2leg

From Proteopedia

(Difference between revisions)

Revision as of 10:09, 12 May 2021

Membrane protein complex DsbB-DsbA structure by joint calculations with solid-state NMR and X-ray experimental data

Structural highlights

2leg is a 2 chain structure with sequence from Ecoli. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	,
Related:	2hi7
Gene:	dsbA, dsf, ppfA, b3860, JW3832 (ECOLI), dsbB, roxB, ycgA, b1185, JW5182 (ECOLI)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[DSBA_ECOLI] Required for disulfide bond formation in some periplasmic proteins such as PhoA or OmpA. Acts by transferring its disulfide bond to other proteins and is reduced in the process. DsbA is reoxidized by DsbB. Required for pilus biogenesis. PhoP-regulated transcription is redox-sensitive, being activated when the periplasm becomes more reducing (deletion of dsbA/dsbB, treatment with dithiothreitol). MgrB acts between DsbA/DsbB and PhoP/PhoQ in this pathway.^[1] ^[2] [DSBB_ECOLI] Required for disulfide bond formation in some periplasmic proteins such as PhoA or OmpA. Acts by oxidizing the DsbA protein.^[3] ^[4]

Publication Abstract from PubMed

X-ray diffraction and nuclear magnetic resonance spectroscopy (NMR) are the staple methods for revealing atomic structures of proteins. Since crystals of biomolecular assemblies and membrane proteins often diffract weakly and such large systems encroach upon the molecular tumbling limit of solution NMR, new methods are essential to extend structures of such systems to high resolution. Here we present a method that incorporates solid-state NMR restraints alongside of X-ray reflections to the conventional model building and refinement steps of structure calculations. Using the 3.7 A crystal structure of the integral membrane protein complex DsbB-DsbA as a test case yielded a significantly improved backbone precision of 0.92 A in the transmembrane region, a 58% enhancement from using X-ray reflections alone. Furthermore, addition of solid-state NMR restraints greatly improved the overall quality of the structure by promoting 22% of DsbB transmembrane residues into the most favored regions of Ramachandran space in comparison to the crystal structure. This method is widely applicable to any protein system where X-ray data are available, and is particularly useful for the study of weakly diffracting crystals.

High-resolution membrane protein structure by joint calculations with solid-state NMR and X-ray experimental data.,Tang M, Sperling LJ, Berthold DA, Schwieters CD, Nesbitt AE, Nieuwkoop AJ, Gennis RB, Rienstra CM J Biomol NMR. 2011 Nov;51(3):227-33. Epub 2011 Sep 22. PMID:21938394^[5]

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

References

↑ Akiyama Y, Kamitani S, Kusukawa N, Ito K. In vitro catalysis of oxidative folding of disulfide-bonded proteins by the Escherichia coli dsbA (ppfA) gene product. J Biol Chem. 1992 Nov 5;267(31):22440-5. PMID:1429594
↑ Lippa AM, Goulian M. Perturbation of the oxidizing environment of the periplasm stimulates the PhoQ/PhoP system in Escherichia coli. J Bacteriol. 2012 Mar;194(6):1457-63. doi: 10.1128/JB.06055-11. Epub 2012 Jan 20. PMID:22267510 doi:http://dx.doi.org/10.1128/JB.06055-11
↑ Bardwell JC, Lee JO, Jander G, Martin N, Belin D, Beckwith J. A pathway for disulfide bond formation in vivo. Proc Natl Acad Sci U S A. 1993 Feb 1;90(3):1038-42. PMID:8430071
↑ Missiakas D, Georgopoulos C, Raina S. Identification and characterization of the Escherichia coli gene dsbB, whose product is involved in the formation of disulfide bonds in vivo. Proc Natl Acad Sci U S A. 1993 Aug 1;90(15):7084-8. PMID:7688471
↑ Tang M, Sperling LJ, Berthold DA, Schwieters CD, Nesbitt AE, Nieuwkoop AJ, Gennis RB, Rienstra CM. High-resolution membrane protein structure by joint calculations with solid-state NMR and X-ray experimental data. J Biomol NMR. 2011 Nov;51(3):227-33. Epub 2011 Sep 22. PMID:21938394 doi:10.1007/s10858-011-9565-6

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2leg"

@@ Line 1: / Line 1: @@
 ==Membrane protein complex DsbB-DsbA structure by joint calculations with solid-state NMR and X-ray experimental data==
-<StructureSection load='2leg' size='340' side='right' caption='[[2leg]], [[NMR_Ensembles_of_Models | 10 NMR models]]' scene=''>
+<StructureSection load='2leg' size='340' side='right'caption='[[2leg]], [[NMR_Ensembles_of_Models | 10 NMR models]]' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2leg]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LEG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2LEG FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2leg]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Ecoli Ecoli]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LEG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2LEG FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=UQ1:UBIQUINONE-1'>UQ1</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=UQ1:UBIQUINONE-1'>UQ1</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2hi7|2hi7]]</td></tr>
+<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2hi7|2hi7]]</div></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">dsbA, dsf, ppfA, b3860, JW3832 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI]), dsbB, roxB, ycgA, b1185, JW5182 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">dsbA, dsf, ppfA, b3860, JW3832 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI]), dsbB, roxB, ycgA, b1185, JW5182 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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=2leg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2leg OCA], [http://pdbe.org/2leg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2leg RCSB], [http://www.ebi.ac.uk/pdbsum/2leg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2leg ProSAT]</span></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=2leg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2leg OCA], [https://pdbe.org/2leg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2leg RCSB], [https://www.ebi.ac.uk/pdbsum/2leg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2leg ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/DSBA_ECOLI DSBA_ECOLI]] Required for disulfide bond formation in some periplasmic proteins such as PhoA or OmpA. Acts by transferring its disulfide bond to other proteins and is reduced in the process. DsbA is reoxidized by DsbB. Required for pilus biogenesis. PhoP-regulated transcription is redox-sensitive, being activated when the periplasm becomes more reducing (deletion of dsbA/dsbB, treatment with dithiothreitol). MgrB acts between DsbA/DsbB and PhoP/PhoQ in this pathway.<ref>PMID:1429594</ref> <ref>PMID:22267510</ref>  [[http://www.uniprot.org/uniprot/DSBB_ECOLI DSBB_ECOLI]] Required for disulfide bond formation in some periplasmic proteins such as PhoA or OmpA. Acts by oxidizing the DsbA protein.<ref>PMID:8430071</ref> <ref>PMID:7688471</ref>
+[[https://www.uniprot.org/uniprot/DSBA_ECOLI DSBA_ECOLI]] Required for disulfide bond formation in some periplasmic proteins such as PhoA or OmpA. Acts by transferring its disulfide bond to other proteins and is reduced in the process. DsbA is reoxidized by DsbB. Required for pilus biogenesis. PhoP-regulated transcription is redox-sensitive, being activated when the periplasm becomes more reducing (deletion of dsbA/dsbB, treatment with dithiothreitol). MgrB acts between DsbA/DsbB and PhoP/PhoQ in this pathway.<ref>PMID:1429594</ref> <ref>PMID:22267510</ref>  [[https://www.uniprot.org/uniprot/DSBB_ECOLI DSBB_ECOLI]] Required for disulfide bond formation in some periplasmic proteins such as PhoA or OmpA. Acts by oxidizing the DsbA protein.<ref>PMID:8430071</ref> <ref>PMID:7688471</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 23: / Line 23: @@
 ==See Also==
 *[[Protein disulfide oxidoreductase|Protein disulfide oxidoreductase]]
+*[[Thiol:disulfide interchange protein 3D structures|Thiol:disulfide interchange protein 3D structures]]
 == References ==
 <references/>
@@ Line 28: / Line 29: @@
 </StructureSection>
 [[Category: Ecoli]]
+[[Category: Large Structures]]
 [[Category: Berthold, D A]]
 [[Category: Gennis, R B]]

2leg

From Proteopedia

Revision as of 10:09, 12 May 2021

Membrane protein complex DsbB-DsbA structure by joint calculations with solid-state NMR and X-ray experimental data

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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