1kn9

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[[Image:1kn9.png|left|200px]]
 
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==CRYSTAL STRUCTURE OF A BACTERIAL SIGNAL PEPTIDASE APO-ENZYME, IMPLICATIONS FOR SIGNAL PEPTIDE BINDING AND THE SER-LYS DYAD MECHANISM.==
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The line below this paragraph, containing "STRUCTURE_1kn9", creates the "Structure Box" on the page.
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<StructureSection load='1kn9' size='340' side='right'caption='[[1kn9]], [[Resolution|resolution]] 2.40&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'>[[1kn9]] 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=1KN9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KN9 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]] 2.4&#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=1kn9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kn9 OCA], [https://pdbe.org/1kn9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kn9 RCSB], [https://www.ebi.ac.uk/pdbsum/1kn9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kn9 ProSAT]</span></td></tr>
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{{STRUCTURE_1kn9| PDB=1kn9 | SCENE= }}
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/LEP_ECOLI LEP_ECOLI]
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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/kn/1kn9_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=1kn9 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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We report here the x-ray crystal structure of a soluble catalytically active fragment of the Escherichia coli type I signal peptidase (SPase-(Delta2-75)) in the absence of inhibitor or substrate (apoenzyme). The structure was solved by molecular replacement and refined to 2.4 A resolution in a different space group (P4(1)2(1)2) from that of the previously published acyl-enzyme inhibitor-bound structure (P2(1)2(1)2) (Paetzel, M., Dalbey, R.E., and Strynadka, N.C.J. (1998) Nature 396, 186-190). A comparison with the acyl-enzyme structure shows significant side-chain and main-chain differences in the binding site and active site regions, which result in a smaller S1 binding pocket in the apoenzyme. The apoenzyme structure is consistent with SPase utilizing an unusual oxyanion hole containing one side-chain hydroxyl hydrogen (Ser-88 OgammaH) and one main-chain amide hydrogen (Ser-90 NH). Analysis of the apoenzyme active site reveals a potential deacylating water that was displaced by the inhibitor. It has been proposed that SPase utilizes a Ser-Lys dyad mechanism in the cleavage reaction. A similar mechanism has been proposed for the LexA family of proteases. A structural comparison of SPase and members of the LexA family of proteases reveals a difference in the side-chain orientation for the general base lysine, both of which are stabilized by an adjacent hydroxyl group. To gain insight into how signal peptidase recognizes its substrates, we have modeled a signal peptide into the binding site of SPase. The model is built based on the recently solved crystal structure of the analogous enzyme LexA (Luo, Y., Pfuetzner, R. A., Mosimann, S., Paetzel, M., Frey, E. A., Cherney, M., Kim, B., Little, J. W., and Strynadka, N. C. J. (2001) Cell 106, 1-10) with its bound cleavage site region.
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===CRYSTAL STRUCTURE OF A BACTERIAL SIGNAL PEPTIDASE APO-ENZYME, IMPLICATIONS FOR SIGNAL PEPTIDE BINDING AND THE SER-LYS DYAD MECHANISM.===
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Crystal structure of a bacterial signal peptidase apoenzyme: implications for signal peptide binding and the Ser-Lys dyad mechanism.,Paetzel M, Dalbey RE, Strynadka NC J Biol Chem. 2002 Mar 15;277(11):9512-9. Epub 2001 Dec 10. PMID:11741964<ref>PMID:11741964</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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The line below this paragraph, {{ABSTRACT_PUBMED_11741964}}, adds the Publication Abstract to the page
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<div class="pdbe-citations 1kn9" style="background-color:#fffaf0;"></div>
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(as it appears on PubMed at http://www.pubmed.gov), where 11741964 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_11741964}}
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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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1KN9 is a [[Single protein]] structure of 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=1KN9 OCA].
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[[Category: Large Structures]]
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[[Category: Dalbey RE]]
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==Reference==
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[[Category: Paetzel M]]
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Crystal structure of a bacterial signal peptidase apoenzyme: implications for signal peptide binding and the Ser-Lys dyad mechanism., Paetzel M, Dalbey RE, Strynadka NC, J Biol Chem. 2002 Mar 15;277(11):9512-9. Epub 2001 Dec 10. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11741964 11741964]
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[[Category: Strynadka NCJ]]
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[[Category: Escherichia coli]]
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[[Category: Signal peptidase I]]
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[[Category: Single protein]]
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[[Category: Dalbey, R E.]]
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[[Category: Paetzel, M.]]
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[[Category: Strynadka, N C.J.]]
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[[Category: Lysine general base]]
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[[Category: Membrane protein]]
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[[Category: Mostly beta-fold]]
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[[Category: Serine protease]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jul 2 10:35:15 2008''
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Current revision

CRYSTAL STRUCTURE OF A BACTERIAL SIGNAL PEPTIDASE APO-ENZYME, IMPLICATIONS FOR SIGNAL PEPTIDE BINDING AND THE SER-LYS DYAD MECHANISM.

PDB ID 1kn9

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