3by7

Protein Summary

Novel protein ECX21941 from the environmental metagenome proteome has unexpected structural similarity to Sm and Sm-like (or Like Sm, LSm) proteins that form a very large and evolutionary diverse protein family with various functions centered around RNA processing. The Sm/LSm family is classified into 23 different groups by the NCBI Conserved Domains Database (cd00600) and into seven structurally characterized families of proteins with Sm-like fold by the SCOP database (sunid: 50181). The sequence based clustering of known Sm-like proteins is shown below.

 

Protein sequence clustering of known Sm and Sm-like proteins, where similar proteins (represented by black dots) are connected by lines. Proteins with known structure are highlighted red and their PDB codes are shown (black labells). Clusters corresponding to previously annotated groups of Sm/LSm proteins are labelled green.

 

ECX21941 forms pentamer in vitro and in the crystal structure, but its quaternary structure in vivo is currently unknown.

The highly conserved residues are indicated by red color on the protein surface of the ECX21941 pentamer. Conserved residues cluster togather predominately in the central part of the ECX21941 pentamer. Conserved residues were labelled on one monomer only.
	The conserved residues are highlighted by white dots on the protein surface of ECX21941 pentamer. The colors represent amino acid properties: basic, blue; acidic, red; polar, light blue; nonpolar and Gly, gray; aromatic, orange.           Schematic representation of ECX21941 pentamer, where monomers are shown in different colors with protein surface as the background.

 

 

Structural similarity to Sm/LSm proteins.

ECX21941 has the highest structural similarity to proteins from four SCOP families of Sm-like ribonucleoproteins and detectable structural similarity to protein structures with SH3-like barrel fold.

 

 

 

Superposition between monomers of ECX21941 3BY7 (red) and the top 4 DALI hits, 1I8F (Z=7; heptamer in crystal structure, cyan), 1D3B (Z=6; magenta), 1B34 (Z=6; yellow), 1Y96 (Z=6), and 1EAR (from FFAS03) were superimposed in COOT by SSM. The DALI hits 1I8F, 1D3B and 1B34 are most similar and closest matches. The proteins are similar in structure but with differences in N and C-term helices. The 1I8F and 1D3B strucures both have only an N-terminal helix. The 1B34 has an N-terminal helix in a similar conformation as the first two and also a C-terminal helix. The 3BY7 does not have the N-term helix but has a C-term helix but it points in a direction almost oppsite to that seen for the C-term of 1B34.

 

The structural similarities, illustrated by structure guided sequence alignment,  indicates that ECX21941 (PDB code 3by7 chain A) function is unlikely to be the same as that of any structurally characterized proteins.

 

 

The protein structure of ECX21941 is representative of several new protein families from the environmental metagenome dataset.

 

The protein sequence clustering indicates that ECX21941 belongs to one of several new protein families with Sm-like fold.

 

ECX21941 is the first protein structure of phage-like Sm-like protein.

The detected sequence similarity between ECX21941 and cyanophage proteins (see table below) and the strong similarity between proteins from ECX21941 conserved genomic neighborhood to cyanophage proteins (accompanied in some cases by identical order of encoded proteins) leads to the conclusion that ECX21941 is the first protein structure of phage Sm-like protein.

 

 

  Table:  Cyanophages and cyanobacteria with ECX21941 and its homologs.

ECX21941 and similar proteins	number of homologs
Synechococcus phage syn9	4
Synechococcus phage S-PM2	3
Prochlorococcus phage P-SSM2	3
Prochlorococcus phage P-SSM4	2
Synechococcus sp. CC9311	1
Synechococcus sp. BL107	1
Synechococcus sp. CC9902	1

          

 

 

 

 Table:  Cyanobacteria with Hfq-like proteins.

ssr3341 and similar proteins	number of homologs
Synechococcus elongatus PCC 7942	1
Synechococcus elongatus PCC 6301	1
Synechococcus sp. WH 7803	1
Synechococcus sp. WH 5701	1
Synechococcus sp. CC9311	1
Synechococcus sp. WH 7805	1
Synechococcus sp. CC9605	1
Synechococcus sp. BL107	1
Synechococcus sp. RS9917	1
Synechococcus sp. JA-3-3Ab	1
Synechococcus sp. JA-2-3B'a(2-13)	1
Synechococcus sp. RS9916	1
Synechococcus sp. RCC307	1
Synechocystis sp. PCC 6803	1

 

Ligand Summary

 

References

 Crystal structure of a novel Sm-like protein of putative cyanophage origin at 2.60 Å resolution

Debanu Das, Piotr Kozbial, Herbert L. Axelrod, Mitchell D. Miller, Daniel McMullan, S. Sri Krishna, Polat Abdubek, Claire Acosta, Tamara Astakhova, Prasad Burra, Dennis Carlton, Connie Chen, Hsiu-Ju Chiu, Thomas Clayton, Marc C. Deller, Lian Duan, Ylva Elias, Marc-Andre Elsliger, Dustin Ernst, Carol Farr, Julie Feuerhelm, Anna Grzechnik, Slawomir K. Grzechnik, Joanna Hale, Gye Won Han, Lukasz Jaroszewski, Kevin K. Jin, Hope A. Johnson, Heath E. Klock, Mark W. Knuth, Abhinav Kumar, David Marciano, Andrew T. Morse, Kevin D. Murphy, Edward Nigoghossian, Amanda Nopakun, Linda Okach, Silvya Oommachen, Jessica Paulsen, Christina Puckett, Ron Reyes, Christopher L. Rife, Natasha Sefcovic, Sebastian Sudek, Henry Tien, Christine Trame, Christina V. Trout, Henry van den Bedem, Dana Weekes, Aprilfawn White, Qingping Xu, Keith O. Hodgson, John Wooley, Ashley M. Deacon, Adam Godzik, Scott A. Lesley, and Ian A. Wilson.  

Accepted for publication (Dec 2008), http://www3.interscience.wiley.com/journal/36176/home