1b4z: Difference between revisions

Revision as of 12:51, 21 February 2008

OLIGO-PEPTIDE BINDING PROTEIN (OPPA) COMPLEXED WITH KDK

OverviewOverview

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.

About this StructureAbout this Structure

1B4Z is a Single protein structure of sequence from Salmonella typhimurium with and as ligands. Full crystallographic information is available from OCA.

ReferenceReference

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

Page seeded by OCA on Thu Feb 21 11:51:30 2008

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OCA

@@ Line 1: / Line 1: @@
-[[Image:1b4z.gif|left|200px]]<br /><applet load="1b4z" size="450" color="white" frame="true" align="right" spinBox="true"
+[[Image:1b4z.gif|left|200px]]<br /><applet load="1b4z" size="350" color="white" frame="true" align="right" spinBox="true"
 caption="1b4z, resolution 1.75&Aring;" />
 '''OLIGO-PEPTIDE BINDING PROTEIN (OPPA) COMPLEXED WITH KDK'''<br />
 ==Overview==
-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.
+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.
 ==About this Structure==
-B4Z is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Salmonella_typhimurium Salmonella typhimurium] with IUM and ACT as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1B4Z OCA].
+B4Z is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Salmonella_typhimurium Salmonella typhimurium] with <scene name='pdbligand=IUM:'>IUM</scene> and <scene name='pdbligand=ACT:'>ACT</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1B4Z OCA].
 ==Reference==
@@ Line 13: / Line 13: @@
 [[Category: Salmonella typhimurium]]
 [[Category: Single protein]]
-[[Category: Sleigh, S.H.]]
+[[Category: Sleigh, S H.]]
-[[Category: Tame, J.R.H.]]
+[[Category: Tame, J R.H.]]
-[[Category: Wilkinson, A.J.]]
+[[Category: Wilkinson, A J.]]
 [[Category: ACT]]
 [[Category: IUM]]
@@ Line 21: / Line 21: @@
 [[Category: peptide transport]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 11:22:00 2007''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 11:51:30 2008''