6XWK

Crystal structure of Phormidium rubidum phycocyanin

This is a non-PDB format compatible entry.

Summary for 6XWK

• Entry DOI: 10.2210/pdb6xwk/pdb
• Descriptor: Phycocyanin alpha subunit, Phycocyanin beta subunit, PHYCOCYANOBILIN, ... (8 entities in total)
• Functional Keywords: phycocyanin, phycocyanobilin, photosynthesis, light harvesting, cyanobacteria
• Biological source: Phormidium rubidum A09DM; More
• Total number of polymer chains: 2
• Total formula weight: 38145.87

Authors

Sonani, R.R.,Roszak, A.W.,Cogdell, R.J.,Madamwar, D.,Liu, H.,Gross, M.L.,Blankenship, R.E. (deposition date: 2020-01-23, release date: 2020-04-29, Last modification date: 2024-01-24)

Primary citation

Sonani, R.R.,Roszak, A.W.,Liu, H.,Gross, M.L.,Blankenship, R.E.,Madamwar, D.,Cogdell, R.J.
Revisiting high-resolution crystal structure of Phormidium rubidum phycocyanin.
Photosyn. Res., 144:349-360, 2020

PubMed Abstract: The crystal structure of phycocyanin (pr-PC) isolated from Phormidium rubidum A09DM (P. rubidum) is described at a resolution of 1.17 Å. Electron density maps derived from crystallographic data showed many clear differences in amino acid sequences when compared with the previously obtained gene-derived sequences. The differences were found in 57 positions (30 in α-subunit and 27 in β-subunit of pr-PC), in which all residues except one (β145Arg) are not interacting with the three phycocyanobilin chromophores. Highly purified pr-PC was then sequenced by mass spectrometry (MS) using LC-MS/MS. The MS data were analyzed using two independent proteomic search engines. As a result of this analysis, complete agreement between the polypeptide sequences and the electron density maps was obtained. We attribute the difference to multiple genes in the bacterium encoding the phycocyanin apoproteins and that the gene sequencing sequenced the wrong ones. We are not implying that protein sequencing by mass spectrometry is more accurate than that of gene sequencing. The final 1.17 Å structure of pr-PC allows the chromophore interactions with the protein to be described with high accuracy.

PubMed: 32303893
DOI: 10.1007/s11120-020-00746-7

Experimental method

X-RAY DIFFRACTION (1.17 Å)