1b58: Difference between revisions
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==OLIGO-PEPTIDE BINDING PROTEIN (OPPA) COMPLEXED WITH KYK== | |||
<StructureSection load='1b58' size='340' side='right'caption='[[1b58]], [[Resolution|resolution]] 1.80Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[1b58]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_Typhimurium Salmonella enterica subsp. enterica serovar Typhimurium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1B58 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1B58 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]] 1.8Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=IUM:URANYL+(VI)+ION'>IUM</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=1b58 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1b58 OCA], [https://pdbe.org/1b58 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1b58 RCSB], [https://www.ebi.ac.uk/pdbsum/1b58 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1b58 ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/OPPA_SALTY OPPA_SALTY] This protein is a component of the oligopeptide permease, a binding protein-dependent transport system, it binds peptides up to five amino acids long with high affinity. | |||
== 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/b5/1b58_consurf.spt"</scriptWhenChecked> | |||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=1b58 ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Isothermal titration calorimetry has been used to study the binding of 20 different peptides to the peptide binding protein OppA, and the crystal structures of the ligand complexes have been refined. This periplasmic binding protein, part of the oligopeptide permease system of Gram negative bacteria, has evolved to bind and enclose small peptides of widely varying sequences. The peptides used in this study have the sequence Lys-X-Lys, where X is any of the 20 commonly occurring amino acids. The various side-chains found at position 2 on the ligand fit into a hydrated pocket. The majority of side-chains are restrained to particular conformations within the pocket. Water molecules act as flexible adapters, matching the hydrogen-bonding requirements of the protein and ligand and shielding charges on the buried ligand. This use of water by OppA to broaden the repertoire of its binding site is not unique, but contrasts sharply with other proteins which use water to help bind ligands highly selectively. Predicting the thermodynamics of binding from the structure of the complexes is highly complicated by the influence of water on the system. | |||
Crystallographic and calorimetric analysis of peptide binding to OppA protein.,Sleigh SH, Seavers PR, Wilkinson AJ, Ladbury JE, Tame JR J Mol Biol. 1999 Aug 13;291(2):393-415. PMID:10438628<ref>PMID:10438628</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 1b58" style="background-color:#fffaf0;"></div> | |||
==See Also== | ==See Also== | ||
*[[ | *[[ABC transporter 3D structures|ABC transporter 3D structures]] | ||
== References == | |||
== | <references/> | ||
< | __TOC__ | ||
[[Category: Salmonella enterica subsp. enterica serovar | </StructureSection> | ||
[[Category: Tame | [[Category: Large Structures]] | ||
[[Category: Wilkinson | [[Category: Salmonella enterica subsp. enterica serovar Typhimurium]] | ||
[[Category: Tame JRH]] | |||
[[Category: Wilkinson AJ]] | |||
Latest revision as of 02:48, 21 November 2024
OLIGO-PEPTIDE BINDING PROTEIN (OPPA) COMPLEXED WITH KYKOLIGO-PEPTIDE BINDING PROTEIN (OPPA) COMPLEXED WITH KYK
Structural highlights
FunctionOPPA_SALTY This protein is a component of the oligopeptide permease, a binding protein-dependent transport system, it binds peptides up to five amino acids long with high affinity. Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedIsothermal titration calorimetry has been used to study the binding of 20 different peptides to the peptide binding protein OppA, and the crystal structures of the ligand complexes have been refined. This periplasmic binding protein, part of the oligopeptide permease system of Gram negative bacteria, has evolved to bind and enclose small peptides of widely varying sequences. The peptides used in this study have the sequence Lys-X-Lys, where X is any of the 20 commonly occurring amino acids. The various side-chains found at position 2 on the ligand fit into a hydrated pocket. The majority of side-chains are restrained to particular conformations within the pocket. Water molecules act as flexible adapters, matching the hydrogen-bonding requirements of the protein and ligand and shielding charges on the buried ligand. This use of water by OppA to broaden the repertoire of its binding site is not unique, but contrasts sharply with other proteins which use water to help bind ligands highly selectively. Predicting the thermodynamics of binding from the structure of the complexes is highly complicated by the influence of water on the system. Crystallographic and calorimetric analysis of peptide binding to OppA protein.,Sleigh SH, Seavers PR, Wilkinson AJ, Ladbury JE, Tame JR J Mol Biol. 1999 Aug 13;291(2):393-415. PMID:10438628[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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