=2LRR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2LRR FirstGlance]. <br>		<table><tr><td colspan='2'>[[2lrr]] 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=2LRR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2LRR FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DGP:2-DEOXYGUANOSINE-5-MONOPHOSPHATE'>DGP</scene></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='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DGP:2-DEOXYGUANOSINE-5-MONOPHOSPHATE'>DGP</scene></td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2lrr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lrr OCA], [https://pdbe.org/2lrr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2lrr RCSB], [https://www.ebi.ac.uk/pdbsum/2lrr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2lrr 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=2lrr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lrr OCA], [https://pdbe.org/2lrr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2lrr RCSB], [https://www.ebi.ac.uk/pdbsum/2lrr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2lrr ProSAT]</span></td></tr>
	</table>		</table>

OCA at 11:14, 15 February 2023

OCA — Wed, 15 Feb 2023 11:14:32 GMT

←Older revision		Revision as of 11:14, 15 February 2023
Line 1:		Line 1:

	==Solution structure of the R3H domain from human Smubp-2 in complex with 2'-deoxyguanosine-5'-monophosphate==		==Solution structure of the R3H domain from human Smubp-2 in complex with 2'-deoxyguanosine-5'-monophosphate==
-	<StructureSection load='2lrr' size='340' side='right'caption='[[2lrr~~]], [[NMR_Ensembles_of_Models \| 20 NMR models~~]]' scene=''>	+	<StructureSection load='2lrr' size='340' side='right'caption='[[2lrr]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2lrr]] 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=2LRR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2LRR FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2lrr]] 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=2LRR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2LRR FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DGP:2-DEOXYGUANOSINE-5-MONOPHOSPHATE'>DGP</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DGP:2-DEOXYGUANOSINE-5-MONOPHOSPHATE'>DGP</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;'>[[1msz\|1msz]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">IGHMBP2, SMBP2, smubp-2, SMUBP2 ([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'>[https://proteopedia.org/fgij/fg.htm?mol=2lrr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lrr OCA], [https://pdbe.org/2lrr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2lrr RCSB], [https://www.ebi.ac.uk/pdbsum/2lrr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2lrr 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=2lrr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lrr OCA], [https://pdbe.org/2lrr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2lrr RCSB], [https://www.ebi.ac.uk/pdbsum/2lrr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2lrr ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
-	[[https://www.uniprot.org/uniprot/SMBP2_HUMAN SMBP2_HUMAN]] Defects in IGHMBP2 are the cause of distal hereditary motor neuronopathy type 6 (HMN6) [MIM:[https://omim.org/entry/604320 604320]]; also known as spinal muscular atrophy distal autosomal recessive 1 (DSMA1) or spinal muscular atrophy with respiratory distress 1 (SMARD1). Distal hereditary motor neuronopathies constitute a heterogeneous group of neuromuscular disorders caused by selective degeneration of motor neurons in the anterior horn of the spinal cord, without sensory deficit in the posterior horn. The overall clinical picture consists of a classical distal muscular atrophy syndrome in the legs without clinical sensory loss. The disease starts with weakness and wasting of distal muscles of the anterior tibial and peroneal compartments of the legs. Later on, weakness and atrophy may expand to the proximal muscles of the lower limbs and/or to the distal upper limbs. The most prominent symptoms of HMN6 are severe respiratory distress resulting from diaphragmatic paralysis with eventration shown on chest x-ray and predominant involvement of the upper limbs and distal muscles.<ref>PMID:19158098</ref> <ref>PMID:11528396</ref> <ref>PMID:14681881</ref> <ref>PMID:15108294</ref> <ref>PMID:15797190</ref> <ref>PMID:17431882</ref> <ref>PMID:18802676</ref>	+	[https://www.uniprot.org/uniprot/SMBP2_HUMAN SMBP2_HUMAN] Defects in IGHMBP2 are the cause of distal hereditary motor neuronopathy type 6 (HMN6) [MIM:[https://omim.org/entry/604320 604320]; also known as spinal muscular atrophy distal autosomal recessive 1 (DSMA1) or spinal muscular atrophy with respiratory distress 1 (SMARD1). Distal hereditary motor neuronopathies constitute a heterogeneous group of neuromuscular disorders caused by selective degeneration of motor neurons in the anterior horn of the spinal cord, without sensory deficit in the posterior horn. The overall clinical picture consists of a classical distal muscular atrophy syndrome in the legs without clinical sensory loss. The disease starts with weakness and wasting of distal muscles of the anterior tibial and peroneal compartments of the legs. Later on, weakness and atrophy may expand to the proximal muscles of the lower limbs and/or to the distal upper limbs. The most prominent symptoms of HMN6 are severe respiratory distress resulting from diaphragmatic paralysis with eventration shown on chest x-ray and predominant involvement of the upper limbs and distal muscles.<ref>PMID:19158098</ref> <ref>PMID:11528396</ref> <ref>PMID:14681881</ref> <ref>PMID:15108294</ref> <ref>PMID:15797190</ref> <ref>PMID:17431882</ref> <ref>PMID:18802676</ref>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/SMBP2_HUMAN SMBP2_HUMAN]] 5' to 3' helicase that unwinds RNA and DNA duplices in an ATP-dependent reaction. Acts as a transcription regulator. Required for the transcriptional activation of the flounder liver-type antifreeze protein gene. Exhibits strong binding specificity to the enhancer element B of the flounder antifreeze protein gene intron. Binds to the insulin II gene RIPE3B enhancer region. May be involved in translation (By similarity). DNA-binding protein specific to 5'-phosphorylated single-stranded guanine-rich sequence related to the immunoglobulin mu chain switch region. Preferentially binds to the 5'-GGGCT-3' motif. Interacts with tRNA-Tyr. Stimulates the transcription of the human neurotropic virus JCV.<ref>PMID:19158098</ref> <ref>PMID:19299493</ref>	+	[https://www.uniprot.org/uniprot/SMBP2_HUMAN SMBP2_HUMAN] 5' to 3' helicase that unwinds RNA and DNA duplices in an ATP-dependent reaction. Acts as a transcription regulator. Required for the transcriptional activation of the flounder liver-type antifreeze protein gene. Exhibits strong binding specificity to the enhancer element B of the flounder antifreeze protein gene intron. Binds to the insulin II gene RIPE3B enhancer region. May be involved in translation (By similarity). DNA-binding protein specific to 5'-phosphorylated single-stranded guanine-rich sequence related to the immunoglobulin mu chain switch region. Preferentially binds to the 5'-GGGCT-3' motif. Interacts with tRNA-Tyr. Stimulates the transcription of the human neurotropic virus JCV.<ref>PMID:19158098</ref> <ref>PMID:19299493</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 26:		Line 24:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Jaudzems, K]]	+	[[Category: Jaudzems K]]
-	[[Category: Liepinsh, E]]	+	[[Category: Liepinsh E]]
-	[[Category: Otting, G]]	+	[[Category: Otting G]]
-	[[Category: Zhulenkovs, D]]	+	[[Category: Zhulenkovs D]]
-	~~[[Category: Dna binding protein]]~~	+
-	~~[[Category: Hydrolase~~]]	+

OCA at 10:17, 12 May 2021

OCA — Wed, 12 May 2021 10:17:07 GMT

←Older revision		Revision as of 10:17, 12 May 2021
Line 1:		Line 1:

	==Solution structure of the R3H domain from human Smubp-2 in complex with 2'-deoxyguanosine-5'-monophosphate==		==Solution structure of the R3H domain from human Smubp-2 in complex with 2'-deoxyguanosine-5'-monophosphate==
-	<StructureSection load='2lrr' size='340' side='right' caption='[[2lrr]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>	+	<StructureSection load='2lrr' size='340' side='right'caption='[[2lrr]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2lrr]] 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=2LRR OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2LRR FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2lrr]] 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=2LRR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2LRR FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DGP:2-DEOXYGUANOSINE-5-MONOPHOSPHATE'>DGP</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DGP:2-DEOXYGUANOSINE-5-MONOPHOSPHATE'>DGP</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1msz\|1msz]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1msz\|1msz]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">IGHMBP2, SMBP2, smubp-2, SMUBP2 ([~~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">IGHMBP2, SMBP2, smubp-2, SMUBP2 ([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=2lrr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lrr OCA], [~~http~~://pdbe.org/2lrr PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2lrr RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2lrr PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2lrr 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=2lrr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lrr OCA], [https://pdbe.org/2lrr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2lrr RCSB], [https://www.ebi.ac.uk/pdbsum/2lrr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2lrr ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
-	[[~~http~~://www.uniprot.org/uniprot/SMBP2_HUMAN SMBP2_HUMAN]] Defects in IGHMBP2 are the cause of distal hereditary motor neuronopathy type 6 (HMN6) [MIM:[~~http~~://omim.org/entry/604320 604320]]; also known as spinal muscular atrophy distal autosomal recessive 1 (DSMA1) or spinal muscular atrophy with respiratory distress 1 (SMARD1). Distal hereditary motor neuronopathies constitute a heterogeneous group of neuromuscular disorders caused by selective degeneration of motor neurons in the anterior horn of the spinal cord, without sensory deficit in the posterior horn. The overall clinical picture consists of a classical distal muscular atrophy syndrome in the legs without clinical sensory loss. The disease starts with weakness and wasting of distal muscles of the anterior tibial and peroneal compartments of the legs. Later on, weakness and atrophy may expand to the proximal muscles of the lower limbs and/or to the distal upper limbs. The most prominent symptoms of HMN6 are severe respiratory distress resulting from diaphragmatic paralysis with eventration shown on chest x-ray and predominant involvement of the upper limbs and distal muscles.<ref>PMID:19158098</ref> <ref>PMID:11528396</ref> <ref>PMID:14681881</ref> <ref>PMID:15108294</ref> <ref>PMID:15797190</ref> <ref>PMID:17431882</ref> <ref>PMID:18802676</ref>	+	[[https://www.uniprot.org/uniprot/SMBP2_HUMAN SMBP2_HUMAN]] Defects in IGHMBP2 are the cause of distal hereditary motor neuronopathy type 6 (HMN6) [MIM:[https://omim.org/entry/604320 604320]]; also known as spinal muscular atrophy distal autosomal recessive 1 (DSMA1) or spinal muscular atrophy with respiratory distress 1 (SMARD1). Distal hereditary motor neuronopathies constitute a heterogeneous group of neuromuscular disorders caused by selective degeneration of motor neurons in the anterior horn of the spinal cord, without sensory deficit in the posterior horn. The overall clinical picture consists of a classical distal muscular atrophy syndrome in the legs without clinical sensory loss. The disease starts with weakness and wasting of distal muscles of the anterior tibial and peroneal compartments of the legs. Later on, weakness and atrophy may expand to the proximal muscles of the lower limbs and/or to the distal upper limbs. The most prominent symptoms of HMN6 are severe respiratory distress resulting from diaphragmatic paralysis with eventration shown on chest x-ray and predominant involvement of the upper limbs and distal muscles.<ref>PMID:19158098</ref> <ref>PMID:11528396</ref> <ref>PMID:14681881</ref> <ref>PMID:15108294</ref> <ref>PMID:15797190</ref> <ref>PMID:17431882</ref> <ref>PMID:18802676</ref>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/SMBP2_HUMAN SMBP2_HUMAN]] 5' to 3' helicase that unwinds RNA and DNA duplices in an ATP-dependent reaction. Acts as a transcription regulator. Required for the transcriptional activation of the flounder liver-type antifreeze protein gene. Exhibits strong binding specificity to the enhancer element B of the flounder antifreeze protein gene intron. Binds to the insulin II gene RIPE3B enhancer region. May be involved in translation (By similarity). DNA-binding protein specific to 5'-phosphorylated single-stranded guanine-rich sequence related to the immunoglobulin mu chain switch region. Preferentially binds to the 5'-GGGCT-3' motif. Interacts with tRNA-Tyr. Stimulates the transcription of the human neurotropic virus JCV.<ref>PMID:19158098</ref> <ref>PMID:19299493</ref>	+	[[https://www.uniprot.org/uniprot/SMBP2_HUMAN SMBP2_HUMAN]] 5' to 3' helicase that unwinds RNA and DNA duplices in an ATP-dependent reaction. Acts as a transcription regulator. Required for the transcriptional activation of the flounder liver-type antifreeze protein gene. Exhibits strong binding specificity to the enhancer element B of the flounder antifreeze protein gene intron. Binds to the insulin II gene RIPE3B enhancer region. May be involved in translation (By similarity). DNA-binding protein specific to 5'-phosphorylated single-stranded guanine-rich sequence related to the immunoglobulin mu chain switch region. Preferentially binds to the 5'-GGGCT-3' motif. Interacts with tRNA-Tyr. Stimulates the transcription of the human neurotropic virus JCV.<ref>PMID:19158098</ref> <ref>PMID:19299493</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 27:		Line 27:
	</StructureSection>		</StructureSection>
	[[Category: Human]]		[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Jaudzems, K]]		[[Category: Jaudzems, K]]
	[[Category: Liepinsh, E]]		[[Category: Liepinsh, E]]

OCA at 19:54, 1 August 2018

OCA — Wed, 01 Aug 2018 19:54:54 GMT

←Older revision		Revision as of 19:54, 1 August 2018
Line 1:		Line 1:
		+
	==Solution structure of the R3H domain from human Smubp-2 in complex with 2'-deoxyguanosine-5'-monophosphate==		==Solution structure of the R3H domain from human Smubp-2 in complex with 2'-deoxyguanosine-5'-monophosphate==
	<StructureSection load='2lrr' size='340' side='right' caption='[[2lrr]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>		<StructureSection load='2lrr' size='340' side='right' caption='[[2lrr]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1msz\|1msz]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1msz\|1msz]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">IGHMBP2, SMBP2, smubp-2, SMUBP2 ([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">IGHMBP2, SMBP2, smubp-2, SMUBP2 ([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=2lrr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lrr OCA], [http://pdbe.org/2lrr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2lrr RCSB], [http://www.ebi.ac.uk/pdbsum/2lrr 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=2lrr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lrr OCA], [http://pdbe.org/2lrr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2lrr RCSB], [http://www.ebi.ac.uk/pdbsum/2lrr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2lrr ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==

OCA at 10:26, 10 September 2015

OCA — Thu, 10 Sep 2015 10:26:51 GMT

←Older revision		Revision as of 10:26, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='2lrr' size='340' side='right' caption='[[2lrr]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>		<StructureSection load='2lrr' size='340' side='right' caption='[[2lrr]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2lrr]] 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=2LRR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2LRR FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2lrr]] 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=2LRR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2LRR FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DGP:2-DEOXYGUANOSINE-5-MONOPHOSPHATE'>DGP</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DGP:2-DEOXYGUANOSINE-5-MONOPHOSPHATE'>DGP</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1msz\|1msz]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1msz\|1msz]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">IGHMBP2, SMBP2, smubp-2, SMUBP2 ([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">IGHMBP2, SMBP2, smubp-2, SMUBP2 ([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=2lrr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lrr OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2lrr RCSB], [http://www.ebi.ac.uk/pdbsum/2lrr 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=2lrr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lrr OCA], [http://pdbe.org/2lrr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2lrr RCSB], [http://www.ebi.ac.uk/pdbsum/2lrr PDBsum]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
Line 20:		Line 20:
	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 2lrr" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Homo sapiens~~]]	+	[[Category: Human]]
	[[Category: Jaudzems, K]]		[[Category: Jaudzems, K]]
	[[Category: Liepinsh, E]]		[[Category: Liepinsh, E]]

OCA at 12:34, 18 December 2014

OCA — Thu, 18 Dec 2014 12:34:16 GMT

←Older revision		Revision as of 12:34, 18 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_2lrr~~\| ~~PDB~~=2lrr \| ~~SCENE~~= }}	+	==Solution structure of the R3H domain from human Smubp-2 in complex with 2'-deoxyguanosine-5'-monophosphate==
-	===Solution structure of the R3H domain from human Smubp-2 in complex with 2'-~~deoxyguanosine~~-5'-~~monophosphate===~~	+	<StructureSection load='2lrr' size='340' side='right' caption='[[2lrr]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
-	~~{{ABSTRACT_PUBMED_22999958}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2lrr]] 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=2LRR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2LRR FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DGP:2-DEOXYGUANOSINE-5-MONOPHOSPHATE'>DGP</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1msz\|1msz]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">IGHMBP2, SMBP2, smubp-2, SMUBP2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</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=2lrr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lrr OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2lrr RCSB], [http://www.ebi.ac.uk/pdbsum/2lrr PDBsum]</span></td></tr>
		+	</table>
		+	== Disease ==
		+	[[http://www.uniprot.org/uniprot/SMBP2_HUMAN SMBP2_HUMAN]] Defects in IGHMBP2 are the cause of distal hereditary motor neuronopathy type 6 (HMN6) [MIM:[http://omim.org/entry/604320 604320]]; also known as spinal muscular atrophy distal autosomal recessive 1 (DSMA1) or spinal muscular atrophy with respiratory distress 1 (SMARD1). Distal hereditary motor neuronopathies constitute a heterogeneous group of neuromuscular disorders caused by selective degeneration of motor neurons in the anterior horn of the spinal cord, without sensory deficit in the posterior horn. The overall clinical picture consists of a classical distal muscular atrophy syndrome in the legs without clinical sensory loss. The disease starts with weakness and wasting of distal muscles of the anterior tibial and peroneal compartments of the legs. Later on, weakness and atrophy may expand to the proximal muscles of the lower limbs and/or to the distal upper limbs. The most prominent symptoms of HMN6 are severe respiratory distress resulting from diaphragmatic paralysis with eventration shown on chest x-ray and predominant involvement of the upper limbs and distal muscles.<ref>PMID:19158098</ref> <ref>PMID:11528396</ref> <ref>PMID:14681881</ref> <ref>PMID:15108294</ref> <ref>PMID:15797190</ref> <ref>PMID:17431882</ref> <ref>PMID:18802676</ref>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/SMBP2_HUMAN SMBP2_HUMAN]] 5' to 3' helicase that unwinds RNA and DNA duplices in an ATP-dependent reaction. Acts as a transcription regulator. Required for the transcriptional activation of the flounder liver-type antifreeze protein gene. Exhibits strong binding specificity to the enhancer element B of the flounder antifreeze protein gene intron. Binds to the insulin II gene RIPE3B enhancer region. May be involved in translation (By similarity). DNA-binding protein specific to 5'-phosphorylated single-stranded guanine-rich sequence related to the immunoglobulin mu chain switch region. Preferentially binds to the 5'-GGGCT-3' motif. Interacts with tRNA-Tyr. Stimulates the transcription of the human neurotropic virus JCV.<ref>PMID:19158098</ref> <ref>PMID:19299493</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The R3H domain is a conserved sequence motif in nucleic acid binding proteins. Previously, we reported the solution structure of the R3H domain and identified a putative nucleic acid binding site composed of three conserved basic residues [Liepinsh, E., Leonchiks, A., Sharipo, A., Guignard, L. & Otting, G. (2003). Solution structure of the R3H domain from human Smubp-2. J. Mol. Biol.326, 217-223]. Here, we determine the binding affinities of mononucleotides and dinucleotides for the R3H domain from human Smubp-2 (Smubp2-R3H) and map their binding sites on the protein's surface. Although the binding affinities show up to 260-fold selectivity between different nucleotides, their binding sites and conformations seem very similar. Further, we report the NMR structure of the Smubp2-R3H in complex with deoxyguanosine 5'-monophosphate (dGMP) mimicking the 5'-end of single-stranded DNA. Pseudocontact shifts from a paramagnetic lanthanide tag attached to residue 731 in the mutant A731C confirmed that binding of dGMP brings a loop of the protein into closer proximity. The structure provides the first structural insight into single-stranded nucleic acid recognition by the R3H domain and shows that the R3H domain specifically binds the phosphorylated 5'-end through electrostatic interactions with the two conserved arginines and stacking interactions with the highly conserved histidine.

-	~~==Disease==~~	+	Structural Basis for 5'-End-Specific Recognition of Single-Stranded DNA by the R3H Domain from Human Smubp-2.,Jaudzems K, Jia X, Yagi H, Zhulenkovs D, Graham B, Otting G, Liepinsh E J Mol Biol. 2012 Sep 18. pii: S0022-2836(12)00760-7. doi:, 10.1016/j.jmb.2012.09.010. PMID:22999958<ref>PMID:22999958</ref>
-	~~[[http://www~~.~~uniprot~~.~~org/uniprot/SMBP2_HUMAN SMBP2_HUMAN]] Defects in IGHMBP2 are the cause of distal hereditary motor neuronopathy type 6~~ (~~HMN6~~) ~~[MIM~~:~~[http://omim~~.~~org~~/~~entry/604320 604320]]; also known as spinal muscular atrophy distal autosomal recessive 1 (DSMA1) or spinal muscular atrophy with respiratory distress 1 (SMARD1)~~. Distal hereditary motor neuronopathies constitute a heterogeneous group of neuromuscular disorders caused by selective degeneration of motor neurons in the anterior horn of the spinal cord, without sensory deficit in the posterior horn. ~~The overall clinical picture consists of a classical distal muscular atrophy syndrome in the legs without clinical sensory loss~~. ~~The disease starts with weakness and wasting of distal muscles of the anterior tibial and peroneal compartments of the legs~~. ~~Later on, weakness and atrophy may expand to the proximal muscles of the lower limbs and/or to the distal upper limbs~~. The most prominent symptoms of HMN6 are severe respiratory distress resulting from diaphragmatic paralysis with eventration shown on chest x-ray and predominant involvement of the upper limbs and distal muscles.<ref>PMID:~~19158098</ref><ref>PMID:11528396</ref><ref>PMID:14681881</ref><ref>PMID:15108294</ref><ref>PMID:15797190</ref><ref>PMID:17431882</ref>~~<ref>PMID:~~18802676~~</ref>	+

-	~~==Function==~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[http:~~/~~/www.uniprot.org/uniprot/SMBP2_HUMAN SMBP2_HUMAN]] 5' to 3' helicase that unwinds RNA and DNA duplices in an ATP-dependent reaction. Acts as~~ a ~~transcription regulator. Required for the transcriptional activation~~ of the ~~flounder liver-type antifreeze protein gene~~. ~~Exhibits strong binding specificity to the enhancer element B of the flounder antifreeze protein gene intron~~. Binds to the insulin II gene RIPE3B enhancer region. May be involved in translation (By similarity). DNA-binding protein specific to 5'-phosphorylated single-stranded guanine-rich sequence related to the immunoglobulin mu chain switch region. Preferentially binds to the 5'-GGGCT-3' motif. Interacts with tRNA-Tyr. Stimulates the transcription of ~~the human neurotropic virus JCV~~.<~~ref~~>~~PMID:19158098~~</~~ref~~>~~<ref>PMID:19299493</ref>~~	+	</div>
-		+	== References ==
-	==~~About this Structure==~~	+	<references/>
-	[[2lrr]] 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=2LRR OCA].	+	__TOC__
-		+	</StructureSection>
-	~~==Reference~~==	+
-	<references ~~group="xtra"~~/><~~references~~/>	+
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
-	[[Category: Jaudzems, K.]]	+	[[Category: Jaudzems, K]]
-	[[Category: Liepinsh, E.]]	+	[[Category: Liepinsh, E]]
-	[[Category: Otting, G.]]	+	[[Category: Otting, G]]
-	[[Category: Zhulenkovs, D.]]	+	[[Category: Zhulenkovs, D]]
	[[Category: Dna binding protein]]		[[Category: Dna binding protein]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]

OCA at 10:06, 24 March 2013

OCA — Sun, 24 Mar 2013 10:06:58 GMT

←Older revision		Revision as of 10:06, 24 March 2013
Line 1:		Line 1:
-	[[Image:2lrr.jpg\|left\|200px]]
-
	{{STRUCTURE_2lrr\| PDB=2lrr \| SCENE= }}		{{STRUCTURE_2lrr\| PDB=2lrr \| SCENE= }}
-
	===Solution structure of the R3H domain from human Smubp-2 in complex with 2'-deoxyguanosine-5'-monophosphate===		===Solution structure of the R3H domain from human Smubp-2 in complex with 2'-deoxyguanosine-5'-monophosphate===
-
	{{ABSTRACT_PUBMED_22999958}}		{{ABSTRACT_PUBMED_22999958}}
		+
		+	==Disease==
		+	[[http://www.uniprot.org/uniprot/SMBP2_HUMAN SMBP2_HUMAN]] Defects in IGHMBP2 are the cause of distal hereditary motor neuronopathy type 6 (HMN6) [MIM:[http://omim.org/entry/604320 604320]]; also known as spinal muscular atrophy distal autosomal recessive 1 (DSMA1) or spinal muscular atrophy with respiratory distress 1 (SMARD1). Distal hereditary motor neuronopathies constitute a heterogeneous group of neuromuscular disorders caused by selective degeneration of motor neurons in the anterior horn of the spinal cord, without sensory deficit in the posterior horn. The overall clinical picture consists of a classical distal muscular atrophy syndrome in the legs without clinical sensory loss. The disease starts with weakness and wasting of distal muscles of the anterior tibial and peroneal compartments of the legs. Later on, weakness and atrophy may expand to the proximal muscles of the lower limbs and/or to the distal upper limbs. The most prominent symptoms of HMN6 are severe respiratory distress resulting from diaphragmatic paralysis with eventration shown on chest x-ray and predominant involvement of the upper limbs and distal muscles.<ref>PMID:19158098</ref><ref>PMID:11528396</ref><ref>PMID:14681881</ref><ref>PMID:15108294</ref><ref>PMID:15797190</ref><ref>PMID:17431882</ref><ref>PMID:18802676</ref>
		+
		+	==Function==
		+	[[http://www.uniprot.org/uniprot/SMBP2_HUMAN SMBP2_HUMAN]] 5' to 3' helicase that unwinds RNA and DNA duplices in an ATP-dependent reaction. Acts as a transcription regulator. Required for the transcriptional activation of the flounder liver-type antifreeze protein gene. Exhibits strong binding specificity to the enhancer element B of the flounder antifreeze protein gene intron. Binds to the insulin II gene RIPE3B enhancer region. May be involved in translation (By similarity). DNA-binding protein specific to 5'-phosphorylated single-stranded guanine-rich sequence related to the immunoglobulin mu chain switch region. Preferentially binds to the 5'-GGGCT-3' motif. Interacts with tRNA-Tyr. Stimulates the transcription of the human neurotropic virus JCV.<ref>PMID:19158098</ref><ref>PMID:19299493</ref>

	==About this Structure==		==About this Structure==
	[[2lrr]] 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=2LRR OCA].		[[2lrr]] 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=2LRR OCA].
		+
		+	==Reference==
		+	<references group="xtra"/><references/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Jaudzems, K.]]		[[Category: Jaudzems, K.]]

OCA at 07:38, 24 October 2012

OCA — Wed, 24 Oct 2012 07:38:27 GMT

←Older revision		Revision as of 07:38, 24 October 2012
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:2lrr.jpg\|left\|200px]]

-	~~The entry~~ 2lrr ~~is ON HOLD~~ ~~until Paper Publication~~	+	{{STRUCTURE_2lrr\| PDB=2lrr \| SCENE= }}

-	~~Authors: Jaudzems, K., Zhulenkovs, D., Otting, G., Liepinsh, E.~~	+	===Solution structure of the R3H domain from human Smubp-2 in complex with 2'-deoxyguanosine-5'-monophosphate===

-	~~Description: Solution~~ structure ~~of the R3H domain~~ from ~~human Smubp~~-~~2 in complex with 2'-deoxyguanosine-5'-monophosphate~~	+	{{ABSTRACT_PUBMED_22999958}}
		+
		+	==About this Structure==
		+	[[2lrr]] 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=2LRR OCA].
		+	[[Category: Homo sapiens]]
		+	[[Category: Jaudzems, K.]]
		+	[[Category: Liepinsh, E.]]
		+	[[Category: Otting, G.]]
		+	[[Category: Zhulenkovs, D.]]
		+	[[Category: Dna binding protein]]
		+	[[Category: Hydrolase]]

OCA at 04:38, 8 August 2012

OCA — Wed, 08 Aug 2012 04:38:05 GMT

←Older revision		Revision as of 04:38, 8 August 2012
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 2lrr is ON HOLD	+	The entry 2lrr is ON HOLD until Paper Publication

	Authors: Jaudzems, K., Zhulenkovs, D., Otting, G., Liepinsh, E.		Authors: Jaudzems, K., Zhulenkovs, D., Otting, G., Liepinsh, E.

	Description: Solution structure of the R3H domain from human Smubp-2 in complex with 2'-deoxyguanosine-5'-monophosphate		Description: Solution structure of the R3H domain from human Smubp-2 in complex with 2'-deoxyguanosine-5'-monophosphate

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

OCA — Wed, 18 Apr 2012 07:15:18 GMT

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

←Older revision

Revision as of 07:15, 18 April 2012