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The Open Protein Structure Annotation Network
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3bjq

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

    Title Crystal structure of phage-related protein (NP_890161.1) from Bordetella bronchiseptica at 2.05 A resolution. To be published
    Site JCSG
    PDB Id 3bjq Target Id 373379
    Molecular Characteristics
    Source Bordetella bronchiseptica rb50
    Alias Ids TPS1620,NP_890161.1, BIG_945, 93053 Molecular Weight 34467.23 Da.
    Residues 315 Isoelectric Point 5.60
    Sequence msqmspgqarvvdpilsthargyrqstligkklfpvapvaqyggkiltfgkeafrlyntkrapgantkr idfgyegdpysivpsaleakvprelmrdasqvpgidlgarsvntvlrimalahehecaqialdpakyna dhkvklvgsarwtspdsdptkdvetakeaiadsigmepnrlmlsrkalsackyhpkliervkytraesi tidmlkalweveeivvgtarvatgandsfgdvwgpdvwlgyvsdnpdpsveepsfgytyqieghplvev pywdnnakswiygvsddntpalsgmlagyliedaglpaa
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 10
    Resolution (Å) 2.05 Rfree 0.227
    Matthews' coefficent 2.54 Rfactor 0.186
    Waters 1337 Solvent Content 51.50

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3bjq
    1. P22 coat protein structures reveal a novel mechanism for capsid maturation: Stability without auxiliary proteins or chemical crosslinks
    KN Parent, R Khayat, LH Tu, MM Suhanovsky - Structure, 2010 - Elsevier
     
    2. The host outer membrane proteins OmpA and OmpC are associated with the Shigella phage Sf6 virion
    H Zhao, RD Sequeira, NA Galeva, L Tang - Virology, 2011 - Elsevier
     
    3. Distributed structure determination at the JCSG
    H van den Bedem, G Wolf, Q Xu - Section D: Biological , 2011 - scripts.iucr.org
     
    4. Characterization of protein function using automated computational methods
    S Wu - 2010 - gradworks.umi.com
     



    Protein Summary

    The BB3626 gene from Bordetella bronchiseptica, an opportunistic pathogen, encodes the NP_890161 protein, a member of the PF03864 group. This family representative is the major capsid protein E, a protein involved in DNA stabilization within bacteriophage heads. Members of the PF03864 family are found in a number of pathogenic bacteria as well as in some double stranded (ds) bacteriophages.

     

    Despite the lack of sequence homology, 3bjq is structurally very similar to virus envelope proteins such as pfV and HK97 gp5 (2e0z with a Dali Zscr=15; and 1ohg, Zscr=13). A surprising observation is that, instead of forming virus envelopes like 2e0z and 1ohg, 3bjq is a decamer in current crystal form. The decamer is formed by tail to tail stacking of two pentamers.


    Compared to 2e0z, 13% seq id, rmsd 3.1, (200 ca out ~300 of 3bjq)
    Compared to 1ohg, 11% seq id, rmsd 2.8 (197 ca out of ~300 of 3bjq)


    So the question is: is 3bjq also a virus envelop protein which will form virus envelope under certain conditions  Or is 3bjq a similar folded protein but with different function? why does such protein exist in pathogenic bacterium?

    The conserved residues are scattered around the whole protein and buried, as a result, there is no easily identifiable highly conserved active site.



    The structure has unusual electrostatic properties.  Both the inside and outside surfaces of the decamer are predominately negatively charged. This property is very similar to 2e0z and 1ohg.

    Thus, from 1) no conserved active site, 2) conserved electrostatic surface for DNA encapsulation, we suggest that 3bjq may also form a virus like particle like 2e0z under certain conditions. The observed pentamer may represent a core for the envelope assembly (TODO: check whether the pentamer is same as the pentamers in HK97 or pfV). In other words, the current structure may represent a pre-assembly intermediate state, eg, HK97 can also exist in solution as pentamers.

    Monomer electrostatic surface


    Electrostatic surface, looking into the inner chamber formed by the pentamer

    Electrostatic surface, looking at the outside surface of the pentamer


    Phage-related protein (3bjq).

    TODO: compare with:
    (a) major capsid protein E is involved with the stabilization of the condensed form of the DNA molecule in phage heads (PF03864).
    (b) Linocin M18 (PF04454).

     

    The most conserved secondary structural element of 3bjq, helix H3, is the one that exhibits the most diversity in similar structures. Superposition of  3bjq with a linocin-like protein from Thermotoga maritima termed encapsulin (PDB id: 3DKT, Dali Z=14), a virus-like particle from the archaeon Pyrococcus furiosus (PDB id: 2E0Z, Z=15) and a putative prophage protein from Escherichia coli cft073 (PDB id 3BQW, Z=14) shows that in all cases H3 is replaced by a conformationally flexible beta-hairpin (see figure below). This region, termed the E-loop, is involved in capsid assembly (Gan 2006) as well as, in the case of the linocin-like protein from T. maritima, in tight interactions critical to the formation of a 60-mer enzyme-encapsulating, bacterial nanocompartment implicated in the oxidative-stress response (Sutter 2008).

     

    3bjq_sups.png

    Stereo ribbon diagram showing superposition of 3BJQ (blue), 3DKT (yellow), 2E0Z (magenta) and 3BQW (cyan).

     

    [Could a conformational switch in the E-loop be responsible for different oligomerization states that could transform BB3626 from e.g. a bona fide viral capsid to an encapsulin or some other function altogether (zinc protease, see below)? In other words, could this be a moonlighting protein with different functions triggered by changes in environmental conditions?]

     

    The genome context (http://string.embl.de) of PF03864 family strongly suggests a bacteriophage origin with all members showing strong predicted functional associations with phage capsid, tail sheath, tail core and portal proteins.

     

    Other computational predictions of function

    SeqFEATURE is a library of 3D protein functional site models built from 1D sequence motifs. 3BJQ had a very high scoring hit for the following model:

    ZINC_PROTEASE.4.GLU.OE1

    (site ID)           (z-score)       (X)     (Y)     (Z)      (res_ID:chain@atom)
    Env_3BJQ.pdb_92     3.7743673860    -89.925 91.923  65.278   GLU123:F@OE1
    Env_3BJQ.pdb_158    3.6719361952    -95.627 115.015 41.195   GLU123:J@OE1
    Env_3BJQ.pdb_22     3.5686598948    -90.287 37.524  27.977   GLU123:B@OE1

     

    This model for a zinc protease active site has an area under the ROC curve of ~ 0.89 and a sensitivity of 50% using a 100% specificity cutoff. Using this cutoff, the model hit 3 of the 10 chains at the same residue (GLU123), suggesting that this residue in each subunit may be functional. The 3 hits score well within the bulk of the positive training site score distribution:

    More information about this model

     

    Below are images of the local structural environment surrounding the predicted functional site.

     3bjq-site.png 3bjq-surface.png

    For comparison, below are images of the local structural environment surrounding a known zinc protease active site (PDB: 1EZM).

    1ezm-site.png 1ezm-surface.png

     

    While the predicted site is very high scoring, it is not necessarily a zinc protease active site. The functional models are based on the presence or absence of significant physichochemical properties as defined by statistically modeling data in a radially averaged form from positive and negative training examples. A high scoring hit for a model indicates that the radial distribution of physicochemical properties at that site in the query structure was very similar to the positive training examples for that model.

    Corroborating evidence for zinc-related functional activity comes from analysis of the structure with a zinc binding site model, also built using the FEATURE system. The figure on the left below show all of the hits (in blue); the 10 highest scoring hits correspond to one hit per subunit, which fall in the direct vicinity of the predicted zinc protease site (as shown in the figure on the right - white = predicted zinc site, red/blue = predicted zinc protease site).

    3bjq_zinc.png  3bjq_zinc_sp_1chain-site.png

    It is thus possible that there is a zinc protease active site in 3BJQ at the location specified, enzymatic activity similar to zinc proteases, zinc or other cation binding activity, or simply an area of interest that may warrant further investigation.

    File:private/var/tmp/folders.501/TemporaryItems/3bjq-site_1.pngFile:private/var/tmp/folders.501/TemporaryItems/3bjq-site.png

    File:Users/shwu/Research/SG_exp_grant/3bjq-site.png

    File:Users/shwu/Research/SG_exp_grant/3bjq-site.png

    Ligand Summary



    References

    Reviews

    References

     

    No references found.

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    Files (13)

    FileSizeDateAttached by 
     1ezm-site.png
    Local environment around known zinc protease active site, 1EZM
    222.51 kB22:23, 14 Oct 2008shwuActions
     1ezm-surface.png
    Local surface around known zinc protease active site, 1EZM
    227.52 kB22:23, 14 Oct 2008shwuActions
     3bjq-site.png
    Local environment around predicted zinc protease active site
    170.59 kB22:23, 14 Oct 2008shwuActions
     3bjq-surface.png
    Local surface view around predicted zinc protease active site
    219.79 kB22:23, 14 Oct 2008shwuActions
     3bjq_sups.png
    No description
    167.41 kB00:50, 22 Oct 2008tinabActions
     3bjq_zinc.png
    Predicted zinc binding sites
    47.71 kB00:00, 23 Oct 2008shwuActions
     3bjq_zinc_sp_1chain-site.png
    Predicted zinc binding site in the vicinity of the predicted zinc protease site
    60.41 kB23:53, 22 Oct 2008shwuActions
    p-e1.png
    No description
    552.13 kB22:04, 30 Jun 2008dweekesActions
    p-e1t.png
    No description
    569.17 kB22:04, 30 Jun 2008dweekesActions
    p-e2.png
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    438.79 kB22:04, 30 Jun 2008dweekesActions
    p-e2t.png
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    430.47 kB22:04, 30 Jun 2008dweekesActions
    ph10216a-a-elec.png
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    295.28 kB22:04, 30 Jun 2008dweekesActions
    ph10216a-consurf.png
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    96.89 kB22:04, 30 Jun 2008dweekesActions
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