3e0f

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[[Image:3e0f.png|left|200px]]
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==Crystal structure of a putative metal-dependent phosphoesterase (bad_1165) from bifidobacterium adolescentis atcc 15703 at 2.40 A resolution==
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<StructureSection load='3e0f' size='340' side='right' caption='[[3e0f]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[3e0f]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bifidobacterium_adolescentis_atcc_15703 Bifidobacterium adolescentis atcc 15703]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3E0F OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3E0F FirstGlance]. <br>
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</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>
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<tr><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
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<tr><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">YP_910028.1, BAD_1165 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=367928 Bifidobacterium adolescentis ATCC 15703])</td></tr>
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<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=3e0f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3e0f OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3e0f RCSB], [http://www.ebi.ac.uk/pdbsum/3e0f PDBsum], [http://www.topsan.org/Proteins/JCSG/3e0f TOPSAN]</span></td></tr>
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<table>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/e0/3e0f_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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The crystal structures of an unliganded and adenosine 5'-monophosphate (AMP) bound, metal-dependent phosphoesterase (YP_910028.1) from Bifidobacterium adolescentis are reported at 2.4 and 1.94 A, respectively. Functional characterization of this enzyme was guided by computational analysis and then confirmed by experiment. The structure consists of a polymerase and histidinol phosphatase (PHP, Pfam: PF02811) domain with a second domain (residues 105-178) inserted in the middle of the PHP sequence. The insert domain functions in binding AMP, but the precise function and substrate specificity of this domain are unknown. Initial bioinformatics analyses yielded multiple potential functional leads, with most of them suggesting DNA polymerase or DNA replication activity. Phylogenetic analysis indicated a potential DNA polymerase function that was somewhat supported by global structural comparisons identifying the closest structural match to the alpha subunit of DNA polymerase III. However, several other functional predictions, including phosphoesterase, could not be excluded. Theoretical microscopic anomalous titration curve shapes, a computational method for the prediction of active sites from protein 3D structures, identified potential reactive residues in YP_910028.1. Further analysis of the predicted active site and local comparison with its closest structure matches strongly suggested phosphoesterase activity, which was confirmed experimentally. Primer extension assays on both normal and mismatched DNA show neither extension nor degradation and provide evidence that YP_910028.1 has neither DNA polymerase activity nor DNA-proofreading activity. These results suggest that many of the sequence neighbors previously annotated as having DNA polymerase activity may actually be misannotated. Proteins 2011. (c) 2011 Wiley-Liss, Inc.
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<!--
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Crystal structure of a metal-dependent phosphoesterase (YP_910028.1) from Bifidobacterium adolescentis: Computational prediction and experimental validation of phosphoesterase activity.,Han GW, Ko J, Farr CL, Deller MC, Xu Q, Chiu HJ, Miller MD, Sefcikova J, Somarowthu S, Beuning PJ, Elsliger MA, Deacon AM, Godzik A, Lesley SA, Wilson IA, Ondrechen MJ Proteins. 2011 Jul;79(7):2146-60. doi: 10.1002/prot.23035. Epub 2011 May, 2. PMID:21538547<ref>PMID:21538547</ref>
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The line below this paragraph, containing "STRUCTURE_3e0f", creates the "Structure Box" on the page.
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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or leave the SCENE parameter empty for the default display.
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-->
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{{STRUCTURE_3e0f| PDB=3e0f | SCENE= }}
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===Crystal structure of a putative metal-dependent phosphoesterase (bad_1165) from bifidobacterium adolescentis atcc 15703 at 2.40 A resolution===
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From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
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</div>
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== References ==
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<!--
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<references/>
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The line below this paragraph, {{ABSTRACT_PUBMED_21538547}}, adds the Publication Abstract to the page
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__TOC__
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(as it appears on PubMed at http://www.pubmed.gov), where 21538547 is the PubMed ID number.
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</StructureSection>
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-->
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{{ABSTRACT_PUBMED_21538547}}
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==About this Structure==
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[[3e0f]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bifidobacterium_adolescentis_atcc_15703 Bifidobacterium adolescentis atcc 15703]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3E0F OCA].
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==Reference==
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<ref group="xtra">PMID:021538547</ref><references group="xtra"/>
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[[Category: Bifidobacterium adolescentis atcc 15703]]
[[Category: Bifidobacterium adolescentis atcc 15703]]
[[Category: JCSG, Joint Center for Structural Genomics.]]
[[Category: JCSG, Joint Center for Structural Genomics.]]

Revision as of 09:50, 21 May 2014

Crystal structure of a putative metal-dependent phosphoesterase (bad_1165) from bifidobacterium adolescentis atcc 15703 at 2.40 A resolution

3e0f, resolution 2.40Å

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