4oct

From Proteopedia

(Difference between revisions)

Revision as of 11:24, 24 December 2014

Crystal structure of human ALKBH5 crystallized in the presence of Mn^{2+} and 2-oxoglutarate

Structural highlights

4oct is a 2 chain structure with sequence from Human. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, ,
Gene:	ALKBH5, ABH5, OFOXD1 (HUMAN)
Resources:	FirstGlance, OCA, RCSB, PDBsum

Function

[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.^[1] ^[2]

Publication Abstract from PubMed

N6-Methyladenosine (m6A) is the most prevalent internal RNA modification in eukaryotes. ALKBH5 belongs to the AlkB family of dioxygenases and has been shown to specifically demethylate m6A in single stranded RNA. Here we report crystal structures of ALKBH5 in the presence of either its cofactors or the ALKBH5 inhibitor citrate. Catalytic assays demonstrate that the ALKBH5 catalytic domain can demethylate both ssRNA and ssDNA. We identify the tricarboxylic acid (TCA) cycle intermediate citrate as a modest inhibitor of ALKHB5 (IC50: ~488 muM). The structural analysis reveals that a loop region of ALKBH5 is immobilized by a disulfide bond which apparently excludes the binding of dsDNA to ALKBH5. We identify the m6A binding pocket of ALKBH5 and the key residues involved in m6A recognition using mutagenesis and ITC binding experiments.

Structures of human ALKBH5 demethylase reveal a unique binding mode for specific single stranded m6A RNA demethylation.,Xu C, Liu K, Tempel W, Demetriades M, Aik W, Schofield CJ, Min J J Biol Chem. 2014 Apr 28. PMID:24778178^[3]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Thalhammer A, Bencokova Z, Poole R, Loenarz C, Adam J, O'Flaherty L, Schodel J, Mole D, Giaslakiotis K, Schofield CJ, Hammond EM, Ratcliffe PJ, Pollard PJ. Human AlkB homologue 5 is a nuclear 2-oxoglutarate dependent oxygenase and a direct target of hypoxia-inducible factor 1alpha (HIF-1alpha). PLoS One. 2011 Jan 14;6(1):e16210. doi: 10.1371/journal.pone.0016210. PMID:21264265 doi:http://dx.doi.org/10.1371/journal.pone.0016210
↑ Zheng G, Dahl JA, Niu Y, Fedorcsak P, Huang CM, Li CJ, Vagbo CB, Shi Y, Wang WL, Song SH, Lu Z, Bosmans RP, Dai Q, Hao YJ, Yang X, Zhao WM, Tong WM, Wang XJ, Bogdan F, Furu K, Fu Y, Jia G, Zhao X, Liu J, Krokan HE, Klungland A, Yang YG, He C. ALKBH5 is a mammalian RNA demethylase that impacts RNA metabolism and mouse fertility. Mol Cell. 2013 Jan 10;49(1):18-29. doi: 10.1016/j.molcel.2012.10.015. Epub 2012, Nov 21. PMID:23177736 doi:http://dx.doi.org/10.1016/j.molcel.2012.10.015
↑ Xu C, Liu K, Tempel W, Demetriades M, Aik W, Schofield CJ, Min J. Structures of human ALKBH5 demethylase reveal a unique binding mode for specific single stranded m6A RNA demethylation. J Biol Chem. 2014 Apr 28. PMID:24778178 doi:http://dx.doi.org/10.1074/jbc.M114.550350

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/4oct"

@@ Line 3: / Line 3: @@
 == Structural highlights ==
 <table><tr><td colspan='2'>[[4oct]] 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=4OCT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4OCT FirstGlance]. <br>
-</td></tr><tr><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>, <scene name='pdbligand=UNX:UNKNOWN+ATOM+OR+ION'>UNX</scene><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>, <scene name='pdbligand=UNX:UNKNOWN+ATOM+OR+ION'>UNX</scene></td></tr>
-<tr><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ALKBH5, ABH5, 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">ALKBH5, ABH5, OFOXD1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
-<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4oct FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4oct OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4oct RCSB], [http://www.ebi.ac.uk/pdbsum/4oct 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=4oct FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4oct OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4oct RCSB], [http://www.ebi.ac.uk/pdbsum/4oct PDBsum]</span></td></tr>
-<table>
+</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>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 13: / Line 15: @@
 Structures of human ALKBH5 demethylase reveal a unique binding mode for specific single stranded m6A RNA demethylation.,Xu C, Liu K, Tempel W, Demetriades M, Aik W, Schofield CJ, Min J J Biol Chem. 2014 Apr 28. PMID:24778178<ref>PMID:24778178</ref>
-From MEDLINEÂ®/PubMedÂ®, a database of the U.S. National Library of Medicine.<br>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
 == References ==
@@ Line 20: / Line 22: @@
 </StructureSection>
 [[Category: Human]]
-[[Category: Arrowsmith, C H.]]
+[[Category: Arrowsmith, C H]]
-[[Category: Bountra, C.]]
+[[Category: Bountra, C]]
-[[Category: Cerovina, T.]]
+[[Category: Cerovina, T]]
-[[Category: Chao, X.]]
+[[Category: Chao, X]]
-[[Category: Dong, A.]]
+[[Category: Dong, A]]
-[[Category: Edwards, A M.]]
+[[Category: Edwards, A M]]
-[[Category: He, H.]]
+[[Category: He, H]]
-[[Category: Liu, K.]]
+[[Category: Liu, K]]
-[[Category: Min, J.]]
+[[Category: Min, J]]
-[[Category: SGC, Structural Genomics Consortium.]]
+[[Category: Structural genomic]]
-[[Category: Tempel, W.]]
+[[Category: Tempel, W]]
 [[Category: Oxidoreductase]]
 [[Category: Rna demethylase]]
 [[Category: Sgc]]
-[[Category: Structural genomic]]
-[[Category: Structural genomics consortium]]

4oct

From Proteopedia

Revision as of 11:24, 24 December 2014

Crystal structure of human ALKBH5 crystallized in the presence of Mn^{2+} and 2-oxoglutarate

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox