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The Open Protein Structure Annotation Network
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4mu9

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

    Title Crystal structure of a putative glycosylhydrolase (BT_3782) from Bacteroides thetaiotaomicron VPI-5482 at 1.89 A resolution. To be published
    Site JCSG
    PDB Id 4mu9 Target Id 396216
    Molecular Characteristics
    Source Bacteroides thetaiotaomicron vpi-5482
    Alias Ids TPS25891,NP_812693.1, BIG_251, 332865 Molecular Weight 41959.37 Da.
    Residues 363 Isoelectric Point 7.18
    Sequence hpfvsiadsildnvlnlyqtedglltetypvnpdqkitylaggaqqngtlkasflwpysgmmsgcvamy qatgdkkyktilekrilpgleqywdgerlpacyqsypvkygqhgryyddniwialdycdyyrltkkady lkkaialyeyiysgwsdelgggifwceqqkeakhtcsnapstvlgvklyrltkdkkylnkaketyawtr khlcdpddflywdninlkgkvskdkyaynsgqmiqagvllyeetgdkdylrdaqktaagtdaffrskad kkdpsvkvhkdmswfnvilfrgfkalekidhnptyvramaenalhawrnyrdangllgrdwsghneepy kwlldnaclielfaeiek
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 1.89 Rfree 0.1916
    Matthews' coefficent 2.11 Rfactor 0.1498
    Waters 713 Solvent Content 41.74

    Ligand Information
    Ligands
    Metals

    Jmol

     

    Protein Summary

     

     

     

    NP_812693.1  from Bacteroides thetaiotaomicron vpi-5482, has highly similar homolog pdbID 3K7X.It is also called

     

     

    harboring the active side. FFAS indicates origin from Glyco-hydro-76 family, but it is also very similar to

    *105 family, represented by 2gh4 pdbID.

     

     

     

    Profunc results in 5 matching sequence motifs:

     

     

    HMMPfam

    PF03663

    Glyco_hydro_76

     

     

     

    superfamily

    SSF48208

    Six-hairpin glycosidases

     

     

     

    HMMPanther

    PTHR12145

    UNCHARACTERIZED

     

     

     

    Gene3D

    G3DSA:1.50.10.10

    no description

     

     

     

    HMMPIR

    PIRSF021505

    Predicted O-glycosyl hydrolase

     

     

     

    DALI RESULTS:

     

        No:  Chain   Z    rmsd lali nres  %id PDB  Description
       1:  3k7x-A 37.2  2.2  323   348   25 PDB  MOLECULE: LIN0763 PROTEIN;                                           
       2:  3vw5-A 29.0  3.0  329   389   11 PDB  MOLECULE: CELLOBIOSE 2-EPIMERASE;                                    
       3:  3vw5-C 28.9  3.0  329   389   11 PDB  MOLECULE: CELLOBIOSE 2-EPIMERASE;                                    
       4:  3vw5-B 28.8  3.0  328   389   11 PDB  MOLECULE: CELLOBIOSE 2-EPIMERASE;                                    
       5:  3gt5-A 28.7  3.4  332   391   10 PDB  MOLECULE: N-ACETYLGLUCOSAMINE 2

     

     

     

    Structural overlap with 2gh4 reveals exact overlap of the RAM ring with the ring of the HEPES ligand present in the PX5927B crystallization. It is remarkable that the piperazine ring's surface from HEPES is ~parallel to ring surface of its nearest aromatic residue, i.e. Trp80 in our target and RAM ring to Tyr41 in 2gh4, see in figures below.

     

     

     

    All helices along the 6-fold barrel are twisted about 40deg relative to the barrel axis. Dipole of the monomer runs through the inner channel, ~parallel to the long axix of HEPES molecule. All radial components of the 6 pairs of dipole moments must cancel out giving rise to that axial resulting vector. It is known that GlycosylTransferases-B fold enzymes use positively charged side chains and/or hydroxyls and helix dipoles for leaving group departure part of their enzymatic reaction.When looking at electrostatic surface of the monomer and dimeric configuration, it becomes clear that it's the same case for this family. Pictures of Delphi output are below. PISA prediction of functional dimer would imply that the dimerizartion is electrostatically driven.

    Ligand Summary

    Reviews

    References

     

    No references found.

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    Files (2)

    FileSizeDateAttached by 
     DELPHI-activePOCKET.png
    Delphi electrostatic surface with bound EPE inside of the barrel
    387.69 kB01:14, 5 Sep 2013cbtrameActions
     PX-TOP.jpg
    Overall fold as seen along the barrel axis
    795.95 kB01:12, 5 Sep 2013cbtrameActions
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