This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


3i3m

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (10:03, 21 February 2024) (edit) (undo)
 
(10 intermediate revisions not shown.)
Line 1: Line 1:
-
'''Unreleased structure'''
 
-
The entry 3i3m is ON HOLD until Paper Publication
+
==Crystal Structure of AlkB in complex with Mn(II), 2-oxoglutarate and methylated trinucleotide T-meC-T==
 +
<StructureSection load='3i3m' size='340' side='right'caption='[[3i3m]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
 +
== Structural highlights ==
 +
<table><tr><td colspan='2'>[[3i3m]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3I3M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3I3M FirstGlance]. <br>
 +
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.5&#8491;</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=ME6:[(2R,3S,5R)-5-(4-AZANYL-3-METHYL-2-OXO-PYRIMIDIN-3-IUM-1-YL)-3-HYDROXY-OXOLAN-2-YL]METHYL+DIHYDROGEN+PHOSPHATE'>ME6</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=3i3m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3i3m OCA], [https://pdbe.org/3i3m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3i3m RCSB], [https://www.ebi.ac.uk/pdbsum/3i3m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3i3m ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/ALKB_ECOLI ALKB_ECOLI] Dioxygenase that repairs alkylated DNA and RNA containing 3-methylcytosine or 1-methyladenine by oxidative demethylation. Has highest activity towards 3-methylcytosine. Has lower activity towards alkylated DNA containing ethenoadenine, and no detectable activity towards 1-methylguanine or 3-methylthymine. Accepts double-stranded and single-stranded substrates. Requires molecular oxygen, alpha-ketoglutarate and iron. Provides extensive resistance to alkylating agents such as MMS and DMS (SN2 agents), but not to MMNG and MNU (SN1 agents).<ref>PMID:12226668</ref> <ref>PMID:12594517</ref> <ref>PMID:16482161</ref> <ref>PMID:19706517</ref> <ref>PMID:21068844</ref> <ref>PMID:20084272</ref>
 +
== 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/i3/3i3m_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/main_output.php?pdb_ID=3i3m ConSurf].
 +
<div style="clear:both"></div>
-
Authors: Yu, B., Hunt, J.F.
+
==See Also==
-
 
+
*[[Dioxygenase 3D structures|Dioxygenase 3D structures]]
-
Description: Crystal Structure of AlkB in complex with Mn(II), 2-oxoglutarate and methylated trinucleotide T-meC-T
+
== References ==
-
 
+
<references/>
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Aug 5 09:47:14 2009''
+
__TOC__
 +
</StructureSection>
 +
[[Category: Escherichia coli K-12]]
 +
[[Category: Large Structures]]
 +
[[Category: Hunt JF]]
 +
[[Category: Yu B]]

Current revision

Crystal Structure of AlkB in complex with Mn(II), 2-oxoglutarate and methylated trinucleotide T-meC-T

PDB ID 3i3m

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3i3m"
Personal tools