5z2l

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of BdcA in complex with NADPH

Structural highlights

5z2l is a 12 chain structure with sequence from Escherichia coli K-12. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.7Å
Ligands:	, , , , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

BDCA_ECOLI Increases biofilm dispersal. Acts by binding directly to the signaling molecule cyclic-di-GMP, which decreases the intracellular concentration of cyclic-di-GMP and leads to biofilm dispersal. Also controls other biofilm-related phenotypes such as cell motility, cell size, cell aggregation and production of extracellular DNA and extracellular polysaccharides (EPS). Does not act as a phosphodiesterase.^[1]

Publication Abstract from PubMed

Biofilm dispersal is characterized by the cell detachment from biofilms and expected to provide novel "anti-biofilm" approaches of prevention and treatment of biofilms in clinical and industrial settings. The E.coli protein BdcA has been identified as a biofilm dispersal factor and designed to be an important component in engineered applications to control biofilm formation. It belongs to short-chain dehydrogenase/reductase (SDR) family with the specific affinity to NADPH. Here, we show the structure of BdcA in complex with NADPH and confirm that NADPH binding is requisite for BdcA facilitating cell motility and increasing biofilm dispersal. Especially, we observe a potential substrate binding pocket surrounded by hydrophobic residues upon NADPH binding and present evidences that this pocket is essential for BdcA binding NADPH and exerting its biological functions. Our study provides the clues for illuminating the molecular mechanism of BdcA regulating biofilm dispersal and better utilizing BdcA to eliminate the biofilms.

A potential substrate binding pocket of BdcA plays a critical role in NADPH recognition and biofilm dispersal.,Yang WS, Hong Y, Zhang Y, Wang DC, Li DF, Hou YJ Biochem Biophys Res Commun. 2018 Mar 11;497(3):863-868. doi:, 10.1016/j.bbrc.2018.02.143. Epub 2018 Feb 17. PMID:29462616^[2]

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

References

↑ Ma Q, Yang Z, Pu M, Peti W, Wood TK. Engineering a novel c-di-GMP-binding protein for biofilm dispersal. Environ Microbiol. 2011 Mar;13(3):631-42. doi: 10.1111/j.1462-2920.2010.02368.x. , Epub 2010 Nov 8. PMID:21059164 doi:http://dx.doi.org/10.1111/j.1462-2920.2010.02368.x
↑ Yang WS, Hong Y, Zhang Y, Wang DC, Li DF, Hou YJ. A potential substrate binding pocket of BdcA plays a critical role in NADPH recognition and biofilm dispersal. Biochem Biophys Res Commun. 2018 Mar 11;497(3):863-868. doi:, 10.1016/j.bbrc.2018.02.143. Epub 2018 Feb 17. PMID:29462616 doi:http://dx.doi.org/10.1016/j.bbrc.2018.02.143

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5z2l"

@@ Line 1: / Line 1: @@
 ==Crystal structure of BdcA in complex with NADPH==
-<StructureSection load='5z2l' size='340' side='right' caption='[[5z2l]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
+<StructureSection load='5z2l' size='340' side='right'caption='[[5z2l]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5z2l]] is a 12 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Z2L OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5Z2L FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5z2l]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Z2L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5Z2L FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PG0:2-(2-METHOXYETHOXY)ETHANOL'>PG0</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</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]] 1.7&#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=5z2l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5z2l OCA], [http://pdbe.org/5z2l PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5z2l RCSB], [http://www.ebi.ac.uk/pdbsum/5z2l PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5z2l ProSAT]</span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PG0:2-(2-METHOXYETHOXY)ETHANOL'>PG0</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</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=5z2l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5z2l OCA], [https://pdbe.org/5z2l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5z2l RCSB], [https://www.ebi.ac.uk/pdbsum/5z2l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5z2l ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/BDCA_ECOLI BDCA_ECOLI]] Increases biofilm dispersal. Acts by binding directly to the signaling molecule cyclic-di-GMP, which decreases the intracellular concentration of cyclic-di-GMP and leads to biofilm dispersal. Also controls other biofilm-related phenotypes such as cell motility, cell size, cell aggregation and production of extracellular DNA and extracellular polysaccharides (EPS). Does not act as a phosphodiesterase.<ref>PMID:21059164</ref>
+[https://www.uniprot.org/uniprot/BDCA_ECOLI BDCA_ECOLI] Increases biofilm dispersal. Acts by binding directly to the signaling molecule cyclic-di-GMP, which decreases the intracellular concentration of cyclic-di-GMP and leads to biofilm dispersal. Also controls other biofilm-related phenotypes such as cell motility, cell size, cell aggregation and production of extracellular DNA and extracellular polysaccharides (EPS). Does not act as a phosphodiesterase.<ref>PMID:21059164</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 22: / Line 23: @@
 __TOC__
 </StructureSection>
-[[Category: Hou, Y J]]
+[[Category: Escherichia coli K-12]]
-[[Category: Li, D F]]
+[[Category: Large Structures]]
-[[Category: Wang, D C]]
+[[Category: Hou YJ]]
-[[Category: Yang, W S]]
+[[Category: Li DF]]
-[[Category: Biofilm dispersal]]
+[[Category: Wang DC]]
-[[Category: Nadph binding]]
+[[Category: Yang WS]]
-[[Category: Oxidoreductase]]

5z2l

From Proteopedia

Current revision

Crystal structure of BdcA in complex with NADPH

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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