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2i5i

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

    Title Crystal structure of hypothetical protein (EF3048) from ENTEROCOCCUS FAECALIS V583 at 1.70 A resolution. To be published
    Site JCSG
    PDB Id 2i5i Target Id
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    Molecular Characteristics
    Source
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    Alias Ids
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    TPS1421,EF3048, PF04794, 285518
    Molecular Weight
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    Da.
    Residues
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    Isoelectric Point
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    Sequence
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      BLAST   FFAS

    Structure Determination
    Method XRAY
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    Chains 2
    Resolution (Å)
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    Rfree
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    Matthews' coefficent 2.25 Rfactor 0.144
    Waters
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    Solvent Content 45.01

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    Ligand Information
    Ligands
    Metals

    Jmol

     
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    Google Scholar output for 2i5i
    1. Domain definition and target classification for CASP7
    ND Clarke, I Ezkurdia, J Kopp, RJ Read - Proteins: Structure, , 2007 - Wiley Online Library
     
    2. Crystal structure of the YdjC-family protein TTHB029 from Thermus thermophilus HB8: Structural relationship with peptidoglycan N-acetylglucosamine deacetylase
    T Imagawa, H Iino, M Kanagawa, A Ebihara - Biochemical and , 2008 - Elsevier
     
    3. Distributed structure determination at the JCSG
    H van den Bedem, G Wolf, Q Xu - Section D: Biological , 2011 - scripts.iucr.org
     
    4. Reconstruction of Protein Backbone with the a-Carbon Coordinates
    JH Wang, CB Yang, CT Tseng - 2007 - asiair.asia.edu.tw
     
    5. Reconstruction of Protein Backbone with the alpha-Carbon Coordinates
    JH Wang, CB Yang, CT Tseng - Journal of Information Science , 2010 - etd.lib.nsysu.edu.tw
     
    6. Refinement of All-atom Backbone Prediction of Proteins
    HY Chang - 2008 - etd.lib.nsysu.edu.tw
     
    7. Importance de l'extrmit N-terminale de la nuclocapside dans l'assemblage du virus de la mosaque de la papaye
    ML Gagn - 2007 - theses.ulaval.ca
     

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    Protein Summary

    Gene EF3048 from E. faecalis V583 encodes the protein NP_816660 that has sequence similarity to YdjC-like proteins (PfamPF04794) and is possibly involved in the cleavage of cellobiose-phosphate.

    EF3048 genomic neighborhood and phylogenetic cooccurrence indicate that its function may be interdependent with the following proteins:
    EF1411[Q835G6], Glycosyl hydrolase (family 4);
    EF1018[Q836T9], PTS system (IIA component);
    EF1159[Q836F5], PTS system (cellobiose-specific IIB component).

    Highly conserved Asp11, Asp12, His63, His129, and His213 are part of a deep cleft and are likely to be important for enzymatic activity.

    2i5i is highly similar to several PDB structures, such as:
    2nly DALI Z-score 17.1; RMSD 3.0; 14% sequence identity for 201 superimposed residues), 2dfa DALI Z-score 15.8; RMSD 2.8; 21% sequence identity for 196 superimposed residues), 1xw8 DALI Z-score 14.2; RMSD 2.6; 20% sequence identity for 180 superimposed residues), 2c1g DALI Z-score 12.4; RMSD 2.7 ;14% sequence identity for 167 superimposed residues). 

    Conserved histidines of 2i5i are superimposed with histidines in PDB structures: 2nly, 2dfa, 1xw8. However highly conserved Gln112 (buried close to the conserved cleft) is only superimposed with glutamine of PDB structures 2dfa and 1xw8.

    Analysis of the crystallographic packing of 2i5i using the PQS server {Henrick, 1998 #73} indicates that an hexamer is the biologically relevant form.

    Ligand Summary



    References

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