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The Open Protein Structure Annotation Network
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1vk9

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

    Title Crystal structure of an ADP-ribosylated protein with a cytidine deaminase-like fold, but unknown function (TM1506), from Thermotoga maritima at 2.70 A resolution. Proteins 71 1546-1552 2008
    Site JCSG
    PDB Id 1vk9 Target Id 283363
    Molecular Characteristics
    Source Thermotoga maritima msb8
    Alias Ids TPS1294,TM1506, 84820 Molecular Weight 15743.74 Da.
    Residues 139 Isoelectric Point 8.89
    Sequence meknllrsalkifekkdlsllaysgrsifeskdsglkpvvelfkrfdnlegslvidkmvgkaaasfllk mkpdhihakviskpalklmneygqsfsydekipfvlgkdgksmcpfeklvlemddpeeiirivlskftsl
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 2.70 Rfree 0.25083
    Matthews' coefficent 5.06 Rfactor 0.20579
    Waters 9 Solvent Content 75.49

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 1vk9
    1. The Buccaneer software for automated model building. 1. Tracing protein chains
    K Cowtan - Acta Crystallographica Section D: Biological , 2006 - scripts.iucr.org
     
    2. 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
     
    3. Prediction of protein structure from ideal forms
    WR Taylor, GJ Bartlett, V Chelliah - Proteins: Structure, , 2008 - Wiley Online Library
     
    4. High-throughput protein production for X-ray crystallography and use of size exclusion chromatography to validate or refute computational biological unit predictions
    D McMullan, JM Canaves, K Quijano - Journal of structural and , 2005 - Springer
     
    5. Ligands in PSI structures
    A Kumar, HJ Chiu, HL Axelrod, A Morse - Section F: Structural , 2010 - scripts.iucr.org
     
    6. Crystal structure of an ADP_ribosylated protein with a cytidine deaminase_like fold, but unknown function (TM1506), from Thermotoga maritima at 2.70 resolution
    Q Xu, P Kozbial, D McMullan - Proteins: Structure, , 2008 - Wiley Online Library
     
    7. A score of the ability of a three-dimensional protein model to retrieve its own sequence as a quantitative measure of its quality and appropriateness
    LP Martnez-Castilla, R Rodrguez-Sotres - PloS one, 2010 - dx.plos.org
     

    Protein Summary

    The TM1506 gene of Thermotoga maritima encodes a protein of unknown function with a molecular weight of 15612.55 Da (residues -10 to 136) and a calculated isoelectric point of 8.89. TM1506 belongs to Pfam family PF08973 (DUF1893) and has members among bacteroides, spirochetes and firmicutes.

    TM1506 has unusually high content of basic residues (19 lysines and 4 arginines) and is encoded by the same operon as acidic protein - TM1470 (transcription termination factor Rho). Proteins with high content of basic residues are well soluble at low pH and often have functions related to nucleic acid binding, but there is no information whether TM1506 and TM1470 functions are interdependent.

    Structure of TM1506 protein consists of 3 layers: ?/?/?; mixed ?-sheet of five strands, order 21345; strand 1 is antiparallel to the rest. Initially it was thought to be a new fold, however, more careful structure analysis revealed that TM1506 structure belongs to the cytydine deaminase fold, which also contains other (deoxycytidylate and guanine) deaminases, AICAR transformylase and proteins from the Mov34/MPN/PAD-1 family of proteasome regulatory subunits, eukaryotic initiation factor 3 (eIF3) subunits and regulators of transcription factors. Sequence similarity between these proteins is extremely small (~5% seq id) and is not detectable by even most sensitive sequence comparison programs.

    Mass spectroscopic analysis suggests that TM1506 is ADP-ribosylated.

    Several nucleotide-binding proteins are targeted for ADP-ribosylation (Krueger and Barbieri 1995). 

    Research ideas for members of scientific community: Is this a tRNA binding protein? The figures below (prepared with Pymol) shows a speculative model of a manually fitted tRNA (from structure with PDB code 2b3j)  into the ligand binding cleft. Protein surface was colored by amino acid type (basic, blue; acidic, red; polar, violet; nonpolar, grey; aromatic, orange, cysteine, yellow). The side chains of Cys113 and Asp56 are indicated as sticks on the cross section  and Asp56 is labeled (first image). ;. Please note that we do not have any direct evidence that this is a tRNA binding protein.


    Figure: cross section showing ligand binding cleft.




    Ligand Summary

    The region of electron density modeled as an unknown ligand (UNL) has been identified by mass spec. as a ribosylated-ADP molecule covalently bound to Asp56.


    References

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