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The Open Protein Structure Annotation Network
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1zup

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

    Title Crystal structure of hypothetical protein (tm1739) from Thermotoga maritima at 2.20 A resolution. To be published
    Site JCSG
    PDB Id 1zup Target Id 283594
    Molecular Characteristics
    Source Thermotoga maritima msb8
    Alias Ids TPS1311,TM1739, 89495 Molecular Weight 34878.26 Da.
    Residues 303 Isoelectric Point 5.30
    Sequence mqvrieraerieseleehvgdqtfveesrfleedeqregeildqiifvdgkrrsfvrittdegitgifa elcvgaviwdreggtktlfspdkppvkervlgfsqsfqeegyeevggilfkvvkegkdamqsidlymrs leieevrkhmdknilivkdgpaarelpfeenvgpiglvknigvtelskedfkklrflkkgkrskmfvss retplkkvgayvklidgegirglvrletyvkddnqipyirkvfddlaktlphltadlpiprlpenilpi qfleenlsyyltdknymntrlfayigr
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 2.20 Rfree 0.266
    Matthews' coefficent 3.18 Rfactor 0.228
    Waters 70 Solvent Content 61.04

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    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 1zup
    1. Structural and functional insights into DNA-end processing by the archaeal HerA helicaseNurA nuclease complex
    JK Blackwood, NJ Rzechorzek, AS Abrams - Nucleic Acids , 2011 - Oxford Univ Press
     
    2. The carboxyl terminal of the archaeal nuclease NurA is involved in the interaction with single-stranded DNA-binding protein and dimer formation
    T Wei, S Zhang, L Hou, J Ni, D Sheng, Y Shen - Extremophiles, 2011 - Springer
     
    3. Crystal structure of the NurAdAMPMn2+ complex
    J Chae, YC Kim, Y Cho - Nucleic Acids Research, 2011 - Oxford Univ Press
     

    Protein Summary

    The TM1739 gene from Thermotoga maritima encodes the NP_229537 protein, a putative NurA nuclease (PF09376) found in bacteroidetes, firmicutes and a wide range of archaea. A homolog from Sulfolobus acidocaldaricus has been shown to exhibit 5'-3' nuclease activity (Constantinesco 2002) with the family itself predicted to be part of a novel restriction-modification system (Iyer 2004, Burroughs 2007). Its genome context indicates a likely functional association (score 0.86) with its neighbors, the GufA (TM1738) and NagD (TM1742) proteins.

    The TM1739 structure, 1zup, adopts a ribonuclease H-like motif fold and the four acidic residues implicated in catalysis by ribonucleases (Kashiwagi 1996) (Asp49, Glu140, Asp157 and Glu280 in TM1739) (Fig. 1) are conserved. DALI top hits are with endonuclease-V 3ga2 (Z=10), the argonaute protein 2f8s (Z=8) and the AF1318 protein 1ytu (Z=7).

    Compared to other bacterial ribonuclease H structures (e.g. 1kvc; Z=3.5), TM1739 contains additional secondary structure elements inserted into the main core of the fold. Two insertions occur at the termini, and are implicated in TM1739 dimerization (2,511 Å^2 of total buried surface area, Figs. 2 and 3) via extended loops and N-terminal strand swapping. Two additional insertions occur within the fold itself (the first following strand-5 in TM1739 (strand-3 in 1kvc), colored in yellow in Fig. 2; the second following strand beta-9 in TM1739 (strand-5 in 1kvc), orange in Fig. 2) and extend the central, 5-stranded beta-sheet on either side. These additions are also likely to influence access to the active site via formation of a large cavity (~5,000 Å^3) between the insertions and the main core of the fold (Fig. 3).

     

     1zup_activesite.png

     

    Fig. 1. Comparison of active sites of Escherichia coli ribonuclease H (PDB id: 1kvc, in magenta) and TM1739 (PDB id: 1zup, in cyan). Numbering is shown for TM1739 and in brackets for 1kvc. The D134N E. coli ribonuclease mutant shown here as overlapping with Glu280, abolishes nuclease activity (Kashiwagi 1996).

     

     

    1zup_1kvc_active site.png 

     

    Fig. 2. The structure of TM1739 shows insertions in the core ribonuclease-H fold. Stereo-view showing a ribbon diagram of the superposition of TM1739 (PDB id: 1zup) and the ribonuclease H from E. coli (Pdb id: 1kvc, in magenta). In cyan, the structural elements shared between TM1739 and 1kvc. In blue, the N-terminal (beta strand and loop) and C-terminal (helix) insertions implicated in TM1739 dimerization (see Fig. 3). In yellow, beta strands inserted at the N-terminal region of the core ribonuclease H beta-sheet, in orange an insertion at the C-terminal region of the sheet. The circle depicts the location of the active site.

     

    1zup_dimer2.png

     

    Fig. 3. The TM1739 dimer. Ribbon diagram and corresponding surface representation showing the overall structure of the TM1739 dimer. Monomers are colored in cyan and red respectively.

    Ligand Summary



    References

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