1dy6: Difference between revisions

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{{Seed}}
[[Image:1dy6.png|left|200px]]


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==Structure of the imipenem-hydrolyzing beta-lactamase SME-1==
The line below this paragraph, containing "STRUCTURE_1dy6", creates the "Structure Box" on the page.
<StructureSection load='1dy6' size='340' side='right'caption='[[1dy6]], [[Resolution|resolution]] 2.13&Aring;' scene=''>
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== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<table><tr><td colspan='2'>[[1dy6]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Serratia_marcescens Serratia marcescens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DY6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DY6 FirstGlance]. <br>
or leave the SCENE parameter empty for the default display.
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.13&#8491;</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=1dy6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dy6 OCA], [https://pdbe.org/1dy6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dy6 RCSB], [https://www.ebi.ac.uk/pdbsum/1dy6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dy6 ProSAT]</span></td></tr>
{{STRUCTURE_1dy6|  PDB=1dy6  |  SCENE=  }}
</table>
== Function ==
[https://www.uniprot.org/uniprot/Q54488_SERMA Q54488_SERMA]
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dy/1dy6_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</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=1dy6 ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The structure of the beta-lactamase SME-1 from Serratia marcescens, a class A enzyme characterized by its significant activity against imipenem, has been determined to 2.13 A resolution. The overall structure of SME-1 is similar to that of other class A beta-lactamases. In the active-site cavity, most of the residues found in SME-1 are conserved among class A beta-lactamases, except at positions 104, 105 and 237, where a tyrosine, a histidine and a serine are found, respectively, and at position 238, which is occupied by a cysteine forming a disulfide bridge with the other cysteine residue located at position 69. The crucial role played by this disulfide bridge in SME-1 was confirmed by site-directed mutagenesis of Cys69 to Ala, which resulted in a mutant unable to confer resistance to imipenem and all other beta-lactam antibiotics tested. Another striking structural feature found in SME-1 was the short distance separating the side chains of the active serine residue at position 70 and the strictly conserved glutamate at position 166, which is up to 1.4 A shorter in SME-1 compared with other class A beta-lactamases. Consequently, the SME-1 structure cannot accommodate the essential catalytic water molecule found between Ser70 and Glu166 in the other class A beta-lactamases described so far, suggesting that a significant conformational change may be necessary in SME-1 to properly position the hydrolytic water molecule involved in the hydrolysis of the acyl-enzyme intermediate.


===STRUCTURE OF THE IMIPENEM-HYDROLYZING BETA-LACTAMASE SME-1===
Structure of the imipenem-hydrolyzing class A beta-lactamase SME-1 from Serratia marcescens.,Sougakoff W, L'Hermite G, Pernot L, Naas T, Guillet V, Nordmann P, Jarlier V, Delettre J Acta Crystallogr D Biol Crystallogr. 2002 Feb;58(Pt 2):267-74. Epub 2002, Jan 24. PMID:11807251<ref>PMID:11807251</ref>


From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1dy6" style="background-color:#fffaf0;"></div>


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==See Also==
The line below this paragraph, {{ABSTRACT_PUBMED_11807251}}, adds the Publication Abstract to the page
*[[Beta-lactamase 3D structures|Beta-lactamase 3D structures]]
(as it appears on PubMed at http://www.pubmed.gov), where 11807251 is the PubMed ID number.
== References ==
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<references/>
{{ABSTRACT_PUBMED_11807251}}
__TOC__
 
</StructureSection>
==About this Structure==
[[Category: Large Structures]]
1DY6 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Serratia_marcescens Serratia marcescens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DY6 OCA].
 
==Reference==
Structure of the imipenem-hydrolyzing class A beta-lactamase SME-1 from Serratia marcescens., Sougakoff W, L'Hermite G, Pernot L, Naas T, Guillet V, Nordmann P, Jarlier V, Delettre J, Acta Crystallogr D Biol Crystallogr. 2002 Feb;58(Pt 2):267-74. Epub 2002, Jan 24. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11807251 11807251]
[[Category: Beta-lactamase]]
[[Category: Serratia marcescens]]
[[Category: Serratia marcescens]]
[[Category: Single protein]]
[[Category: Billy I]]
[[Category: Billy, I.]]
[[Category: Delettre J]]
[[Category: Delettre, J.]]
[[Category: Guillet V]]
[[Category: Guillet, V.]]
[[Category: Jarlier V]]
[[Category: Hermite, G L.]]
[[Category: L'Hermite G]]
[[Category: Jarlier, V.]]
[[Category: Naas T]]
[[Category: Naas, T.]]
[[Category: Nordman P]]
[[Category: Nordman, P.]]
[[Category: Sougakoff W]]
[[Category: Sougakoff, W.]]
[[Category: Antibiotic]]
[[Category: Carbapenem]]
[[Category: Hydrolase]]
[[Category: Imipenem]]
[[Category: Lactamase]]
 
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Retrieved from "https://proteopedia.org/1dy6"