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The Open Protein Structure Annotation Network
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3hrp

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

    Title Crystal structure of Structural genomics protein of unknown function (NP_812590.1) from Bacteroides thetaiotaomicron VPI-5482 at 1.70 A resolution. To be Published
    Site JCSG
    PDB Id 3hrp Target Id 392959
    Molecular Characteristics
    Source Bacteroides thetaiotaomicron vpi-5482
    Alias Ids TPS20259,NP_812590.1, 324892 Molecular Weight 44939.95 Da.
    Residues 408 Isoelectric Point 4.90
    Sequence sddnkttgatydpnqpvtvesfmpvegklrekvivkgsnfgtdkskvkvyfvdeaaerlstvigidnnt lyclaprqlpggnrikvivdgkevttdgtfkyeqaqnvstisgsaskdgnddgdlasakfkymwgiaav gnntvlayqrddprvrlisvddnkvttvhpgfkggkpavtkdkqrvysigwegthtvyvymkasgwapt rigqlgstfsgkigavaldeteewlyfvdsnknfgrfnvktqevtlikqlelsgslgtnpgpyliyyfv dsnfymsdqnlssvykitpdgecewfcgsatqktvqdglreealfaqpngmtvdedgnfyivdgfkgyc lrkldildgyvstvagqvdvasqidgtpleatfnypydicydgeggywiaeawgkairkyave
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 1.70 Rfree 0.195
    Matthews' coefficent 2.26 Rfactor 0.169
    Waters 358 Solvent Content 45.58

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3hrp
    1. Plasma membrane proteomes of differentially matured dendritic cells identified by LC-MS/MS combined with iTRAQ labelling
    S Ferret-Bernard, W Castro-Borges, AA Dowle - Journal of , 2011 - Elsevier
     

    Protein Summary

    The BT_3769 gene from Bacteroides thetaiotaomicron encodes a two-domain protein. The N-terminal domain adopts an immunoglobulin-like structure and belongs to PF01833 while the C-terminal domain adopts a beta-propeller fold and contains two NHL repeats that belong to Pfam PF01436. The four-stranded antiparallel, twisted beta-sheets of the propeller are radially arranged around a central  tunnel with positive charged  central cavity facing the interface to the 'attachment' domain. While many propellers maintain their active side in that central cavity, this starget has the bound MPD in a cavity between the propeller body and the beta-barrel attachment domain. While Profunc assigns this protein within the NHL-repeat family, the first stricking feature of this fold are sets of TYR's aligned in pairs of 3 in most of the blade segments of the propeller. Surface calculations reveal no opening at the bottom of the propeller, where additional 3 TYR's line out the exit of that internal central cavity. The beta-barrel 'attachment' domain has the most ligands bound, favouring the negative charged groove along the side of the barrel, where there would be a place for a complementary beta-sheet closing the barrel cavity. The last characteristic feature of this fold is the 'alignment' and strong contacts of the C-terminal with the N-terminal strand, in which the GLU430 makes 4 close contacts with a strand connecting the attachment to the propeller body. These are to ALS126,TYR123 and multiple waters in the adjacent space. It's like that connection 'fixes' the 2 big structures relative to each other. The MPD bound in the internal cavity besides of water contacts has the only bond to ASP352.

    A DALI search for similar structures gave PDB id 1Q7F (Brain Tumor NHL domain) as the top hit follwed by 1RWL (serine/threonine-protein kinase), within 2.6 Å rmsd. The Brain Tumor functions in which the NHL-propeller seems to be an essential scaffold for both tranlational repression and cell growth inhibitory activities in Drosophila.  It is also known (Genes Dev. 2003 Oct 15;17(20):2508-13) that NHL domain carries the tumour suppressor function of Brat25 and bam25 ad is required for regulation of germ cell differentation. All that might tiie the current target at least partially (through the preserved propeller domain) to RNA metabolism.

    Profunc serach results:

    4 motifs matched in scan against PROSITE, PRINTS, PFam-A, TIGRFAM, PROFILES and PRODOM motifs
          Type     Motif     Name
    1.     HMMPfam     PF01436x2     NHL
    2.     superfamily     SSF101898     NHL repeat
    3.     superfamily     SSF81296     E set domains
    4.     Gene3D     G3DSA:2.120.10.30     no description

     

    Search of sequence vs Superfamily HMM library. Chain A

    1 motif matched in scan against the Superfamily HMM library
          Residue range(s)                        Motif     Superfamily name
    1.     84-95, 100-121, 144-220,
            222-239, 244-279, 288-306,
            310-324, 338-386, 399-430     50974     Nitrous oxide reductase,
                                                                            N-terminal domainBLAST search vs Uniprot. Chain A

    88 matching sequences found by BLAST search
          Ref. no.     E-value     %-tage id     Overlap     Name
    1.     Q8A1I2_BACTN         100.000     400     Q8A1I2 Putative uncharacterized protein OS=Bacteroides
    2.     Q8A3A7_BACTN         39.416     411     Q8A3A7 NHL repeat containing protein OS=Bacteroides
    3.     Q8A550_BACTN         32.701     422     Q8A550 NHL repeat-containing protein OS=Bacteroides
    4.     A5ZJP9_9BACE         29.484     407     A5ZJP9 Putative uncharacterized protein OS=Bacteroides caccae ATCC
    5.     B3C9G7_9BACE         30.332     422     B3C9G7 Putative uncharacterized protein OS=Bacteroides intestinalis
     

    Matching folds detected by SSM

        Matching folds. Chain A

    633 significant structural matches
          Q-score     Rmsd          No. SSE     Z-score     PDB     Name
    1.     0.324       2.41A                 18            8.4     1rwl     Extracellular domain of mycobacterium tuberculosis pknd
    2.     0.321       2.44A                 18            8.2     1rwi     Extracellular domain of mycobacterium tuberculosis pknd
    3.     0.311       2.66A                  20           8.2     1q7f     Brain tumor nhl domain
    4.     0.291       2.31A                  21           8.7     3e5z     X-ray structure of the putative gluconolactonase in protein family pf08450. Northeast structural genomics consortium target drr130.
    5.     0.286       2.13A                   22          9.7     2p4o     Crystal structure of hypothetical protein (zp_00111901.1) from nostoc punctiforme pcc 73102 at 1.90 a resolution
     

    13 nests located in the structure
          Score     No.resid.     Ave.accessibility     Cleft     Ave. conservation     Residues
    1.     3.252     3     0.27     2     0.585     Asp409(A), Gly410(A), Glu411(A)
    2.     2.841     4     0.20     2     0.340     Asp202(A), Lys203(A), Gln204(A), Arg205(A)
    3.     2.257     3     0.19     -     0.924     Asn61(A), Phe62(A), Gly63(A)
    4.     2.086     3     0.19     3     0.420     Asp375(A), Gly376(A), Tyr377(A)
    5.     1.761     3     0.21     -     0.428     Thr270(A), Gln271(A), Glu272(A)

    Ligand Summary

    Reviews

    References

     

    No references found.

    Tag page

    Files (8)

    FileSizeDateAttached by 
     109-buttom-electrostats.tif
    Electrostatics from the bottom-no 6-fold symmetry
    4.61 MB22:33, 5 Mar 2009cbtrameActions
     109-HEAD-II-ligands-electrostats.tif
    Electrostatics of the 'head' with bound ethylene glycol molecules
    4.61 MB22:33, 5 Mar 2009cbtrameActions
     109-top-electrostats.tif
    Electrostatics (CHIMERA UCSF) from the top looking into central tunnel
    4.47 MB22:33, 5 Mar 2009cbtrameActions
     GS13221C-109-side.jpg
    Side view of the NHL domain looking target GS13221C
    313.31 kB22:40, 5 Mar 2009cbtrameActions
    GS13221C-109-side.tiff
    Side view of the 'modified' propeller fold
    4.47 MB22:36, 5 Mar 2009cbtrameActions
     GS13221C-109-TOP.jpg
    Top View of the 6-fold beta-propeller with beta-barrel attachment
    333.23 kB22:40, 5 Mar 2009cbtrameActions
    GS13221C-109-TOP.tiff
    Top view of the GS13221C
    4.47 MB22:36, 5 Mar 2009cbtrameActions
     MPD-cavity.jpg
    MPD cavity above the central tunnel
    163.01 kB22:36, 5 Mar 2009cbtrameActions
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