5akp

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of the dark-adapted full-length bacteriophytochrome XccBphP from Xanthomonas campestris bound to BV chromophore

Structural highlights

5akp is a 2 chain structure with sequence from Xanthomonas campestris pv. campestris str. 8004. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 3.25Å
Ligands:	, ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

BPHY_XANC8 Photoreceptor which exists in two forms that are reversibly interconvertible by light: far-red light (733 nm) converts protein to the red-absorbing (Pr) form, while red light (630 nm) partly converts the protein to the far-red-absorbing (Pfr) form (PubMed:27107635). Regulates virulence of X.campestris pv. campestris on its host plants, perhaps by fine-tuning expression to ambient light levels and/or spatial cues (PubMed:27621284). The Pr form may sense light and partially inhibit virulence; in the dark (Pfr form) biofilm and xanathan production rise and bacteria are more virulent (PubMed:27621284). Strains overexpressing this protein have significantly decreased amounts of extracellular beta-1,4-endoglucanase, produce less xanthin and have decreased transcription of genes involved in virulence such as endoglucanases, type 2 secretion systems, xanthan production and flagellar-dependent motility (PubMed:27621284).^[1] ^[2] ^[3]

Publication Abstract from PubMed

Phytochromes constitute a major superfamily of light-sensing proteins that are reversibly photoconverted between a red-absorbing (Pr) and a far-red-absorbing (Pfr) state. Bacteriophytochromes (BphPs) are found among photosynthetic and non-photosynthetic bacteria, including pathogens. To date, several BphPs have been biophysically characterized. However, it is still not fully understood how structural changes are propagated from the photosensory module to the output module during the signal transduction event. Most phytochromes share a common architecture consisting of an N-terminal photosensor that includes the PAS2-GAF-PHY domain triad and a C-terminal variable output module. Here we present the crystal structure of the full-length BphP from the plant pathogen Xanthomonas campestris pv. campestris (XccBphP) bearing its photosensor and its complete output module, a PAS9 domain. In the crystals, the protein was found to be in the Pr state, whereas diffraction data together with resonance Raman spectroscopic and theoretical results indicate a ZZZssa and a ZZEssa chromophore configuration corresponding to a mixture of Pr and Meta-R state, the precursor of Pfr. The XccBphP quaternary assembly reveals a head-to-head dimer in which the output module contributes to the helical dimer interface. The photosensor, which is shown to be a bathy-like BphP, is influenced in its dark reactions by the output module. Our structural analyses suggest that the photoconversion between the Pr and Pfr states in the full-length XccBphP may involve changes in the relative positioning of the output module. This work contributes to understand the light-induced structural changes propagated from the photosensor to the output modules in phytochrome signaling.

Structure of the Full-Length Bacteriophytochrome from the Plant Pathogen Xanthomonas campestris Provides Clues to its Long-Range Signaling Mechanism.,Otero LH, Klinke S, Rinaldi J, Velazquez-Escobar F, Mroginski MA, Fernandez Lopez M, Malamud F, Vojnov AA, Hildebrandt P, Goldbaum FA, Bonomi HR J Mol Biol. 2016 Apr 20. pii: S0022-2836(16)30071-7. doi:, 10.1016/j.jmb.2016.04.012. PMID:27107635^[4]

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

References

↑ Otero LH, Klinke S, Rinaldi J, Velazquez-Escobar F, Mroginski MA, Fernandez Lopez M, Malamud F, Vojnov AA, Hildebrandt P, Goldbaum FA, Bonomi HR. Structure of the Full-Length Bacteriophytochrome from the Plant Pathogen Xanthomonas campestris Provides Clues to its Long-Range Signaling Mechanism. J Mol Biol. 2016 Apr 20. pii: S0022-2836(16)30071-7. doi:, 10.1016/j.jmb.2016.04.012. PMID:27107635 doi:http://dx.doi.org/10.1016/j.jmb.2016.04.012
↑ Bonomi HR, Toum L, Sycz G, Sieira R, Toscani AM, Gudesblat GE, Leskow FC, Goldbaum FA, Vojnov AA, Malamud F. Xanthomonas campestris attenuates virulence by sensing light through a bacteriophytochrome photoreceptor. EMBO Rep. 2016 Nov;17(11):1565-1577. doi: 10.15252/embr.201541691. Epub 2016 Sep , 12. PMID:27621284 doi:http://dx.doi.org/10.15252/embr.201541691
↑ Bonomi HR, Toum L, Sycz G, Sieira R, Toscani AM, Gudesblat GE, Leskow FC, Goldbaum FA, Vojnov AA, Malamud F. Xanthomonas campestris attenuates virulence by sensing light through a bacteriophytochrome photoreceptor. EMBO Rep. 2016 Nov;17(11):1565-1577. doi: 10.15252/embr.201541691. Epub 2016 Sep , 12. PMID:27621284 doi:http://dx.doi.org/10.15252/embr.201541691
↑ Otero LH, Klinke S, Rinaldi J, Velazquez-Escobar F, Mroginski MA, Fernandez Lopez M, Malamud F, Vojnov AA, Hildebrandt P, Goldbaum FA, Bonomi HR. Structure of the Full-Length Bacteriophytochrome from the Plant Pathogen Xanthomonas campestris Provides Clues to its Long-Range Signaling Mechanism. J Mol Biol. 2016 Apr 20. pii: S0022-2836(16)30071-7. doi:, 10.1016/j.jmb.2016.04.012. PMID:27107635 doi:http://dx.doi.org/10.1016/j.jmb.2016.04.012

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/5akp"

@@ Line 1: / Line 1: @@
 ==Crystal structure of the dark-adapted full-length bacteriophytochrome XccBphP from Xanthomonas campestris bound to BV chromophore==
-<StructureSection load='5akp' size='340' side='right' caption='[[5akp]], [[Resolution|resolution]] 3.25&Aring;' scene=''>
+<StructureSection load='5akp' size='340' side='right'caption='[[5akp]], [[Resolution|resolution]] 3.25&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5akp]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5AKP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5AKP FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5akp]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Xanthomonas_campestris_pv._campestris_str._8004 Xanthomonas campestris pv. campestris str. 8004]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5AKP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5AKP FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BLA:BILIVERDINE+IX+ALPHA'>BLA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</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]] 3.25&#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=5akp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5akp OCA], [http://pdbe.org/5akp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5akp RCSB], [http://www.ebi.ac.uk/pdbsum/5akp PDBsum]</span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BLA:BILIVERDINE+IX+ALPHA'>BLA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</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=5akp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5akp OCA], [https://pdbe.org/5akp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5akp RCSB], [https://www.ebi.ac.uk/pdbsum/5akp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5akp ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/BPHY_XANC8 BPHY_XANC8] Photoreceptor which exists in two forms that are reversibly interconvertible by light: far-red light (733 nm) converts protein to the red-absorbing (Pr) form, while red light (630 nm) partly converts the protein to the far-red-absorbing (Pfr) form (PubMed:27107635). Regulates virulence of X.campestris pv. campestris on its host plants, perhaps by fine-tuning expression to ambient light levels and/or spatial cues (PubMed:27621284). The Pr form may sense light and partially inhibit virulence; in the dark (Pfr form) biofilm and xanathan production rise and bacteria are more virulent (PubMed:27621284). Strains overexpressing this protein have significantly decreased amounts of extracellular beta-1,4-endoglucanase, produce less xanthin and have decreased transcription of genes involved in virulence such as endoglucanases, type 2 secretion systems, xanthan production and flagellar-dependent motility (PubMed:27621284).<ref>PMID:27107635</ref> <ref>PMID:27621284</ref> <ref>PMID:27621284</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 20: / Line 23: @@
 __TOC__
 </StructureSection>
-[[Category: Bonomi, H R]]
+[[Category: Large Structures]]
-[[Category: Goldbaum, F A]]
+[[Category: Xanthomonas campestris pv. campestris str. 8004]]
-[[Category: Klinke, S]]
+[[Category: Bonomi HR]]
-[[Category: Otero, L H]]
+[[Category: Goldbaum FA]]
-[[Category: Bacterial protein]]
+[[Category: Klinke S]]
-[[Category: Photoreceptor]]
+[[Category: Otero LH]]
-[[Category: Photosensor]]
-[[Category: Phytochrome]]
-[[Category: Phytopathogen]]
-[[Category: Protein structure]]
-[[Category: Red/far-red light]]
-[[Category: Signal transduction]]
-[[Category: Signaling protein]]
-[[Category: Xanthomona]]

5akp

From Proteopedia

Current revision

Crystal structure of the dark-adapted full-length bacteriophytochrome XccBphP from Xanthomonas campestris bound to BV chromophore

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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