This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

1qka

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Revision as of 22:25, 10 September 2015

OLIGO-PEPTIDE BINDING PROTEIN (OPPA) COMPLEXED WITH KRK

Structural highlights

1qka is a 2 chain structure. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Related:	1qkb, 1ola, 2olb, 1olc, 1jet, 1jeu, 1jev, 1rkm, 2rkm, 1b05, 1b0h, 1b1h, 1b2h, 1b3f, 1b3g, 1b3h, 1b3l, 1b4h, 1b4z, 1b5h, 1b5i, 1b5j, 1b6h, 1b7h, 1b9j, 1b32, 1b40, 1b46, 1b51, 1b52, 1b58
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum

Function

[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

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

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^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Sleigh SH, Seavers PR, Wilkinson AJ, Ladbury JE, Tame JR. Crystallographic and calorimetric analysis of peptide binding to OppA protein. J Mol Biol. 1999 Aug 13;291(2):393-415. PMID:10438628 doi:10.1006/jmbi.1999.2929

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1qka"

Categories: Tame, J R.H | Wilkinson, A J | Peptide transport | Protein transport

@@ Line 2: / Line 2: @@
 <StructureSection load='1qka' size='340' side='right' caption='[[1qka]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1qka]] is a 2 chain structure with sequence from [http://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=1QKA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1QKA FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1qka]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QKA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1QKA FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=IUM:URANYL+(VI)+ION'>IUM</scene></td></tr>
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1qkb|1qkb]], [[1ola|1ola]], [[2olb|2olb]], [[1olc|1olc]], [[1jet|1jet]], [[1jeu|1jeu]], [[1jev|1jev]], [[1rkm|1rkm]], [[2rkm|2rkm]], [[1b05|1b05]], [[1b0h|1b0h]], [[1b1h|1b1h]], [[1b2h|1b2h]], [[1b3f|1b3f]], [[1b3g|1b3g]], [[1b3h|1b3h]], [[1b3l|1b3l]], [[1b4h|1b4h]], [[1b4z|1b4z]], [[1b5h|1b5h]], [[1b5i|1b5i]], [[1b5j|1b5j]], [[1b6h|1b6h]], [[1b7h|1b7h]], [[1b9j|1b9j]], [[1b32|1b32]], [[1b40|1b40]], [[1b46|1b46]], [[1b51|1b51]], [[1b52|1b52]], [[1b58|1b58]]</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">OPPA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=90371 Salmonella enterica subsp. enterica serovar Typhimurium])</td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1qka FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qka OCA], [http://pdbe.org/1qka PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1qka RCSB], [http://www.ebi.ac.uk/pdbsum/1qka PDBsum]</span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1qka FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qka OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1qka RCSB], [http://www.ebi.ac.uk/pdbsum/1qka PDBsum]</span></td></tr>
 </table>
 == Function ==
@@ Line 28: / Line 27: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 1qka" style="background-color:#fffaf0;"></div>
 ==See Also==
@@ Line 35: / Line 35: @@
 __TOC__
 </StructureSection>
-[[Category: Salmonella enterica subsp. enterica serovar typhimurium]]
 [[Category: Tame, J R.H]]
 [[Category: Wilkinson, A J]]
 [[Category: Peptide transport]]
 [[Category: Protein transport]]

1qka

From Proteopedia

Revision as of 22:25, 10 September 2015

OLIGO-PEPTIDE BINDING PROTEIN (OPPA) COMPLEXED WITH KRK

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox