This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

6jpr

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Current revision

Crystal structure of Phycocyanin from Nostoc sp. R76DM

Structural highlights

6jpr is a 12 chain structure with sequence from Nostoc. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.35Å
Ligands:	, , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

A0A5H1ZR40_9NOSO Light-harvesting photosynthetic bile pigment-protein from the phycobiliprotein complex (phycobilisome, PBS). Phycocyanin is the major phycobiliprotein in the PBS rod.[ARBA:ARBA00003579]

Publication Abstract from PubMed

The distinct sequence feature and spectral blue-shift (~10 nm) of phycocyanin, isolated from Nostoc sp. R76DM (N-PC), were investigated by phylogenetic and crystallographic analyses. Twelve conserved substitutions in N-PC sequence were found distributed unequally among alpha- and beta-subunit (3 in alpha- and 9 in beta-subunit). The phylogenetic analysis suggested that molecular evolution of alpha- and beta-subunit of Nostoc-phycocyanin is faster than evolution of Nostoc-species. The divergence events seem to have occurred more frequently in beta-subunit, compared to alpha-subunit (relative divergence, 7.38 for alpha-subunit and 9.66 for beta-subunit). Crystal structure of N-PC was solved at 2.35 A resolution to reasonable R-factors (Rwork/RFree = 0.199/0.248). Substitutions congregate near interface of two alphabeta-monomer in N-PC trimer and are of compensatory nature. Six of the substitutions in beta-subunit may be involved in maintaining topology of beta-subunit, one in inter-monomer interaction and one in interaction with linker-protein. The beta153Cys-attached chromophore adopts high-energy conformational state resulting due to reduced coplanarity of B- and C-pyrrole rings. Distortion in chromophore conformation can result in blue-shift in N-PC spectral properties. N-PC showed significant in-vitro and in-vivo antioxidant activity comparable with other phycocyanin. Since Nostoc-species constitute a distinct phylogenetic clade, the present structure would provide a better template to build a model for phycocyanins of these species.

Phylogenetic and crystallographic analysis of Nostoc phycocyanin having blue-shifted spectral properties.,Sonani RR, Rastogi RP, Patel SN, Chaubey MG, Singh NK, Gupta GD, Kumar V, Madamwar D Sci Rep. 2019 Jul 8;9(1):9863. doi: 10.1038/s41598-019-46288-4. PMID:31285455^[1]

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

References

↑ Sonani RR, Rastogi RP, Patel SN, Chaubey MG, Singh NK, Gupta GD, Kumar V, Madamwar D. Phylogenetic and crystallographic analysis of Nostoc phycocyanin having blue-shifted spectral properties. Sci Rep. 2019 Jul 8;9(1):9863. doi: 10.1038/s41598-019-46288-4. PMID:31285455 doi:http://dx.doi.org/10.1038/s41598-019-46288-4

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/6jpr"

@@ Line 3: / Line 3: @@
 <StructureSection load='6jpr' size='340' side='right'caption='[[6jpr]], [[Resolution|resolution]] 2.35&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6jpr]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Nostoc Nostoc]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JPR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6JPR FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6jpr]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Nostoc Nostoc]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JPR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6JPR FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CYC:PHYCOCYANOBILIN'>CYC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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]] 2.35&#8491;</td></tr>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MEN:N-METHYL+ASPARAGINE'>MEN</scene></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CYC:PHYCOCYANOBILIN'>CYC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MEN:N-METHYL+ASPARAGINE'>MEN</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></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=6jpr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jpr OCA], [http://pdbe.org/6jpr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6jpr RCSB], [http://www.ebi.ac.uk/pdbsum/6jpr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6jpr 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=6jpr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jpr OCA], [https://pdbe.org/6jpr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6jpr RCSB], [https://www.ebi.ac.uk/pdbsum/6jpr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6jpr ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/A0A5H1ZR40_9NOSO A0A5H1ZR40_9NOSO] Light-harvesting photosynthetic bile pigment-protein from the phycobiliprotein complex (phycobilisome, PBS). Phycocyanin is the major phycobiliprotein in the PBS rod.[ARBA:ARBA00003579]
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 17: / Line 19: @@
 </div>
 <div class="pdbe-citations 6jpr" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Phycocyanin|Phycocyanin]]
 == References ==
 <references/>
@@ Line 23: / Line 28: @@
 [[Category: Large Structures]]
 [[Category: Nostoc]]
-[[Category: Gupta, G D]]
+[[Category: Gupta GD]]
-[[Category: Kumar, V]]
+[[Category: Kumar V]]
-[[Category: Madamwar, D]]
+[[Category: Madamwar D]]
-[[Category: Patel, S N]]
+[[Category: Patel SN]]
-[[Category: Rastogi, R P]]
+[[Category: Rastogi RP]]
-[[Category: Sonani, R R]]
+[[Category: Sonani RR]]
-[[Category: Cyanobacteria]]
-[[Category: Light harvesting]]
-[[Category: Photosynthesis]]
-[[Category: Phycobiliprotein]]
-[[Category: Phycocyanobilin]]

6jpr

From Proteopedia

Current revision

Crystal structure of Phycocyanin from Nostoc sp. R76DM

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox