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The Open Protein Structure Annotation Network
PDB Keyword
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3lyc

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

    Title Crystal structure of Putative pectinase (YP_001304412.1) from Parabacteroides distasonis ATCC 8503 at 2.30 A resolution. To be published
    Site JCSG
    PDB Id 3lyc Target Id 394781
    Molecular Characteristics
    Source Parabacteroides distasonis atcc 8503
    Alias Ids TPS25362,YP_001304412.1, 325885 Molecular Weight 25903.76 Da.
    Residues 240 Isoelectric Point 5.11
    Sequence gdgnittenipvseydclelegggmvvnytqsdapegleiktdrnifekyefnvenhklkirpkkefrk htnfrptefmvtansrnlkklaaagsthvninsplqaeefeaglagsgiiqfhdtasftnlkieiagsg dfvghkvyceelngdmagsntivlggtvgiaefsiagsgtvrafdctmdeleckiagsgdieafvvnki kaeiagsgsvkykgdpqdiqkkvmgsgkiekve
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 16
    Resolution (Å) 2.30 Rfree 0.280
    Matthews' coefficent 2.55 Rfactor 0.244
    Waters 850 Solvent Content 51.83

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3lyc

    Protein Summary

     

    Update from Pfam:  Has been updated the annotation for our DUF2897, PF10988, family. However, family not renamed.

    Gene BDI_3084 (YP_001304412) from Parabacteroides distasonis attc 8503, a species of anaerobic bacteria that are predominant components of the bacterial florae of mucous membrane and are a common cause of several endogenous infections encodes a protein belonging to PFAM family of domains of unknown functions  DUF2807 (PF10988). Its one of the three proteins from this family whose structures were recently solved by JCSG (3jx8, 3ljy and 3lyc). Most extensive discussion of the possible function of proteins from this family can be found on the TOPSAN page http://www.topsan.org/Proteins/JCSG/3jx8.

     

    The 3lyc structure was determined by three-wavelength Se-multiwavelength anomalous diffraction at a resolution of 2.3 Angstroms from an orthorhombic (P212121) crystal form. Shown below are two views of the 3lyc structure. The ribbon representations are color coded with the N-terminal region in blue and the C-terminal region in red.

    monomer1.png

     

     

    monomer2.png

    The crystal structure indicates that a dimer is a significant oligomerization state. Shown below is a ribbons representation of a dimer in the crystal structure with the individual subunits colored in blue and yellow.

    dimer.png

     

    A DALI seach shows the crystal structure of 3lyc is similar to the putative lipoprotein 3jx8 (Z-scr=32), the pectate lyase 1ee6 (Z-scr=12), followed by those shown in the table below.

    PDB ID Z-Score rmsd (Ang) Lalign %seq id Description
    2wlf 12.3 10.6 142 13 Polysialic acid o-acetyl transferase from Neisseria menintigitis
    1ib4 11.3 2.8 169 5 Polygalactouronase from Aspergillus aculeatus
    1kcd 11.2 3.0 173 8 Endopolygalactouronase I from Sterenum purpernum
    2yuh 11.0 4.1 134 10 Solution structure of Human Tubulin-specific Chaperone C
    2bx6 10.9 3.0 131 8 Human retinitis pigmentosa 2 protein and its intreraction with Arl3
    1k8f 10.5 3.0 120 10 Human C-Terminal CAP-I Adenylyl Cyclase Associated Protein

     

    The 3lyc structure  can be classified as belonging to the SCOP all beta class, single-stranded right-handed beta-helix fold, pectin lyase-like superfamily. Preliminary inspection of the structure shows that a portion of the structure corresponding to residues (114-266) forms a single-stranded right-handed beta helix.

    Ligand Summary

    Reviews

    References

     

    No references found.

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