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The Open Protein Structure Annotation Network
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3by7

    Table of contents
    1. 1. Protein Summary
    2. 2. Ligand Summary
    3. 3. References

    Title Crystal structure of a novel Sm-like protein of putative cyanophage origin at 2.60 A resolution. Proteins 75 296-307 2009
    Site JCSG
    PDB Id 3by7 Target Id
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    Molecular Characteristics
    Source
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    Alias Ids
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    TPS1751,JCVI_PEP_1096686650277
    Molecular Weight
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    Da.
    Residues
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    Isoelectric Point
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    Sequence
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      BLAST   FFAS

    Structure Determination
    Method XRAY
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    Chains 1
    Resolution (Å)
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    Rfree
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    Matthews' coefficent 2.45 Rfactor 0.235
    Waters
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    Solvent Content 49.80

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    Ligand Information
    Ligands
    Metals

    Jmol

     
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    Google Scholar output for 3by7
    1. Integration of open access literature into the RCSB Protein Data Bank using BioLit
    A Prli_, M Martinez, D Dimitropoulos, B Beran - BMC , 2010 - biomedcentral.com
     
    2. Crystal structure of a novel Sm_like protein of putative cyanophage origin at 2.60 resolution
    D Das, P Kozbial, HL Axelrod, MD Miller - Proteins: Structure, , 2009 - Wiley Online Library
     

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    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.

     

     clans_of_sm-like.jpg

    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.

     conserved_surface2.png

    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.

    GN7729A-Fig2-structural-ali-ver04g.jpg

     

    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.

     

     

    Fig_structural_alignment.png

     

    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.

     

    clans48091-3by7-all.fa-with-hits-to-other.png

    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

    Reviews

    References

     

    No references found.

    Tag page

    Files (6)

    FileSizeDateAttached by 
     clans48091-3by7-all.fa-with-hits-to-other.png
    Clustering of ECX21941 homologs
    394.72 kB21:02, 1 Dec 2008pkozbialActions
     clans_of_sm-like.jpg
    Clustering of known Sm-like proteins
    852.03 kB21:08, 1 Dec 2008pkozbialActions
     conserved_surface2.png
    Conservation pattern
    446.21 kB21:02, 1 Dec 2008pkozbialActions
     Fig_structural_alignment.png
    Structure based sequence alignment
    50.49 kB21:06, 1 Dec 2008pkozbialActions
     GN7729A-Fig2-structural-ali-ver04g.jpg
    Amino acid properties (top) and schematic representation of the pentamer (bottom).
    1170.38 kB21:02, 1 Dec 2008pkozbialActions
    GN7729red_i8fcyan_d3bmagenta_b34yellow.png
    Structural superposition
    276.15 kB22:05, 30 Jun 2008dweekesActions
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