.
The Open Protein Structure Annotation Network
PDB Keyword
.

3gza

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

    Title Crystal structure of putative alpha-L-fucosidase (NP_812709.1) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 1.60 A resolution. To be Published
    Site JCSG
    PDB Id 3gza Target Id 393043
    Molecular Characteristics
    Source Bacteroides thetaiotaomicron vpi-5482
    Alias Ids TPS20952,NP_812709.1, 332635 Molecular Weight 50385.45 Da.
    Residues 442 Isoelectric Point 6.94
    Sequence aqqqelpvpkphqlkwheaemgavfhydlhvfdgirygqgnnrinpiedynifnptelntdqwvqaaka agckfavltathetgfglwqsdvnpyclkavkwrdgkgdivrdfvnscrkyglqpgiyigirwnsllgi hnfkaegegafarnrqawykrlcekmvtelctrygdlymiwfdggaddpradgpdvepivnkyqpnclf yhnidradfrwggsetgtveypcwstfpvpcshhkriessidqlellkhgdkngrywvpamadtplrga ngrhewfwepddenniyplntlmdkyeksvgrnatlilgltpdptglipagdaqrlkemgdeinrrfss piarisgqkksltlklgkeqsvnyciiqenikngerirqyqieakvngkwqtvckgesvghkriekfep veatalrltvsesialpdiinfsaysvk
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 1.60 Rfree 0.168
    Matthews' coefficent 2.55 Rfactor 0.139
    Waters 1252 Solvent Content 51.72

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3gza
    1. Analysis of the Reaction Coordinate of _-l-Fucosidases: A Combined Structural and Quantum Mechanical Approach
    AL van Bueren, A Arde_vol, J Fayers-Kerr, B Luo - J. Am. Chem. , 2010 - ACS Publications
     
    2. Bifidobacterium longum subsp. infantis ATCC 15697 _-Fucosidases Are Active on Fucosylated Human Milk Oligosaccharides
    DA Sela, D Garrido, L Lerno, S Wu, K Tan - Applied and , 2012 - Am Soc Microbiol
     

    Protein Summary

    The structure of Bacteroides thetaiotaomicron protein BT_3798 (accession number NP_812709.1) has been determined at a resolution of 1.6 Angstroms using multiwavelength anomalous disperson methods. Its a two domain protein, with N-terminal Alpha-L-fucosidase (PF01120) domains and C-terminal domain showing sub-threshold similarity to the F5/8 type C (PF00754) domains. Alpha-L-fucosidase is also classified as glycosyl hydrolase family #29. F5/8 type C domain is found in the C-terminal domains of  Blood coagulation factors V and VIII, where it is duplicated, but it is also present in bacteria, for instance in Streptococcus pneumoniae  virulence factors.

     monomer_ribbons.bmp

     Pfam update: This protein is now in families PF01120.10 Alpha_L_fucos, CL0058; PF00754.18 F5_F8_type_C CL0202 both with other structures.

    Shown here is a ribbon representation of the monomer of BT_3798 (NP_812709.1) color coded with the N-terminal end in blue and the C-terminal end in red. The most significant feature of the structure is a larger N-terminal domain (residues 1-360) and a smaller C-terminal domain (residues 360-460). BT_3798 has at least six paralogs in  Bacteroides thetaiotaomicron vpi-5482, one of which (BT_2192) was recently solved by NYSGXRC and deposited in PDB with the code 3eyp. Structure analysis confirms the PFAM domain assignments, with a N-terminal domain showing signficant structural similarity to TIM barrels from (Trans)glycosidases superfamily and C-terminal showing significant similarity to various F5/8 type C domains, classified by SCOP as having Galactose-binding domain-like fold.

    Shown here is a ribbon representation of the structure of NP_812709.1 surrounding the putative active site for one subunit in the asymmetric unit.  2Fo-Fc electron density contoured at 1 sigma (cyan) is shown corresponding to a molecules of HEPES buffer from the crystallization and ethylene glycol (EDO) used as a cryoprotectant. The labeled residues, (Glu 240, Tyr 145, and Asp 199) are conserved in the structure of PDB ID 1hl9, a putative alpha-fucosidase from Thermotoga maritima.

     putative_active_site (3).bmp

     

     

     

    Shown below is a least squares overlap of the N-terminal domains of the structures of BT_3798 (NP_812709.1) (green) and PDB ID 1hl9. The structures of N-terminal domains of both proteins are similar; however, its worth noting that the folds of C-terminal domains of both proteins are different: C-terminal domain of BT_3798 (NP_812709.1) has a Galactose-binding domain-like, jelly-roll beta sandwich with 9 strands in 2 sheets, fold and a C-terminal of T. maritima TM_0306 forms a 8- stranded greek-key beta barrel. 

     

    1hl9_GS13839B_overlap.png

     

     

     

    The figure below show a comparison of the active site of PDB ID 1hl9 (blue) on the N-terminal domain with the putative active site of BT_3798 (NP_812709.1)(green) described here. The structure of 1hl9 was determined in the presence of a substrate analog fucosyl floride (FUF). Kinetic and mutagenic studies implicated the active site residues in 1hl9, Asp 244 and Glu 266 as catalytic nucleophiles. The structural comparison described here indicates that Asp 199 and Glu 240 in the structure of BT_3798 (NP_812709.1) would play a similar role in catalysis.

     

     

     

     

     

    Reference

    Sulzenbacher et. al. "Crystal Structure of Thermotoga maritima alpha-L-fucosidase" J. Biol Chem (2004) Vol 279, No 13 pp. 13119-13128

     

     

     

     

     

     

     

     

     

     

     

     

    Ligand Summary

    Reviews

    References

     

    No references found.

    Tag page
    You must login to post a comment.
    All content on this site is licensed under a Creative Commons Attribution 3.0 License
    Powered by MindTouch