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[[Image:3ldb.png|left|200px]]
==Structure of JMJD6 complexd with ALPHA-KETOGLUTARATE and Fab Fragment.==
<StructureSection load='3ldb' size='340' side='right' caption='[[3ldb]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[3ldb]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Cricetulus_migratorius Cricetulus migratorius] and [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LDB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3LDB 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=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HG:MERCURY+(II)+ION'>HG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3ld8|3ld8]]</td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">JMJD6, JMJD6 (1-403), KIAA0585, PTDSR ([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=3ldb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ldb OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ldb RCSB], [http://www.ebi.ac.uk/pdbsum/3ldb PDBsum]</span></td></tr>
</table>
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ld/3ldb_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
JMJD6 is a Jumonji C domain-containing hydroxylase. JMJD6 binds alpha-ketoglutarate and iron and has been characterized as either a histone arginine demethylase or U2AF65 lysyl hydroxylase. Here, we describe the structures of JMJD6 with and without alpha-ketoglutarate, which revealed a novel substrate binding groove and two positively charged surfaces. The structures also contain a stack of aromatic residues located near the active center. The side chain of one residue within this stack assumed different conformations in the two structures. Interestingly, JMJD6 bound efficiently to single-stranded RNA, but not to single-stranded DNA, double-stranded RNA, or double-stranded DNA. These structural features and truncation analysis of JMJD6 suggest that JMJD6 may bind and modify single-stand RNA rather than the previously reported peptide substrates.


{{STRUCTURE_3ldb|  PDB=3ldb  |  SCENE=  }}
Interaction of JMJD6 with single-stranded RNA.,Hong X, Zang J, White J, Wang C, Pan CH, Zhao R, Murphy RC, Dai S, Henson P, Kappler JW, Hagman J, Zhang G Proc Natl Acad Sci U S A. 2010 Aug 17;107(33):14568-72. Epub 2010 Aug 2. PMID:20679243<ref>PMID:20679243</ref>


===Structure of JMJD6 complexd with ALPHA-KETOGLUTARATE and Fab Fragment.===
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 
</div>
{{ABSTRACT_PUBMED_20679243}}
 
==About this Structure==
[[3ldb]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Cricetulus_migratorius Cricetulus migratorius] and [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LDB OCA].


==See Also==
==See Also==
*[[Antibody|Antibody]]
*[[Monoclonal Antibody|Monoclonal Antibody]]
*[[Monoclonal Antibody|Monoclonal Antibody]]
 
== References ==
==Reference==
<references/>
<ref group="xtra">PMID:020679243</ref><references group="xtra"/>
__TOC__
</StructureSection>
[[Category: Cricetulus migratorius]]
[[Category: Cricetulus migratorius]]
[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
[[Category: Hong, X.]]
[[Category: Hong, X]]
[[Category: Kappler, J W.]]
[[Category: Kappler, J W]]
[[Category: Wang, C.]]
[[Category: Wang, C]]
[[Category: White, J.]]
[[Category: White, J]]
[[Category: Zang, J.]]
[[Category: Zang, J]]
[[Category: Zhang, G.]]
[[Category: Zhang, G]]
[[Category: Alpha-ketoglutarate]]
[[Category: Alpha-ketoglutarate]]
[[Category: Fab fragment]]
[[Category: Fab fragment]]
[[Category: Immune system]]
[[Category: Immune system]]
[[Category: Jmj6d]]
[[Category: Jmj6d]]

Revision as of 13:04, 9 December 2014

Structure of JMJD6 complexd with ALPHA-KETOGLUTARATE and Fab Fragment.Structure of JMJD6 complexd with ALPHA-KETOGLUTARATE and Fab Fragment.

Structural highlights

3ldb is a 3 chain structure with sequence from Cricetulus migratorius and Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:, , , ,
Gene:JMJD6, JMJD6 (1-403), KIAA0585, PTDSR (Homo sapiens)
Resources:FirstGlance, OCA, RCSB, PDBsum

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

JMJD6 is a Jumonji C domain-containing hydroxylase. JMJD6 binds alpha-ketoglutarate and iron and has been characterized as either a histone arginine demethylase or U2AF65 lysyl hydroxylase. Here, we describe the structures of JMJD6 with and without alpha-ketoglutarate, which revealed a novel substrate binding groove and two positively charged surfaces. The structures also contain a stack of aromatic residues located near the active center. The side chain of one residue within this stack assumed different conformations in the two structures. Interestingly, JMJD6 bound efficiently to single-stranded RNA, but not to single-stranded DNA, double-stranded RNA, or double-stranded DNA. These structural features and truncation analysis of JMJD6 suggest that JMJD6 may bind and modify single-stand RNA rather than the previously reported peptide substrates.

Interaction of JMJD6 with single-stranded RNA.,Hong X, Zang J, White J, Wang C, Pan CH, Zhao R, Murphy RC, Dai S, Henson P, Kappler JW, Hagman J, Zhang G Proc Natl Acad Sci U S A. 2010 Aug 17;107(33):14568-72. Epub 2010 Aug 2. PMID:20679243[1]

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

See Also

References

  1. ↑ Hong X, Zang J, White J, Wang C, Pan CH, Zhao R, Murphy RC, Dai S, Henson P, Kappler JW, Hagman J, Zhang G. Interaction of JMJD6 with single-stranded RNA. Proc Natl Acad Sci U S A. 2010 Aug 17;107(33):14568-72. Epub 2010 Aug 2. PMID:20679243 doi:10.1073/pnas.1008832107

3ldb, resolution 2.70Å

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