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3kzs

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

    Title Crystal structure of glycosyl hydrolase family 5 (NP_809925.1) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 2.10 A resolution. To be published
    Site JCSG
    PDB Id 3kzs Target Id 393067
    Molecular Characteristics
    Source Bacteroides thetaiotaomicron vpi-5482
    Alias Ids TPS20966,NP_809925.1, 332634 Molecular Weight 53714.73 Da.
    Residues 462 Isoelectric Point 6.31
    Sequence aqkktqktyipwsngklvvseegrylkhengtpffwlgetgwllperlnrdeaeyyleqckrrgynviq vqtlnnvpsmniygqysmtdgynfkninqkgvygywdhmdyiirtaakkglyigmvciwgspvshgemn vdqakaygkflaerykdepniiwfiggdirgdvktaewealatsikaidknhlmtfhprgrttsatwfn napwldfnmfqsghrrygqrfgdgdypieenteednwrfversmamkpmkpvidgepiyeeiphglhde nellwkdydvrryaywsvfagsfghtyghnsimqfikpgvggaygakkpwydalndpgynqmkylknlm ltfpffervpdqsviagqngerydraiatrgndylmvynytgrpmevdfskisgakknawwyttkdgkl eyigefdngvhkfqhdsgyssgndhvlivvdsskdyvkkdcyqidthe
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 4
    Resolution (Å) 2.10 Rfree 0.222
    Matthews' coefficent 2.77 Rfactor 0.185
    Waters 1208 Solvent Content 55.58

    Ligand Information
    Ligands
    Metals

    Jmol

     

    Protein Summary

    Summary from Pfam: Built this as two separate domains, both now in different, known clans, with other structures:
    ID Glyco_hydro_101
    AC PF12905
    DE Putative endoglucanase
    AU Coggill P
    SE JCSG_target_393067_3kzs
    GA 21.00 21.00;
    TC 21.00 21.10;
    NC 20.80 20.80;
    BM hmmbuild --amino -o /dev/null HMM SEED
    SM hmmsearch -Z 9421015 -E 1000 --cpu 4 HMM pfamseq
    TP Domain
    CL CL0058
    RN [1] RM 9718293 RT Snapshots along an enzymatic reaction coordinate: analysis of a RT retaining beta-glycoside hydrolase. RA Davies GJ, Mackenzie L, Varrot A, Dauter M, Brzozowski AM, Schulein RA M, Withers SG; RL Biochemistry. 1998;37:11707-11713. This is the N-terminal part of the PDB:3kzs structure from Swiss:Q8A905, the C-terminal being family Collagen_bind_2, Pfam:PF12904. It appears to have a TIM beta-l-alpha barrel fold, and to function as a beta-glycanase (information derived from TOPSAN).
    ID Collagen_bind_2
    AC PF12904
    DE Putative collagen-binding domain of a collagenase
    AU Coggill P
    SE JCSG_target_393067_3kzs
    GA 21.70 21.70;
    TC 21.70 27.90;
    NC 20.90 20.50;
    BM hmmbuild --amino -o /dev/null HMM SEED
    SM hmmsearch -Z 9421015 -E 1000 --cpu 4 HMM pfamseq
    TP Domain
    CL CL0204
    This domain is likely to be the collagen-binding domain of a family of bacterial collagenase enzymes. It is the C-terminal part of the PDB:3kzs structure determined from Swiss:Q8A905 (information derived from TOPSAN).

     

     

     

    NP_809925.1 is a 483 amino acid long hypothetical protein encoded by Bacteriodes thetaiotaomicron vpi-5482. The structure described here was determined at a resolution of 2.1 Angtsroms using multiwavelength anomalous dispersion methods. The expression construct from which protein was purfied and crystallized was comprised of amino acids 22-483. NP_809925.1 belongs to an uncharacterized Pfam group. Shown here is a ribbon representation of the monomeric structure of NP_809925.1 color coded with the N-terminal region in blue and the C-terminal region in red.

    GS14055A.png

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

    The most significant structural feature are two domains. The larger N-terminal domain  is comprised primarily of alpha-helices from residues 27-370, and the smaller C-terminal domain is comprised of a beta-sandwich between residues 370-483. A search of the fastSCOP database using the refined coordinates of the NP_809925.1 shows that the N-terminal domain is quite similar to PDB ID 7A3H, an endoglucanase Cel5a from Bacillus agaradhaerens. Thus, the N-terminal domain of NP_809925.1 shows a TIM betal/alpha barrel fold, and belongs to the beta-glycanases SCOP superfamily.
     

     

    Shown below is an alpha-carbon superpositioning of the structures of NP_809925.1 (green) and PDB ID 7AH3, the endoglucanase Cel5a from Bacillus agaradhaerens. The overlap show that the N-terminal domain of NP_809925.1 is likely to perform a similar endoglucanase function as that of PDB ID 7AH3. Cellulases,  from most organisms contain multiple domains with a  catalytic core domain and  accessory domains. These additional domains, such as the smaller C-terminal domain of NP_809925.1 are thought to be involved in substrate binding.

    7a3h_overlap.png

     A search of the fastSCOP evolutionary classification database using only the coordinates of the C-terminal domain of NP_809925.1 (residues 380-483), indicate this smaller domain shows structural similarity to PDB ID 1NQJ, the crystal structure a collagen-binding domain of COLG collagenase from Clostridium  histolyticum. Shown below is a SSM superposition of the ribbon representations of the C-terminal domain of NP_8099256.1 (green) and the structure of PDB ID 1NQJ

    C_term_overlap.png

     

     

     

     

     

     

     

     

     

     

     

    References

    Davies GJ, Mackenzie L, Varrot A, Dauter M, Brzozowski AM, Schülein M, Withers
    SG. Snapshots along an enzymatic reaction coordinate: analysis of a retaining
    beta-glycoside hydrolase. Biochemistry. 1998 Aug 25;37(34):11707-13.

    Ligand Summary

    Reviews

    References

     

    No references found.

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    Files (3)

    FileSizeDateAttached by 
     7a3h_overlap.png
    overlap 7a3h
    261.69 kB04:54, 27 Feb 2009haxelrodActions
     C_term_overlap.png
    1NQJ overlap with C-terminal domain of GS14055A
    156.26 kB20:09, 27 Feb 2009haxelrodActions
     GS14055A.png
    Monomer ribbons
    231.09 kB03:53, 27 Feb 2009haxelrodActions
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