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5k5b

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Revision as of 09:19, 25 June 2020

Wild-type PAS-GAF fragment from Deinococcus radiodurans BphP

Structural highlights

5k5b is a 1 chain structure with sequence from Deira. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, ,
Gene:	bphP, DR_A0050 (DEIRA)
Activity:	Histidine kinase, with EC number 2.7.13.3
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[BPHY_DEIRA] Photoreceptor which exists in two forms that are reversibly interconvertible by light: the R form that absorbs maximally in the red region of the spectrum and the FR form that absorbs maximally in the far-red region. Has also a slight blue shift for the far-red maximum. Could also absorb green light. May participate in regulating pigment synthesis like the carotenoid deinoxanthin which could protect the bacterium from intense visible light.

Publication Abstract from PubMed

Phytochromes are a family of photoreceptors that control light responses of plants, fungi and bacteria. A sequence of structural changes, which is not yet fully understood, leads to activation of an output domain. Time-resolved serial femtosecond crystallography (SFX) can potentially shine light on these conformational changes. Here we report the room temperature crystal structure of the chromophore-binding domains of the Deinococcus radiodurans phytochrome at 2.1 A resolution. The structure was obtained by serial femtosecond X-ray crystallography from microcrystals at an X-ray free electron laser. We find overall good agreement compared to a crystal structure at 1.35 A resolution derived from conventional crystallography at cryogenic temperatures, which we also report here. The thioether linkage between chromophore and protein is subject to positional ambiguity at the synchrotron, but is fully resolved with SFX. The study paves the way for time-resolved structural investigations of the phytochrome photocycle with time-resolved SFX.

The room temperature crystal structure of a bacterial phytochrome determined by serial femtosecond crystallography.,Edlund P, Takala H, Claesson E, Henry L, Dods R, Lehtivuori H, Panman M, Pande K, White T, Nakane T, Berntsson O, Gustavsson E, Bath P, Modi V, Roy-Chowdhury S, Zook J, Berntsen P, Pandey S, Poudyal I, Tenboer J, Kupitz C, Barty A, Fromme P, Koralek JD, Tanaka T, Spence J, Liang M, Hunter MS, Boutet S, Nango E, Moffat K, Groenhof G, Ihalainen J, Stojkovic EA, Schmidt M, Westenhoff S Sci Rep. 2016 Oct 19;6:35279. doi: 10.1038/srep35279. PMID:27756898^[1]

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

References

↑ Edlund P, Takala H, Claesson E, Henry L, Dods R, Lehtivuori H, Panman M, Pande K, White T, Nakane T, Berntsson O, Gustavsson E, Bath P, Modi V, Roy-Chowdhury S, Zook J, Berntsen P, Pandey S, Poudyal I, Tenboer J, Kupitz C, Barty A, Fromme P, Koralek JD, Tanaka T, Spence J, Liang M, Hunter MS, Boutet S, Nango E, Moffat K, Groenhof G, Ihalainen J, Stojkovic EA, Schmidt M, Westenhoff S. The room temperature crystal structure of a bacterial phytochrome determined by serial femtosecond crystallography. Sci Rep. 2016 Oct 19;6:35279. doi: 10.1038/srep35279. PMID:27756898 doi:http://dx.doi.org/10.1038/srep35279

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/5k5b"

@@ Line 1: / Line 1: @@
 ==Wild-type PAS-GAF fragment from Deinococcus radiodurans BphP==
-<StructureSection load='5k5b' size='340' side='right' caption='[[5k5b]], [[Resolution|resolution]] 1.35&Aring;' scene=''>
+<StructureSection load='5k5b' size='340' side='right'caption='[[5k5b]], [[Resolution|resolution]] 1.35&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5k5b]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K5B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5K5B FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5k5b]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Deira Deira]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K5B OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5K5B FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=LBV:3-[2-[(Z)-[3-(2-CARBOXYETHYL)-5-[(Z)-(4-ETHENYL-3-METHYL-5-OXIDANYLIDENE-PYRROL-2-YLIDENE)METHYL]-4-METHYL-PYRROL-1-IUM-2-YLIDENE]METHYL]-5-[(Z)-[(3E)-3-ETHYLIDENE-4-METHYL-5-OXIDANYLIDENE-PYRROLIDIN-2-YLIDENE]METHYL]-4-METHYL-1H-PYRROL-3-YL]PROPANOIC+ACID'>LBV</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=LBV:3-[2-[(Z)-[3-(2-CARBOXYETHYL)-5-[(Z)-(4-ETHENYL-3-METHYL-5-OXIDANYLIDENE-PYRROL-2-YLIDENE)METHYL]-4-METHYL-PYRROL-1-IUM-2-YLIDENE]METHYL]-5-[(Z)-[(3E)-3-ETHYLIDENE-4-METHYL-5-OXIDANYLIDENE-PYRROLIDIN-2-YLIDENE]METHYL]-4-METHYL-1H-PYRROL-3-YL]PROPANOIC+ACID'>LBV</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene></td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">bphP, DR_A0050 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=243230 DEIRA])</td></tr>
 <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Histidine_kinase Histidine kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.13.3 2.7.13.3] </span></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=5k5b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k5b OCA], [http://pdbe.org/5k5b PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5k5b RCSB], [http://www.ebi.ac.uk/pdbsum/5k5b PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5k5b ProSAT]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5k5b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k5b OCA], [http://pdbe.org/5k5b PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5k5b RCSB], [http://www.ebi.ac.uk/pdbsum/5k5b PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5k5b ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 23: / Line 24: @@
 __TOC__
 </StructureSection>
+[[Category: Deira]]
 [[Category: Histidine kinase]]
+[[Category: Large Structures]]
 [[Category: Claesson, E]]
 [[Category: Edlund, P]]

5k5b

From Proteopedia

Revision as of 09:19, 25 June 2020

Wild-type PAS-GAF fragment from Deinococcus radiodurans BphP

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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