8ckp: Difference between revisions

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-'''Unreleased structure'''
-The entry 8ckp is ON HOLD
+==X-ray structure of the crystallization-prone form of subfamily III haloalkane dehalogenase DhmeA from Haloferax mediterranei==
+<StructureSection load='8ckp' size='340' side='right'caption='[[8ckp]], [[Resolution|resolution]] 3.31&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[8ckp]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Haloferax_mediterranei Haloferax mediterranei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8CKP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8CKP 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]] 3.31&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</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=8ckp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8ckp OCA], [https://pdbe.org/8ckp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8ckp RCSB], [https://www.ebi.ac.uk/pdbsum/8ckp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8ckp ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/I3R766_HALMT I3R766_HALMT]
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Haloalkane dehalogenase (HLD) enzymes employ an S(N) 2 nucleophilic substitution mechanism to erase halogen substituents in diverse organohalogen compounds. Subfamily I and II HLDs are well-characterized enzymes, but a mode and purpose of multimerization of subfamily III HLDs are unknown. Here we probe the structural organization of DhmeA, a subfamily III HLD-like enzyme from the archaeon Haloferax mediterranei, by combining cryo-electron microscopy (cryo-EM) and X-ray crystallography. We show that full-length wild-type DhmeA forms diverse quaternary structures, ranging from small oligomers to large supramolecular ring-like assemblies of various sizes and symmetries. We optimized sample preparation steps, enabling three-dimensional reconstructions of an oligomeric species by single-particle cryo-EM. Moreover, we engineered a crystallizable mutant (DhmeA(DeltaGG) ) that provided diffraction-quality crystals. The 3.3 A crystal structure reveals that DhmeA(DeltaGG) forms a ring-like 20-mer structure with outer and inner diameter of ~200 A and ~80 A, respectively. An enzyme homodimer represents a basic repeating building unit of the crystallographic ring. Three assembly interfaces (dimerization, tetramerization and multimerization) were identified to form the supramolecular ring that displays a negatively charged exterior, while its interior part harboring catalytic sites is positively charged. Localization and exposure of catalytic machineries suggest a possible processing of large negatively charged macromolecular substrates. This article is protected by copyright. All rights reserved.
-Authors: Marek, M., Chmelova, K., Schenkmayerova, A., Croll, T., Read, R.J., Diederichs, K.
+Multimeric structure of a subfamily III haloalkane dehalogenase-like enzyme solved by combination of cryo-EM and X-ray crystallography.,Chmelova K, Gao T, Polak M, Schenkmayerova A, Croll TI, Shaikh TR, Skarupova J, Chaloupkova R, Diederichs K, Read RJ, Damborsky J, Novacek J, Marek M Protein Sci. 2023 Aug 13:e4751. doi: 10.1002/pro.4751. PMID:37574754<ref>PMID:37574754</ref>
-Description: X-ray structure of the crystallization-prone form of subfamily III haloalkane dehalogenase DhmeA from Haloferax mediterranei
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
-[[Category: Read, R.J]]
+<div class="pdbe-citations 8ckp" style="background-color:#fffaf0;"></div>
-[[Category: Diederichs, K]]
+== References ==
-[[Category: Chmelova, K]]
+<references/>
-[[Category: Schenkmayerova, A]]
+__TOC__
-[[Category: Croll, T]]
+</StructureSection>
-[[Category: Marek, M]]
+[[Category: Haloferax mediterranei]]
+[[Category: Large Structures]]
+[[Category: Chmelova K]]
+[[Category: Croll T]]
+[[Category: Diederichs K]]
+[[Category: Marek M]]
+[[Category: Read RJ]]
+[[Category: Schenkmayerova A]]