2k8i

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==Solution structure of E.Coli SlyD==
==Solution structure of E.Coli SlyD==
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<StructureSection load='2k8i' size='340' side='right'caption='[[2k8i]], [[NMR_Ensembles_of_Models | 10 NMR models]]' scene=''>
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<StructureSection load='2k8i' size='340' side='right'caption='[[2k8i]]' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[2k8i]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2K8I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2K8I FirstGlance]. <br>
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<table><tr><td colspan='2'>[[2k8i]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2K8I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2K8I FirstGlance]. <br>
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</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">slyD, Ecok1_33310, APECO1_3105 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
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<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Peptidylprolyl_isomerase Peptidylprolyl isomerase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.2.1.8 5.2.1.8] </span></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=2k8i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2k8i OCA], [https://pdbe.org/2k8i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2k8i RCSB], [https://www.ebi.ac.uk/pdbsum/2k8i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2k8i ProSAT]</span></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=2k8i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2k8i OCA], [https://pdbe.org/2k8i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2k8i RCSB], [https://www.ebi.ac.uk/pdbsum/2k8i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2k8i ProSAT]</span></td></tr>
</table>
</table>
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== Function ==
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[https://www.uniprot.org/uniprot/SLYD_ECOLI SLYD_ECOLI] Folding helper with both chaperone and peptidyl-prolyl cis-trans isomerase (PPIase) activities. Chaperone activity prevents aggregation of unfolded or partially folded proteins and promotes their correct folding. PPIases catalyze the cis-trans isomerization of Xaa-Pro bonds of peptides, which accelerates slow steps of protein folding and thus shortens the lifetime of intermediates. Both strategies lower the concentration of intermediates and increase the productivity and yield of the folding reaction. SlyD could be involved in Tat-dependent translocation, by binding to the Tat-type signal of folded proteins. The PPIase substrate specificity, carried out with synthetic peptides of the 'suc-Ala-Xaa-Pro-Phe-4NA' type (where Xaa is the AA tested), was found to be Phe > Ala > Leu.<ref>PMID:12100551</ref> <ref>PMID:15569666</ref> <ref>PMID:16388577</ref> <ref>PMID:17720786</ref> <ref>PMID:17215254</ref> <ref>PMID:19356587</ref> Required for lysis of phiX174 infected cells by stabilizing the hydrophobic viral lysis protein E and allowing it to accumulate to the levels required to exert its lytic effect. May act by a chaperone-like mechanism.<ref>PMID:12100551</ref> <ref>PMID:15569666</ref> <ref>PMID:16388577</ref> <ref>PMID:17720786</ref> <ref>PMID:17215254</ref> <ref>PMID:19356587</ref> Also involved in hydrogenase metallocenter assembly, probably by participating in the nickel insertion step. This function in hydrogenase biosynthesis requires chaperone activity and the presence of the metal-binding domain, but not PPIase activity.<ref>PMID:12100551</ref> <ref>PMID:15569666</ref> <ref>PMID:16388577</ref> <ref>PMID:17720786</ref> <ref>PMID:17215254</ref> <ref>PMID:19356587</ref>
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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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=2k8i ConSurf].
</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=2k8i ConSurf].
<div style="clear:both"></div>
<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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SlyD (sensitive to lysis D) is a putative folding helper from the bacterial cytosol and harbors prolyl isomerase and chaperone activities. We determined the solution NMR structure of a truncated version of SlyD (1-165) from Escherichia coli (SlyD*) that lacks the presumably unstructured C-terminal tail. SlyD* consists of two well-separated domains: the FKBP domain, which harbors the prolyl isomerase activity, and the insert-in-flap (IF) domain, which harbors the chaperone activity. The IF domain is inserted into a loop of the FKBP domain near the prolyl isomerase active site. The NMR structure of SlyD* showed no distinct orientation of the two domains relative to each other. In the FKBP domain, Tyr68 points into the active site, which might explain the lowered intrinsic prolyl isomerase activity and the much lower FK506 binding affinity of the protein compared with archetype human FKBP12 (human FK506 binding protein with 12 kDa). The thermodynamics and kinetics of substrate binding by SlyD* were quantified by fluorescence resonance energy transfer. NMR titration experiments revealed that the IF domain recognizes and binds unfolded or partially folded proteins and peptides. Insulin aggregation is markedly slowed by SlyD* as evidenced by two-dimensional NMR spectroscopy in real time, probably due to SlyD* binding to denatured insulin. The capacity of the IF domain to establish an initial encounter-collision complex, together with the flexible orientation of the two interacting domains, makes SlyD* a very powerful catalyst of protein folding.
 
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NMR solution structure of SlyD from Escherichia coli: spatial separation of prolyl isomerase and chaperone function.,Weininger U, Haupt C, Schweimer K, Graubner W, Kovermann M, Bruser T, Scholz C, Schaarschmidt P, Zoldak G, Schmid FX, Balbach J J Mol Biol. 2009 Mar 27;387(2):295-305. Epub 2009 Jan 27. PMID:19356587<ref>PMID:19356587</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 2k8i" style="background-color:#fffaf0;"></div>
 
==See Also==
==See Also==
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Bacillus coli migula 1895]]
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[[Category: Escherichia coli]]
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Peptidylprolyl isomerase]]
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[[Category: Balbach J]]
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[[Category: Balbach, J]]
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[[Category: Weininger U]]
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[[Category: Weininger, U]]
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[[Category: Chaperone]]
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[[Category: Isomerase]]
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[[Category: Ppiase]]
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[[Category: Rotamase]]
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Current revision

Solution structure of E.Coli SlyD

PDB ID 2k8i

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