2dri: Difference between revisions

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==PROBING PROTEIN-PROTEIN INTERACTIONS: THE RIBOSE BINDING PROTEIN IN BACTERIAL TRANSPORT AND CHEMOTAXIS==
==PROBING PROTEIN-PROTEIN INTERACTIONS: THE RIBOSE BINDING PROTEIN IN BACTERIAL TRANSPORT AND CHEMOTAXIS==
<StructureSection load='2dri' size='340' side='right' caption='[[2dri]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
<StructureSection load='2dri' size='340' side='right'caption='[[2dri]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[2dri]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1dri 1dri]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DRI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DRI FirstGlance]. <br>
<table><tr><td colspan='2'>[[2dri]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1dri 1dri]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DRI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DRI FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=RIP:RIBOSE(PYRANOSE+FORM)'>RIP</scene></td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.6&#8491;</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=2dri FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dri OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2dri RCSB], [http://www.ebi.ac.uk/pdbsum/2dri PDBsum]</span></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=RIP:RIBOSE(PYRANOSE+FORM)'>RIP</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=2dri FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dri OCA], [https://pdbe.org/2dri PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dri RCSB], [https://www.ebi.ac.uk/pdbsum/2dri PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dri ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[http://www.uniprot.org/uniprot/RBSB_ECOLI RBSB_ECOLI]] Involved in the high-affinity D-ribose membrane transport system and also serves as the primary chemoreceptor for chemotaxis.  
[https://www.uniprot.org/uniprot/RBSB_ECOLI RBSB_ECOLI] Involved in the high-affinity D-ribose membrane transport system and also serves as the primary chemoreceptor for chemotaxis.
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
Check<jmol>
   <jmolCheckbox>
   <jmolCheckbox>
     <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dr/2dri_consurf.spt"</scriptWhenChecked>
     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dr/2dri_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
   </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/chain_selection.php?pdb_ID=2ata 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=2dri ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
A number of mutations at Gly134 of the periplasmic ribose-binding protein of Escherichia coli were examined by a combined biochemical and structural approach. Different mutations gave rise to different patterns of effects on the chemotaxis and transport functions. The smallest residue (alanine) had the least effect on transport, whereas large hydrophobic residues had the smallest effect on chemotaxis. Comparison of the x-ray crystal structure of the G134R mutant protein (2.5-A resolution) to that of the wild type (1.6-A resolution) showed that the basic structure of the protein was unaltered. The loss of chemotaxis and transport functions in this and similar mutant proteins must therefore be caused by relatively simple surface effects, which include a change in local main chain conformation. The loss of chemotaxis and transport functions resulting from the introduction of an alanine residue at position 134 was suppressed by an additional isoleucine to threonine mutation at residue 132. An x-ray structure of the I132T/G134A double mutant protein (2.2-A resolution) showed that the changes in local structure were accompanied by a diffuse pattern of structural changes in the surrounding region, implying that the suppression derives from a combination of sources.
Probing protein-protein interactions. The ribose-binding protein in bacterial transport and chemotaxis.,Bjorkman AJ, Binnie RA, Zhang H, Cole LB, Hermodson MA, Mowbray SL J Biol Chem. 1994 Dec 2;269(48):30206-11. PMID:7982928<ref>PMID:7982928</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>


==See Also==
==See Also==
*[[Journal:JBSD:22|Journal:JBSD:22]]
*[[Molecular Playground/RBP|Molecular Playground/RBP]]
*[[Ribose-binding protein|Ribose-binding protein]]
*[[Ribose-binding protein|Ribose-binding protein]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
[[Category: Cole, L B]]
[[Category: Large Structures]]
[[Category: Mowbray, S L]]
[[Category: Cole LB]]
[[Category: Sugar transport]]
[[Category: Mowbray SL]]

Latest revision as of 12:19, 14 February 2024

PROBING PROTEIN-PROTEIN INTERACTIONS: THE RIBOSE BINDING PROTEIN IN BACTERIAL TRANSPORT AND CHEMOTAXISPROBING PROTEIN-PROTEIN INTERACTIONS: THE RIBOSE BINDING PROTEIN IN BACTERIAL TRANSPORT AND CHEMOTAXIS

Structural highlights

2dri is a 1 chain structure with sequence from Escherichia coli. This structure supersedes the now removed PDB entry 1dri. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.6Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RBSB_ECOLI Involved in the high-affinity D-ribose membrane transport system and also serves as the primary chemoreceptor for chemotaxis.

Evolutionary Conservation

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

See Also

2dri, resolution 1.60Å

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