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3b5j

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Crystal Structures of the S504A Mutant of an Isolated ABC-ATPase in Complex with TNP-ADP

Structural highlights

3b5j is a 1 chain structure with sequence from Escherichia coli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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

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

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.

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^[1]

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

References

↑ Oswald C, Jenewein S, Smits SH, Holland IB, Schmitt L. Water-mediated protein-fluorophore interactions modulate the affinity of an ABC-ATPase/TNP-ADP complex. J Struct Biol. 2008 Apr;162(1):85-93. Epub 2007 Nov 21. PMID:18155559 doi:http://dx.doi.org/10.1016/j.jsb.2007.11.006

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/3b5j"

@@ Line 3: / Line 3: @@
 <StructureSection load='3b5j' size='340' side='right'caption='[[3b5j]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3b5j]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. 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>
+<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>
-</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>
+</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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2pmk|2pmk]]</div></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>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">hlyB ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=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.
+[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]]
@@ Line 37: / Line 36: @@
 __TOC__
 </StructureSection>
-[[Category: Bacillus coli migula 1895]]
+[[Category: Escherichia coli]]
 [[Category: Large Structures]]
-[[Category: Holland, I B]]
+[[Category: Holland IB]]
-[[Category: Jenewein, S]]
+[[Category: Jenewein S]]
-[[Category: Oswald, C]]
+[[Category: Oswald C]]
-[[Category: Schmitt, L]]
+[[Category: Schmitt L]]
-[[Category: Smits, S H.J]]
+[[Category: Smits SHJ]]
-[[Category: Abc-transporter]]
-[[Category: Atp-binding]]
-[[Category: Atpase]]
-[[Category: Hydrolase]]
-[[Category: Inner membrane]]
-[[Category: Membrane]]
-[[Category: Nucleotide-binding doamin]]
-[[Category: Transmembrane]]
-[[Category: Transport protein]]

3b5j

From Proteopedia

Current revision

Crystal Structures of the S504A Mutant of an Isolated ABC-ATPase in Complex with TNP-ADP

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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