3b5j: Difference between revisions

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-{{Seed}}
-[[Image:3b5j.png|left|200px]]
-<!--
+==Crystal Structures of the S504A Mutant of an Isolated ABC-ATPase in Complex with TNP-ADP==
-The line below this paragraph, containing "STRUCTURE_3b5j", creates the "Structure Box" on the page.
+<StructureSection load='3b5j' size='340' side='right'caption='[[3b5j]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[3b5j]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3B5J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3B5J FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=12D:2,3-O-[(1R,6R)-2,4,6-TRINITROCYCLOHEXA-2,4-DIENE-1,1-DIYL]ADENOSINE+5-(TRIHYDROGEN+DIPHOSPHATE)'>12D</scene></td></tr>
-{{STRUCTURE_3b5j|  PDB=3b5j  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3b5j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3b5j OCA], [https://pdbe.org/3b5j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3b5j RCSB], [https://www.ebi.ac.uk/pdbsum/3b5j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3b5j ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/HLYBP_ECOLX HLYBP_ECOLX] Part of the ABC transporter complex HlyBD involved in hemolysin export. Transmembrane domains (TMD) form a pore in the inner membrane and the ATP-binding domain (NBD) is responsible for energy generation.
+== 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/b5/3b5j_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=3b5j ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+TNP-modified nucleotides have been used extensively to study protein-nucleotide interactions. In the case of ABC-ATPases, application of these powerful tools has been greatly restricted due to the significantly higher affinity of the TNP-nucleotide for the corresponding ABC-ATPase in comparison to the non-modified nucleotides. To understand the molecular changes occurring upon binding of the TNP-nucleotide to an ABC-ATPase, we have determined the crystal structure of the TNP-ADP/HlyB-NBD complex at 1.6A resolution. Despite the higher affinity of TNP-ADP, no direct fluorophore-protein interactions were observed. Unexpectedly, only water-mediated interactions were detected between the TNP moiety and Tyr(477), that is engaged in pi-pi stacking with the adenine ring, as well as with two serine residues (Ser(504) and Ser(509)) of the Walker A motif. Interestingly, the side chains of these two serine residues adopt novel conformations that are not observed in the corresponding ADP structure. However, in the crystal structure of the S504A mutant, which binds TNP-ADP with similar affinity to the wild type enzyme, a novel TNP-water interaction compensates for the missing serine side chain. Since this water molecule is not present in the wild type enzyme, these results suggest that only water-mediated interactions provide a structural explanation for the increased affinity of TNP-nucleotides towards ABC-ATPases. However, our results also imply that in silico approaches such as docking or modeling cannot directly be applied to generate 'affinity-adopted' ADP- or ATP-analogs for ABC-ATPases.
-===Crystal Structures of the S504A Mutant of an Isolated ABC-ATPase in Complex with TNP-ADP===
+Water-mediated protein-fluorophore interactions modulate the affinity of an ABC-ATPase/TNP-ADP complex.,Oswald C, Jenewein S, Smits SH, Holland IB, Schmitt L J Struct Biol. 2008 Apr;162(1):85-93. Epub 2007 Nov 21. PMID:18155559<ref>PMID:18155559</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3b5j" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_18155559}}, adds the Publication Abstract to the page
+*[[ABC transporter 3D structures|ABC transporter 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 18155559 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_18155559}}
+__TOC__
+</StructureSection>
-==About this Structure==
-B5J is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3B5J OCA].
-==Reference==
-<ref group="xtra">PMID:18155559</ref><references group="xtra"/>
 [[Category: Escherichia coli]]
-[[Category: Holland, I B.]]
+[[Category: Large Structures]]
-[[Category: Jenewein, S.]]
+[[Category: Holland IB]]
-[[Category: Oswald, C.]]
+[[Category: Jenewein S]]
-[[Category: Schmitt, L.]]
+[[Category: Oswald C]]
-[[Category: Smits, S H.J.]]
+[[Category: Schmitt L]]
-[[Category: Abc-transporter]]
+[[Category: Smits SHJ]]
-[[Category: Atp-binding]]
-[[Category: Atpase]]
-[[Category: Hydrolase]]
-[[Category: Inner membrane]]
-[[Category: Membrane]]
-[[Category: Nucleotide-binding doamin]]
-[[Category: Plasmid]]
-[[Category: Transmembrane]]
-[[Category: Transport protein]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 11:29:08 2009''