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3qxg

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==Crystal structure of pyrophosphatase from bacteroides thetaiotaomicron complexed with calcium, a closed cap conformation==
==Crystal structure of pyrophosphatase from bacteroides thetaiotaomicron complexed with calcium, a closed cap conformation==
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<StructureSection load='3qxg' size='340' side='right' caption='[[3qxg]], [[Resolution|resolution]] 1.24&Aring;' scene=''>
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<StructureSection load='3qxg' size='340' side='right'caption='[[3qxg]], [[Resolution|resolution]] 1.24&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[3qxg]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_thetaiotaomicron"_distaso_1912 "bacillus thetaiotaomicron" distaso 1912]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QXG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3QXG FirstGlance]. <br>
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<table><tr><td colspan='2'>[[3qxg]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacteroides_thetaiotaomicron Bacteroides thetaiotaomicron]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QXG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3QXG FirstGlance]. <br>
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</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=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=TLA:L(+)-TARTARIC+ACID'>TLA</scene></td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.24&#8491;</td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3qu2|3qu2]], [[3qu4|3qu4]], [[3qu5|3qu5]], [[3qu7|3qu7]], [[3qu9|3qu9]], [[3qub|3qub]], [[3quc|3quc]], [[3quq|3quq]], [[3qut|3qut]], [[3qyp|3qyp]], [[3qx7|3qx7]], [[3r9k|3r9k]]</td></tr>
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<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=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=TLA:L(+)-TARTARIC+ACID'>TLA</scene></td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">BT_2127 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=818 "Bacillus thetaiotaomicron" Distaso 1912])</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3qxg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qxg OCA], [https://pdbe.org/3qxg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3qxg RCSB], [https://www.ebi.ac.uk/pdbsum/3qxg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3qxg ProSAT]</span></td></tr>
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<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Inorganic_diphosphatase Inorganic diphosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.1.1 3.6.1.1] </span></td></tr>
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<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=3qxg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qxg OCA], [http://pdbe.org/3qxg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3qxg RCSB], [http://www.ebi.ac.uk/pdbsum/3qxg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3qxg ProSAT]</span></td></tr>
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</table>
</table>
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<div style="background-color:#fffaf0;">
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== Function ==
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== Publication Abstract from PubMed ==
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[https://www.uniprot.org/uniprot/Q8A5V9_BACTN Q8A5V9_BACTN]
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The explosion of protein sequence information requires that current strategies for function assignment evolve to complement experimental approaches with computationally based function prediction. This necessitates the development of strategies based on the identification of sequence markers in the form of specificity determinants and a more informed definition of orthologues. Herein, we have undertaken the function assignment of the unknown haloalkanoate dehalogenase superfamily member BT2127 (Uniprot accession code Q8A5 V9) from Bacteroides thetaiotaomicron using an integrated bioinformatics-structure-mechanism approach. The substrate specificity profile and steady-state rate constants of BT2127 (with a k(cat)/K(m) value for pyrophosphate of ~1 x 10(5) M(-1) s(-1)), together with the gene context, support the assigned in vivo function as an inorganic pyrophosphatase. The X-ray structural analysis of wild-type BT2127 and several variants generated by site-directed mutagenesis shows that substrate discrimination is based, in part, on active site space restrictions imposed by the cap domain (specifically by residues Tyr76 and Glu47). Structure-guided site-directed mutagenesis coupled with kinetic analysis of the mutant enzymes identified the residues required for catalysis, substrate binding, and domain-domain association. On the basis of this structure-function analysis, the catalytic residues Asp11, Asp13, Thr113, and Lys147 as well the metal binding residues Asp171, Asn172, and Glu47 were used as markers to confirm BT2127 orthologues identified via sequence searches. This bioinformatic analysis demonstrated that the biological range of BT2127 orthologue is restricted to the phylum Bacteroidetes/Chlorobi. The key structural determinants in the divergence of BT2127 and its closest homologue, beta-phosphoglucomutase, control the leaving group size (phosphate vs glucose phosphate) and the position of the Asp acid/base in the open versus closed conformations. HADSF pyrophosphatases represent a third mechanistic and fold type for bacterial pyrophosphatases.
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Divergence of structure and function in the haloacid dehalogenase enzyme superfamily: Bacteroides thetaiotaomicron BT2127 is an inorganic pyrophosphatase.,Huang H, Patskovsky Y, Toro R, Farelli JD, Pandya C, Almo SC, Allen KN, Dunaway-Mariano D Biochemistry. 2011 Oct 18;50(41):8937-49. Epub 2011 Sep 21. PMID:21894910<ref>PMID:21894910</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 3qxg" style="background-color:#fffaf0;"></div>
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==See Also==
==See Also==
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*[[Inorganic pyrophosphatase|Inorganic pyrophosphatase]]
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*[[Inorganic pyrophosphatase 3D structures|Inorganic pyrophosphatase 3D structures]]
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Bacillus thetaiotaomicron distaso 1912]]
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[[Category: Bacteroides thetaiotaomicron]]
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[[Category: Inorganic diphosphatase]]
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[[Category: Large Structures]]
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[[Category: Almo, S C]]
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[[Category: Almo SC]]
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[[Category: Burley, S K]]
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[[Category: Burley SK]]
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[[Category: Dunaway-Mariano, D]]
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[[Category: Dunaway-Mariano D]]
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[[Category: EFI, Enzyme Function Initiative]]
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[[Category: Gerlt JA]]
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[[Category: Gerlt, J A]]
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[[Category: Huang H]]
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[[Category: Huang, H]]
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[[Category: Patskovsky Y]]
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[[Category: Structural genomic]]
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[[Category: Toro R]]
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[[Category: Patskovsky, Y]]
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[[Category: Toro, R]]
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[[Category: Efi]]
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[[Category: Enzyme function initiative]]
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[[Category: Hydrolase]]
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[[Category: Magnesium binding site]]
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[[Category: NYSGXRC, New York SGX Research Center for Structural Genomics]]
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[[Category: PSI, Protein structure initiative]]
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[[Category: Pyrophosphatase]]
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Current revision

Crystal structure of pyrophosphatase from bacteroides thetaiotaomicron complexed with calcium, a closed cap conformation

PDB ID 3qxg

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