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| | ==Crystal structure of a putative metal-dependent phosphoesterase (bad_1165) from bifidobacterium adolescentis atcc 15703 at 2.40 A resolution== | | ==Crystal structure of a putative metal-dependent phosphoesterase (bad_1165) from bifidobacterium adolescentis atcc 15703 at 2.40 A resolution== |
| - | <StructureSection load='3e0f' size='340' side='right' caption='[[3e0f]], [[Resolution|resolution]] 2.40Å' scene=''> | + | <StructureSection load='3e0f' size='340' side='right'caption='[[3e0f]], [[Resolution|resolution]] 2.40Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3e0f]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bifaa Bifaa]. 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> | + | <table><tr><td colspan='2'>[[3e0f]] is a 1 chain structure with sequence from [https://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 [https://proteopedia.org/fgij/fg.htm?mol=3E0F FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><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></td></tr> | + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</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=3e0f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3e0f OCA], [https://pdbe.org/3e0f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3e0f RCSB], [https://www.ebi.ac.uk/pdbsum/3e0f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3e0f ProSAT], [https://www.topsan.org/Proteins/JCSG/3e0f TOPSAN]</span></td></tr> |
| - | <tr id='gene'><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 BIFAA])</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=3e0f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3e0f OCA], [http://pdbe.org/3e0f PDBe], [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> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/A1A2L3_BIFAA A1A2L3_BIFAA] |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
| | Check<jmol> | | Check<jmol> |
| | <jmolCheckbox> | | <jmolCheckbox> |
| - | <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/e0/3e0f_consurf.spt"</scriptWhenChecked> | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/e0/3e0f_consurf.spt"</scriptWhenChecked> |
| | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> |
| | <text>to colour the structure by Evolutionary Conservation</text> | | <text>to colour the structure by Evolutionary Conservation</text> |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bifaa]] | + | [[Category: Bifidobacterium adolescentis ATCC 15703]] |
| - | [[Category: Structural genomic]] | + | [[Category: Large Structures]] |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: Jcsg]]
| + | |
| - | [[Category: PSI, Protein structure initiative]]
| + | |
| Structural highlights
3e0f is a 1 chain structure with sequence from Bifidobacterium adolescentis ATCC 15703. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Ligands: | , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT, TOPSAN |
Function
A1A2L3_BIFAA
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
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.
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[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ 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. Crystal structure of a metal-dependent phosphoesterase (YP_910028.1) from Bifidobacterium adolescentis: Computational prediction and experimental validation of phosphoesterase activity. Proteins. 2011 Jul;79(7):2146-60. doi: 10.1002/prot.23035. Epub 2011 May, 2. PMID:21538547 doi:10.1002/prot.23035
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