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The Open Protein Structure Annotation Network
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1vpq

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

    Title Crystal structure of hypothetical protein (TM1631) from Thermotoga maritima at 2.20 A resolution. To be published
    Site JCSG
    PDB Id 1vpq Target Id
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    Molecular Characteristics
    Source
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    Alias Ids
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    TPS1306,TM1631, _0050.001329_, 85056
    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 1
    Resolution (Å)
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    Rfree
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    Matthews' coefficent 2.20 Rfactor 0.20602
    Waters
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    Solvent Content 44.02

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    Ligand Information
    Ligands
    Metals

    Jmol

     
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    Google Scholar output for 1vpq
    1. Fast and accurate algorithms for protein side-chain packing
    J Xu, B Berger - Journal of the ACM (JACM), 2006 - dl.acm.org
     
    2. Computational modeling of laminin N_terminal domains using sparse distance constraints from disulfide bonds and chemical cross_linking
    S Kalkhof, S Haehn, M Paulsson - Proteins: Structure, , 2010 - Wiley Online Library
     
    3. Protein structure prediction based on the sliced lattice model
    CC Wang, CB Yang, HY Ann - 2008 Conference on , 2005 - etd.lib.nsysu.edu.tw
     
    4. Dimensionality reduction in computational demarcation of protein tertiary structures
    RR Joshi, PR Panigrahi, RN Patil - Journal of Molecular Modeling, 2011 - Springer
     
    5. Prediction of Protein Backbone Based on the Sliced Lattice Model
    CC Wang, CB Yang, HY Ann, HY Chang - 2008 - csie.npu.edu.tw
     
    6. Nonredundant 3D Structure Datasets for RNA Knowledge Extraction and Benchmarking
    NB Leontis, CL Zirbel - RNA 3D Structure Analysis and Prediction, 2012 - Springer
     

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    Protein Summary

    The TM1631 gene from Thermotoga maritima encodes a protein belonging to a large (~500 homologs, ~400 species) and widely distributed (archaea, eukaryotes, prokaryotes, viruses) family of domains of unknown function (DUF72, PF01904, COG1801) that adopt a TIM alpha/beta barrel fold. A BLAST search provides a hit (e-val=4e-85; 30% seq. id.) with the BselDRAFT_2940 sequence annotated as uracil-xanthine permease.

    A search with HHpred suggests remote homology with PF07825, a family of phage-encoded excisionase proteins (P-value 0.00094) and PF09797, a family of proteins found adjacent to short, palindromic repeat clusters that are thought to constitute mobile DNA elements (P-value 0.0015).

    The structure of EF0266, a DUF72 homolog from Enterococcus faecalis (PDB id: 1vpy), shows strong similarity with the TM1631 structure (main-chain rmsd of 1.6 Å over 219 residues, 33% sequence identity, DALI Z=28). A search with FATCAT shows the highest structural similarity as occurring with a bacterial DNA repair enzyme (UV repair endonuclease, PDB id: 2j6v; Z=12) [Ref] with a main-chain rmsd of 3 Å over 189 residues and a sequence identity of 10%. Similar values are obtained for DUF692 family (PDB id: 3bww) which is also predicted to function in DNA protection or repair. A DALI search provides hits with the putative dehydratase AsbF 3dx5 (Z=13) [Ref], the D-mannonate dehydratase 3ban (Z=13), and the L-ribulose 5-phosphate 3-epimerase UlaE 3cqi (Z=13) [Ref].

    Comparison of DUF72 sequence homologs shows a number of charged and aromatic of residues centered at the top of the barrel that are either invariant (Arg145 in TM1631) or highly conserved (Tyr48, Gln114, Glu143, Tyr208). By analogy with 2j6v, we suggest that this cavity could constitute the active or binding site for this family.

     

    To do: look at UNL in 1VPY, run suspected binding cavity through IsoCleft or similar algorithm.

    Ligand Summary

     

     
     

    Reviews

    References

     

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