3mkm

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[[Image:3mkm.png|left|200px]]
 
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==Crystal structure of the E. coli pyrimidine nucleoside hydrolase YeiK (Apo-form)==
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The line below this paragraph, containing "STRUCTURE_3mkm", creates the "Structure Box" on the page.
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<StructureSection load='3mkm' size='340' side='right'caption='[[3mkm]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
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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'>[[3mkm]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3MKM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3MKM FirstGlance]. <br>
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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]] 2.2&#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=CA:CALCIUM+ION'>CA</scene></td></tr>
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{{STRUCTURE_3mkm| PDB=3mkm | 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=3mkm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3mkm OCA], [https://pdbe.org/3mkm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3mkm RCSB], [https://www.ebi.ac.uk/pdbsum/3mkm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3mkm ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/C3T3U2_ECOLX C3T3U2_ECOLX] Hydrolyzes cytidine or uridine to ribose and cytosine or uracil, respectively. Has a clear preference for cytidine over uridine. Strictly specific for ribonucleosides (By similarity).[HAMAP-Rule:MF_01433]
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Conformational changes modulate macromolecular function by promoting the specific binding of ligands (such as in antigen recognition) or the stabilization of transition states in enzymatic reactions. However, quantitative characterization of the energetics underlying dynamic structural interconversions is still challenging and lacks a unified method. Here, we introduce a novel in silico approach based on the combined use of essential dynamics sampling and nonequilibrium free-energy calculations to obtain quantitative data on conformational energy landscapes. This technique allows the unbiased investigation of highly complex rearrangements, and does not require the crucial definition of user-defined collective variables. We show that free-energy values derived from profiles connecting the unliganded and ligand-bound X-ray structures of a bacterial nucleoside hydrolase match the experimental binding constant. This approach also provides first evidence for a rate-limiting character of the conformational transition in this enzyme, and an unexpected role of the protonation state of a single residue in regulating substrate binding and product release.
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===Crystal structure of the E. coli pyrimidine nucleoside hydrolase YeiK (Apo-form)===
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Energy Landscapes Associated with Macromolecular Conformational Changes from Endpoint Structures.,Fornili A, Giabbai B, Garau G, Degano M J Am Chem Soc. 2010 Nov 17. PMID:21082835<ref>PMID:21082835</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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The line below this paragraph, {{ABSTRACT_PUBMED_21082835}}, adds the Publication Abstract to the page
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<div class="pdbe-citations 3mkm" style="background-color:#fffaf0;"></div>
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(as it appears on PubMed at http://www.pubmed.gov), where 21082835 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_21082835}}
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__TOC__
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</StructureSection>
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==About this Structure==
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[[Category: Escherichia coli K-12]]
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[[3mkm]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3MKM OCA].
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[[Category: Large Structures]]
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[[Category: Degano M]]
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==Reference==
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[[Category: Fornili A]]
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<ref group="xtra">PMID:21082835</ref><ref group="xtra">PMID:15130467</ref><ref group="xtra">PMID:16411753</ref><ref group="xtra">PMID:9572842</ref><references group="xtra"/>
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[[Category: Garau G]]
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[[Category: Escherichia coli]]
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[[Category: Giabbai B]]
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[[Category: Ribosylpyrimidine nucleosidase]]
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[[Category: Degano, M.]]
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[[Category: Fornili, A.]]
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[[Category: Garau, G.]]
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[[Category: Giabbai, B.]]
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[[Category: Bacterial nucleosidase]]
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[[Category: Hydrolase]]
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[[Category: Metalloenzyme]]
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[[Category: Nucleotide metabolism]]
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[[Category: Pyrimidine nucleoside hydrolase]]
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Current revision

Crystal structure of the E. coli pyrimidine nucleoside hydrolase YeiK (Apo-form)

PDB ID 3mkm

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