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The Open Protein Structure Annotation Network
PDB Keyword
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2hsz

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

    Title Crystal structure of novel predicted phosphatase from Haemophilus somnus 129PT at 1.90 A resolution. To be published
    Site JCSG
    PDB Id 2hsz Target Id 366906
    Molecular Characteristics
    Source Haemophilus somnus 129pt
    Alias Ids TPS1487,YP_718383.1, 291564 Molecular Weight 25028.33 Da.
    Residues 224 Isoelectric Point 5.18
    Sequence mtqfkligfdldgtlvnslpdlalsinsalkdvnlpqasenlvmtwigngadvlsqravdwackqaeke ltedefkyfkrqfgfyygenlcnisrlypnvketlealkaqgyilavvtnkptkhvqpiltafgidhlf semlggqslpeikphpapfyylcgkfglypkqilfvgdsqndifaahsagcavvgltygynynipiaqs kpdwifddfadilkitq
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 1.90 Rfree 0.205
    Matthews' coefficent 2.93 Rfactor 0.169
    Waters 334 Solvent Content 57.68

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 2hsz
    1. Decision-making in structure solution using Bayesian estimates of map quality: the PHENIX AutoSol wizard
    TC Terwilliger, PD Adams, RJ Read - Section D: Biological , 2009 - scripts.iucr.org
     
    2. High accuracy template based modeling by global optimization
    K Joo, J Lee, S Lee, JH Seo, SJ Lee - : Structure, Function, and , 2007 - Wiley Online Library
     
    3. Using inferred residue contacts to distinguish between correct and incorrect protein models
    CS Miller, D Eisenberg - Bioinformatics, 2008 - Oxford Univ Press
     
    4. Domain definition and target classification for CASP7
    ND Clarke, I Ezkurdia, J Kopp, RJ Read - Proteins: Structure, , 2007 - Wiley Online Library
     
    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. High Yield Recombinant Expression, Characterization and Homology Modeling of Two Types of Cis-epoxysuccinic Acid Hydrolases
    GZ Cui, S Wang, Y Li, YJ Tian, Y Feng, Q Cui - The Protein Journal, 2012 - Springer
     
    7. Reconstruction of Protein Backbone with the a-Carbon Coordinates
    JH Wang, CB Yang, CT Tseng - 2007 - asiair.asia.edu.tw
     
    8. Refinement of All-atom Backbone Prediction of Proteins
    HY Chang - 2008 - etd.lib.nsysu.edu.tw
     
    9. Relative Packing Groups in Template-Based Structure Prediction: Cooperative Effects of True Positive Constraints
    R Day, X Qu, R Swanson, Z Bohannan - Journal of , 2011 - online.liebertpub.com
     
    10. Analysis of Protein Structure using Geometric and Machine Learning Techniques
    A Tendulkar - 2007 - it.iitb.ac.in
     

    Protein Summary

    The HS_0176 gene of H. somnus 129PT encodes the YP_718383 protein with sequence and structure similar to predicted phosphoglycolate phosphatases (COG0546) (SCOP). Genome context analysis shows a strong functional link (score 0.9) with the ribulose-phosphate 3-epimerase (HS_0175).

    Residues conserved between YP_718383 and COG0546 (Thr118, Lys151, Gly175, Asp176, and Asp180) are clustered together around central part of a deep cleft. This cleft has two openings and is partly occupied by UNL. The other residues that were found (using SAM-T06 server) to be conserved between YP_718383 and similar sequences are also located around the same cleft (Asp10, Asp12, Gly13, Thr118, Asn119, Lys151, Asp176, and Asp180) or clustered together (Phe9, Leu15, Leu104, and Ile219) next to the cleft surrounding residues.

    The 2hsz structure has significant structural similarity to proteins with beta-phosphoglucomutase-like structures, such as for example: phosphonoacetaldehyde hydrolase (PDB:1fez-A; DALI Z-score 22.2; RMSD 2.4; 11% sequence identity within 215 superimposed residues), and beta-phosphoglucomutase (PDB:1o03-A; DALI Z-score 19.8; RMSD 2.9 ; 16% sequence identity within 199 superimposed residues).

    Analysis of the crystallographic packing of 2hsz using the PQS server {Henrick, 1998 #73} indicates that a tetramer is the biologically relevant form.

    Ligand Summary

    The UNL occupies one side of a deep cleft. This cleft has two entrances and several conserved residues in the middle.

    References

    Reviews

    References

     

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