4nro - Revision history

OCA at 14:49, 8 November 2023

2023-11-08T14:49:22Z

←Older revision		Revision as of 14:49, 8 November 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4nro]] is a 1 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=4NRO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4NRO FirstGlance]. <br>		<table><tr><td colspan='2'>[[4nro]] is a 1 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=4NRO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4NRO FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AKG:2-OXOGLUTARIC+ACID'>AKG</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.3Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AKG:2-OXOGLUTARIC+ACID'>AKG</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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=4nro FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nro OCA], [https://pdbe.org/4nro PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4nro RCSB], [https://www.ebi.ac.uk/pdbsum/4nro PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4nro 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=4nro FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nro OCA], [https://pdbe.org/4nro PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4nro RCSB], [https://www.ebi.ac.uk/pdbsum/4nro PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4nro ProSAT]</span></td></tr>
	</table>		</table>

OCA at 08:35, 18 January 2023

2023-01-18T08:35:35Z

←Older revision		Revision as of 08:35, 18 January 2023
Line 1:		Line 1:
		+
	==Crystal structure of human ALKBH5 in complex with alpha-ketoglutarate==		==Crystal structure of human ALKBH5 in complex with alpha-ketoglutarate==
-	<StructureSection load='4nro' size='340' side='right' caption='[[4nro]], [[Resolution\|resolution]] 2.30Å' scene=''>	+	<StructureSection load='4nro' size='340' side='right'caption='[[4nro]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4nro]] is a 1 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=4NRO OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4NRO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4nro]] is a 1 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=4NRO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4NRO FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AKG:2-OXOGLUTARIC+ACID'>AKG</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AKG:2-OXOGLUTARIC+ACID'>AKG</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4nrm\|4nrm]], [[4nrp\|4nrp]], [[4nrq\|4nrq]]</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=4nro FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nro OCA], [https://pdbe.org/4nro PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4nro RCSB], [https://www.ebi.ac.uk/pdbsum/4nro PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4nro ProSAT]</span></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ABH5, ALKBH5, OFOXD1 ([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=4nro FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nro OCA], [~~http~~://pdbe.org/4nro PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4nro RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4nro PDBsum]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/ALKB5_HUMAN ALKB5_HUMAN]] Dioxygenase that demethylates RNA by oxidative demethylation: specifically demethylates N(6)-methyladenosine (m(6)A) RNA, the most prevalent internal modification of messenger RNA (mRNA) in higher eukaryotes. Requires molecular oxygen, alpha-ketoglutarate and iron. Demethylation of m(6)A mRNA affects mRNA processing and export and is required for spermatogenesis.<ref>PMID:21264265</ref> <ref>PMID:23177736</ref>	+	[https://www.uniprot.org/uniprot/ALKB5_HUMAN ALKB5_HUMAN] Dioxygenase that demethylates RNA by oxidative demethylation: specifically demethylates N(6)-methyladenosine (m(6)A) RNA, the most prevalent internal modification of messenger RNA (mRNA) in higher eukaryotes. Requires molecular oxygen, alpha-ketoglutarate and iron. Demethylation of m(6)A mRNA affects mRNA processing and export and is required for spermatogenesis.<ref>PMID:21264265</ref> <ref>PMID:23177736</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 21:		Line 20:

	==See Also==		==See Also==
-	*[[Dioxygenase\|Dioxygenase]]	+	*[[Dioxygenase 3D structures\|Dioxygenase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
-	[[Category: ~~Chen, Z~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Feng, C~~]]	+	[[Category: Chen Z]]
-	[[Category: ~~Liu, Y~~]]	+	[[Category: Feng C]]
-	[[Category: ~~6-methyl adenosine]]~~	+	[[Category: Liu Y]]
-	~~[[Category: Alkbh5]]~~	+
-	~~[[Category: Demethylation]]~~	+
-	~~[[Category: Human dioxygenase]]~~	+
-	~~[[Category: Metal-binding]]~~	+
-	~~[[Category: Nucleus]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Protein/dna interaction]]~~	+
-	~~[[Category: Rna repair~~]]	+

OCA at 23:38, 21 October 2015

2015-10-21T23:38:27Z

←Older revision		Revision as of 23:38, 21 October 2015
Line 6:		Line 6:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4nrm\|4nrm]], [[4nrp\|4nrp]], [[4nrq\|4nrq]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4nrm\|4nrm]], [[4nrp\|4nrp]], [[4nrq\|4nrq]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ABH5, ALKBH5, OFOXD1 ([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">ABH5, ALKBH5, OFOXD1 ([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=4nro FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nro OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4nro RCSB], [http://www.ebi.ac.uk/pdbsum/4nro 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=4nro FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nro OCA], [http://pdbe.org/4nro PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4nro RCSB], [http://www.ebi.ac.uk/pdbsum/4nro PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/ALKB5_HUMAN ALKB5_HUMAN]] Dioxygenase that demethylates RNA by oxidative demethylation: specifically demethylates N(6)-methyladenosine (m(6)A) RNA, the most prevalent internal modification of messenger RNA (mRNA) in higher eukaryotes. Requires molecular oxygen, alpha-ketoglutarate and iron. Demethylation of m(6)A mRNA affects mRNA processing and export and is required for spermatogenesis.<ref>PMID:21264265</ref> <ref>PMID:23177736</ref>		[[http://www.uniprot.org/uniprot/ALKB5_HUMAN ALKB5_HUMAN]] Dioxygenase that demethylates RNA by oxidative demethylation: specifically demethylates N(6)-methyladenosine (m(6)A) RNA, the most prevalent internal modification of messenger RNA (mRNA) in higher eukaryotes. Requires molecular oxygen, alpha-ketoglutarate and iron. Demethylation of m(6)A mRNA affects mRNA processing and export and is required for spermatogenesis.<ref>PMID:21264265</ref> <ref>PMID:23177736</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	N(6)-Methylation of adenosine is the most ubiquitous and abundant modification of nucleoside in eukaryotic mRNA and long non-coding RNA. This modification plays an essential role in the regulation of mRNA translation and RNA metabolism. Recently, human AlkB homolog 5 (Alkbh5) and fat mass- and obesity-associated protein (FTO) were shown to erase this methyl modification on mRNA. Here, we report five high resolution crystal structures of the catalytic core of Alkbh5 in complex with different ligands. Compared with other AlkB proteins, Alkbh5 displays several unique structural features on top of the conserved double-stranded beta-helix fold typical of this protein family. Among the unique features, a distinct "lid" region of Alkbh5 plays a vital role in substrate recognition and catalysis. An unexpected disulfide bond between Cys-230 and Cys-267 is crucial for the selective binding of Alkbh5 to single-stranded RNA/DNA by bringing a "flipping" motif toward the central beta-helix fold. We generated a substrate binding model of Alkbh5 based on a demethylation activity assay of several structure-guided site-directed mutants. Crystallographic and biochemical studies using various analogs of alpha-ketoglutarate revealed that the active site cavity of Alkbh5 is much smaller than that of FTO and preferentially binds small molecule inhibitors. Taken together, our findings provide a structural basis for understanding the substrate recognition specificity of Alkbh5 and offer a foundation for selective drug design against AlkB members.
		+
		+	Crystal structures of the human RNA demethylase Alkbh5 reveal basis for substrate recognition.,Feng C, Liu Y, Wang G, Deng Z, Zhang Q, Wu W, Tong Y, Cheng C, Chen Z J Biol Chem. 2014 Apr 25;289(17):11571-83. doi: 10.1074/jbc.M113.546168. Epub, 2014 Mar 10. PMID:24616105<ref>PMID:24616105</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 4nro" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Dioxygenase\|Dioxygenase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 21:23, 24 December 2014

2014-12-24T21:23:20Z

←Older revision		Revision as of 21:23, 24 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_4nro\| PDB=4nro \| SCENE= }}~~	+	==Crystal structure of human ALKBH5 in complex with alpha-ketoglutarate==
-	===Crystal structure of human ALKBH5 in complex with alpha-ketoglutarate===	+	<StructureSection load='4nro' size='340' side='right' caption='[[4nro]], [[Resolution\|resolution]] 2.30Å' scene=''>
-		+	== Structural highlights ==
-	==Function==	+	<table><tr><td colspan='2'>[[4nro]] is a 1 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=4NRO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4NRO FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AKG:2-OXOGLUTARIC+ACID'>AKG</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4nrm\|4nrm]], [[4nrp\|4nrp]], [[4nrq\|4nrq]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ABH5, ALKBH5, OFOXD1 ([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=4nro FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nro OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4nro RCSB], [http://www.ebi.ac.uk/pdbsum/4nro PDBsum]</span></td></tr>
		+	</table>
		+	== Function ==
	[[http://www.uniprot.org/uniprot/ALKB5_HUMAN ALKB5_HUMAN]] Dioxygenase that demethylates RNA by oxidative demethylation: specifically demethylates N(6)-methyladenosine (m(6)A) RNA, the most prevalent internal modification of messenger RNA (mRNA) in higher eukaryotes. Requires molecular oxygen, alpha-ketoglutarate and iron. Demethylation of m(6)A mRNA affects mRNA processing and export and is required for spermatogenesis.<ref>PMID:21264265</ref> <ref>PMID:23177736</ref>		[[http://www.uniprot.org/uniprot/ALKB5_HUMAN ALKB5_HUMAN]] Dioxygenase that demethylates RNA by oxidative demethylation: specifically demethylates N(6)-methyladenosine (m(6)A) RNA, the most prevalent internal modification of messenger RNA (mRNA) in higher eukaryotes. Requires molecular oxygen, alpha-ketoglutarate and iron. Demethylation of m(6)A mRNA affects mRNA processing and export and is required for spermatogenesis.<ref>PMID:21264265</ref> <ref>PMID:23177736</ref>
-		+	== References ==
-	==~~About this Structure==~~	+	<references/>
-	~~[[4nro]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NRO OCA].~~	+	__TOC__
-		+	</StructureSection>
-	~~==Reference~~==	+	[[Category: Human]]
-	<references ~~group="xtra"~~/><~~references~~/>	+	[[Category: Chen, Z]]
-	[[Category: Chen, Z.]]	+	[[Category: Feng, C]]
-	[[Category: Feng, C.]]	+	[[Category: Liu, Y]]
-	[[Category: Liu, Y.]]	+
	[[Category: 6-methyl adenosine]]		[[Category: 6-methyl adenosine]]
	[[Category: Alkbh5]]		[[Category: Alkbh5]]

OCA at 09:41, 19 March 2014

2014-03-19T09:41:27Z

←Older revision		Revision as of 09:41, 19 March 2014
Line 1:		Line 1:
-	~~'''Unreleased~~ structure~~'''~~	+	{{STRUCTURE_4nro\| PDB=4nro \| SCENE= }}
		+	===Crystal structure of human ALKBH5 in complex with alpha-ketoglutarate===

-	~~The entry 4nro~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	==Function==
		+	[[http://www.uniprot.org/uniprot/ALKB5_HUMAN ALKB5_HUMAN]] Dioxygenase that demethylates RNA by oxidative demethylation: specifically demethylates N(6)-methyladenosine (m(6)A) RNA, the most prevalent internal modification of messenger RNA (mRNA) in higher eukaryotes. Requires molecular oxygen, alpha-ketoglutarate and iron. Demethylation of m(6)A mRNA affects mRNA processing and export and is required for spermatogenesis.<ref>PMID:21264265</ref> <ref>PMID:23177736</ref>

-	~~Authors~~: ~~Feng, C~~.~~, Chen, Z~~.~~, Liu, Y~~.	+	==About this Structure==
		+	[[4nro]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4NRO OCA].

-	~~Description~~: ~~Crystal structure of human ALKBH5 in complex with alpha~~-~~ketoglutarate~~	+	==Reference==
		+	<references group="xtra"/><references/>
		+	[[Category: Chen, Z.]]
		+	[[Category: Feng, C.]]
		+	[[Category: Liu, Y.]]
		+	[[Category: 6-methyl adenosine]]
		+	[[Category: Alkbh5]]
		+	[[Category: Demethylation]]
		+	[[Category: Human dioxygenase]]
		+	[[Category: Metal-binding]]
		+	[[Category: Nucleus]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Protein/dna interaction]]
		+	[[Category: Rna repair]]

OCA at 07:37, 15 January 2014

2014-01-15T07:37:54Z

←Older revision		Revision as of 07:37, 15 January 2014
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4nro is ON HOLD	+	The entry 4nro is ON HOLD until Paper Publication

	Authors: Feng, C., Chen, Z., Liu, Y.		Authors: Feng, C., Chen, Z., Liu, Y.

	Description: Crystal structure of human ALKBH5 in complex with alpha-ketoglutarate		Description: Crystal structure of human ALKBH5 in complex with alpha-ketoglutarate

OCA at 09:20, 18 December 2013

2013-12-18T09:20:52Z

←Older revision		Revision as of 09:20, 18 December 2013
Line 3:		Line 3:
	The entry 4nro is ON HOLD		The entry 4nro is ON HOLD

-	Authors: ~~chong feng~~, ~~zhongzhou chen~~, ~~yang liu~~	+	Authors: Feng, C., Chen, Z., Liu, Y.

	Description: Crystal structure of human ALKBH5 in complex with alpha-ketoglutarate		Description: Crystal structure of human ALKBH5 in complex with alpha-ketoglutarate

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

2013-12-04T06:53:54Z

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

←Older revision

Revision as of 06:53, 4 December 2013

OCA: New page: '''Unreleased structure''' The entry 4nro is ON HOLD Authors: chong feng, zhongzhou chen, yang liu Description: Crystal structure of human ALKBH5 in complex with alpha-ketoglutarate

2013-12-04T06:53:53Z

New page: '''Unreleased structure''' The entry 4nro is ON HOLD Authors: chong feng, zhongzhou chen, yang liu Description: Crystal structure of human ALKBH5 in complex with alpha-ketoglutarate

New page

'''Unreleased structure'''

The entry 4nro is ON HOLD

Authors: chong feng, zhongzhou chen, yang liu

Description: Crystal structure of human ALKBH5 in complex with alpha-ketoglutarate