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The Open Protein Structure Annotation Network
PDB Keyword
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3hrg

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

    Title Crystal structure of Bacteroides thetaiotaomicron BT_3980, protein with actin-like ATPase fold and unknown function (NP_812891.1) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 1.85 A resolution. To be Published
    Site JCSG
    PDB Id 3hrg Target Id 396692
    Molecular Characteristics
    Source Bacteroides thetaiotaomicron vpi-5482
    Alias Ids TPS25963,NP_812891.1, 332898 Molecular Weight 30313.09 Da.
    Residues 256 Isoelectric Point 5.41
    Sequence midftkskqytlsirlstdgfsfsiynpindnsqslfekevdtslsltanlknvfhesdflsysykrvn imiaskrftmiplelfeeeqaellfyhnhqkreneivmynilkknnvviifgidkstytflneqypear fysqstplieyfsiksrlgnskkmyasvrkdaidiycfergqlllansfecmqtedriyyllyvwkqle fnqerdelhltgtlsdketlmnelkkfilqvfimnpannidmqalltce
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 1.85 Rfree 0.240
    Matthews' coefficent 2.33 Rfactor 0.193
    Waters 250 Solvent Content 47.13

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3hrg
    1. Ligands in PSI structures
    A Kumar, HJ Chiu, HL Axelrod, A Morse - Section F: Structural , 2010 - scripts.iucr.org
     

    Protein Summary

    Bacteroides thetaiotaomicron protein BT_3980 (Target DB ID 396692, JCSG target GE15694A, genbank accession code NP_812891.1) is a 256-amino acid long, 30.3 kDa protein that is putatively secreted (based on the predicted N-terminal signalling peptide) from Bacteriodes thetaiotaomicron, a gram-negative, anaerobic bacteria that resides in the human intestinal tract.

    BT_3980 is a first solved representative of a new protein family of ~100 proteins, present mostly in human gut, marine and soil Bacteroidetes, as well as metagenomics samples from the ocean and human gut. The protein has been assigned to Pfam families DUF3822 and PF12864.  The family partly overlaps with PfamB PB022506

    BT_3980 is found in a conserved genomic neighborhood, between methyltransferase, hypothetical protein BT_3981 (protein with unknown function and identical phylogenetic distribution as BT_3980, suggesting that BT_3980 and BT_3981 form a functional unit) and ATP-dependent exoDNAse (exonuclease V). 

    The structure of BT_3980, solved by the Se-Met MAD method to a resolution of 1.85 Angstroms, adopts an alpha-beta fold shown in Figure 1a.   The protein most probably functions as a monomer (as assessed by the EBI PISA server), with each monomer consisting of three distinct structural domains -- domain 1 comprises residues 1-74, 124-141, and 246-256, domain 2 residues 75-123, and domain 3 residues 142-245 (Figure 1b). 

    Figure 1.  Structure of NP_812891.1 monomer (a) gradiently colored from N-terminus (blue) to C-terminus (red) and (b) divided into three distinct structural domains: 1 (blue), 2 (yellow) and 3 (red).

    (a)                                                                                                (b)

    GE15694A-gradient-labeled.png            GE15694A-domains-labeled (1).png

    Proteins with significant structural similarity to BT_3980 that were found by DALI and SSM (Tables 1 and 2) are proteins that are classified in SCOP as belonging to the actin-like ATPase domain superfamily.

     

    Table 1.  Proteins with significant structural similarity to BT_3980, as assessed by DALI.

    N PDB Z-score RMSD LALI NRES %ID TITLE
    1 1e4g 15.2 3.3 225 380 9 CELL DIVISION PROTEIN FTSA
    2 1e4f 15.1 3.2 222 378 9 CELL DIVISION PROTEIN FTSA
    3 2bh1 11.9 3.7 199 238 12 GENERAL SECRETION PATHWAY PROTEIN L
    4 1yf5 11.7 3.7 199 238 12 GENERAL SECRETION PATHWAY PROTEIN L
    5 1w97 11.6 3.7 197 229 12 GENERAL SECRETION PATHWAY PROTEIN L
    6 3bf3 11.1 3.5 172 248 10 TYPE III PANTOTHENATE KINASE
    7 3bf1 11.1 3.6 173 248 10 TYPE III PANTOTHENATE KINASE
    8 3bex 11.1 3.6 174 248 10 TYPE III PANTOTHENATE KINASE
    9 1jcg 11.1 3.7 195 334 9 ROD SHAPE-DETERMINING PROTEIN MREB
    10 1jcf 11.1 3.6 196 335 9 ROD SHAPE-DETERMINING PROTEIN MREB

     

    Table 2.  Proteins with significant structural similarity to BT_3980, as assessed by SSM.

    N PDB Q-score RMSD TITLE
    1 1yf5 0.2543 3.331 CYTO-EPSL: THE CYTOPLASMIC DOMAIN OF EPSL, AN INNER MEMBRANE COMPONENT OF THE TYPE II SECRETION SYSTEM OF VIBRIO CHOLERAE
    2 2bh1 0.2498 3.417 X-RAY STRUCTURE OF THE GENERAL SECRETION PATHWAY COMPLEX OF THE N-TERMINAL DOMAIN OF EPSE AND THE CYTOSOLIC DOMAIN OF EPSL OF VIBRIO CHOLERAE
    3 2ews 0.1976 3.235 S.AUREUS PANTOTHENATE KINASE
    4 2e2o 0.1752 3.188 SULFOLOBUS TOKODAII HEXOKINASE IN COMPLEX WITH GLUCOSE
    5 2e2q 0.1685 3.219 SULFOLOBUS TOKODAII HEXOKINASE IN COMPLEX WITH XYLOSE, MG2+, AND ADP
    6 1sz2 0.1255 4.009 E. COLI GLUCOKINASE IN COMPLEX WITH GLUCOSE

     

    Superposition of NP_812891.1 with several of the top DALI and SSM identified proteins reveals similarities to other actin-like fold proteins; however, it is missing a couple of the domains that other proteins with a canonical actin-like fold have (Figure 2).

    Figure 2.  Superposition of target NP_812891.1 (blue) with structurally similar 1e4g (red), 1yf5 (green), 3bf1 (magenta), and 1jcg (yellow).

    GE15694A-superpose.png

    The structure of NP_812891.1 is similar to other proteins with actin-like folds in that domains 1 and 3 of NP_812891.1 each adopt an RNaseH-like fold.  However, unlike proteins with a canonical actin-like fold, NP_812891.1 is missing domains 1B and 2B (yellow and green in Figure 3a) and contains a unique strand-helix-strand-strand (SHS2) insert domain 2 (Figure 3b).

    Figure 3.  Comparison of domain organization between (a) 1jcg, (b) NP_812891.1, and (c) 1yf5.  Corresponding domains in all three structures are colored the same.  1jcg has the typical actin-like fold with four domains (1A, 1B, 2A, and 2B) whereas NP_812891.1 and 1yf5 differ from the typical actin-like fold in that they lack domain 2B (green) but have a unique additional strand-helix-strand-strand (SHS2) domain 2 (yellow)

    (a)                                                                    (b)                                                            (c)

    1jcg-domains-comparison-labeled.png  GE15694A-domains-comparison-labeled.png  1yf5-domains-comparison-labeled.png

     

    In terms of overall topology, NP_812891.1 is most similar to 1yf5, which is the cytoplasmic domain of a membrane protein that is part of the type-II secretion system in V. cholerae (Abendroth et al. 2004; Abendroth et al. 2005). (Figures 3b and 3c)

     

    An unidentified ligand (UNL) whose density resembles that of a citrate molecule has been modeled into the structure of NP_812891.1 at what perhaps could be the active site.  This electron density was modeled as a UNL because when NP_812891.1 was superimposed with the structural homolog 3bf1 (a type-III pantothenate kinase; Yang et al. 2008), the density was near where the pantothenate substrate molecule was bound in 3bf1 (Figure 4).  The residues surrounding this region between the two structures, however, do not correlate to one another.

    Figure 4.  Superposition of NP_812891.1 (yellow) with 3bf1 (blue) at the active site of 3bf1.  Unidentified electron density (blue mesh) was found near where the substrate pantothenate (PAU; green sticks) was bound in 3bf1.  UNL is shown in ball-and-stick represention (red).

     

    GE15694A-UNL.png

     

    References:

    The structure of the cytoplasmic domain of EpsL, an inner membrane component of the type II secretion system of Vibrio cholerae: an unusual member of the actin-like ATPase superfamily.  Abendroth J, Bagdasarian M, Sandkvist M, Hol WG.  J Mol Biol. 2004 Nov 26;344(3):619-33.

    The X-ray structure of the type II secretion system complex formed by the N-terminal domain of EpsE and the cytoplasmic domain of EpsL of Vibrio cholerae.  Abendroth J, Murphy P, Sandkvist M, Bagdasarian M, Hol WG.  J Mol Biol. 2005 May 13; 348(4):845-55.

    Structural basis for substrate binding and the catalytic mechanism of type III pantothenate kinase.  Yang K, Strauss E, Huerta C, Zhang H.  Biochemistry. 2008 Feb 5;47(5):1369-80. Epub 2008 Jan 11.

    Ligand Summary

    Reviews

    References

     

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