2qmo

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[[Image:2qmo.png|left|200px]]
 
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==Crystal structure of dethiobiotin synthetase (bioD) from Helicobacter pylori==
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The line below this paragraph, containing "STRUCTURE_2qmo", creates the "Structure Box" on the page.
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<StructureSection load='2qmo' size='340' side='right'caption='[[2qmo]], [[Resolution|resolution]] 1.47&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[2qmo]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Helicobacter_pylori_26695 Helicobacter pylori 26695]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QMO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2QMO FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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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]] 1.47&#8491;</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=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
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{{STRUCTURE_2qmo| PDB=2qmo | SCENE= }}
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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=2qmo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qmo OCA], [https://pdbe.org/2qmo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2qmo RCSB], [https://www.ebi.ac.uk/pdbsum/2qmo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2qmo ProSAT], [https://www.topsan.org/Proteins/MCSG/2qmo TOPSAN]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/BIOD_HELPY BIOD_HELPY] Catalyzes a mechanistically unusual reaction, the ATP-dependent insertion of CO2 between the N7 and N8 nitrogen atoms of 7,8-diaminopelargonic acid (DAPA) to form an ureido ring (By similarity).[HAMAP-Rule:MF_00336]
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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/qm/2qmo_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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/main_output.php?pdb_ID=2qmo 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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Dethiobiotin synthetase (DTBS) is involved in the biosynthesis of biotin in bacteria, fungi, and plants. As humans lack this pathway, DTBS is a promising antimicrobial drug target. We determined structures of DTBS from Helicobacter pylori (hpDTBS) bound with cofactors and a substrate analog, and described its unique characteristics relative to other DTBS proteins. Comparison with bacterial DTBS orthologs revealed considerable structural differences in nucleotide recognition. The C-terminal region of DTBS proteins, which contains two nucleotide-recognition motifs, differs greatly among DTBS proteins from different species. The structure of hpDTBS revealed that this protein is unique and does not contain a C-terminal region containing one of the motifs. The single nucleotide-binding motif in hpDTBS is similar to its counterpart in GTPases; however, isothermal titration calorimetry binding studies showed that hpDTBS has a strong preference for ATP. The structural determinants of ATP specificity were assessed with X-ray crystallographic studies of hpDTBS.ATP and hpDTBS.GTP complexes. The unique mode of nucleotide recognition in hpDTBS makes this protein a good target for H. pylori-specific inhibitors of the biotin synthesis pathway. Database Coordinates and structure factors for structures presented in this article have been deposited in the Protein Data Bank under the following accession codes: 2QMO - apo-form; 3MLE - hpDTBS.8-ac.ADP. in P2(1) 2(1) 2(1) form; 3QXC - hpDTBS.ATP; 3QXH - hpDTBS.8-ac:ADP. in C2 form; 3QXJ - hpDTBS.GTP; 3QXS - hpDTBS.ANP; 3QXX - 8-ac.GDP.; and 3QY0 - hpDTBS.GDP.. Structured digital abstract * hpDTBS and hpDTBS bind by x-ray crystallography (View interaction).
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===Crystal structure of dethiobiotin synthetase (bioD) from Helicobacter pylori===
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Structural characterization of Helicobacter pylori dethiobiotin synthetase reveals differences between family members.,Porebski PJ, Klimecka M, Chruszcz M, Nicholls RA, Murzyn K, Cuff ME, Xu X, Cymborowski M, Murshudov GN, Savchenko A, Edwards A, Minor W FEBS J. 2012 Jan 27. doi: 10.1111/j.1742-4658.2012.08506.x. PMID:22284390<ref>PMID:22284390</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 2qmo" style="background-color:#fffaf0;"></div>
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==See Also==
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The line below this paragraph, {{ABSTRACT_PUBMED_22284390}}, adds the Publication Abstract to the page
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*[[Dethiobiotin synthetase 3D structures|Dethiobiotin synthetase 3D structures]]
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(as it appears on PubMed at http://www.pubmed.gov), where 22284390 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_22284390}}
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__TOC__
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</StructureSection>
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==About this Structure==
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[[Category: Helicobacter pylori 26695]]
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[[2qmo]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Helicobacter_pylori Helicobacter pylori]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QMO OCA].
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[[Category: Large Structures]]
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[[Category: Chruszcz M]]
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==Reference==
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[[Category: Cuff M]]
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<ref group="xtra">PMID:022284390</ref><references group="xtra"/>
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[[Category: Cymborowski M]]
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[[Category: Dethiobiotin synthase]]
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[[Category: Edwards A]]
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[[Category: Helicobacter pylori]]
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[[Category: Joachimiak A]]
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[[Category: Chruszcz, M.]]
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[[Category: Minor W]]
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[[Category: Cuff, M.]]
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[[Category: Savchenko A]]
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[[Category: Cymborowski, M.]]
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[[Category: Xu X]]
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[[Category: Edwards, A.]]
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[[Category: Zheng H]]
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[[Category: Joachimiak, A.]]
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[[Category: MCSG, Midwest Center for Structural Genomics.]]
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[[Category: Minor, W.]]
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[[Category: Savchenko, A.]]
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[[Category: Xu, X.]]
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[[Category: Zheng, H.]]
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[[Category: Atp-binding]]
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[[Category: Biotin biosynthesis]]
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[[Category: Dethiobiotin synthetase]]
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[[Category: Ligase]]
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[[Category: Magnesium]]
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[[Category: Mcsg]]
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[[Category: Midwest center for structural genomic]]
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[[Category: Nucleotide-binding]]
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[[Category: Protein structure initiative]]
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[[Category: Psi-2]]
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[[Category: Structural genomic]]
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Current revision

Crystal structure of dethiobiotin synthetase (bioD) from Helicobacter pylori

PDB ID 2qmo

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