The Open Protein Structure Annotation Network
PDB Keyword


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

    Title Crystal structure of 4-nitrophenylphosphatase (TM1742) from Thermotoga maritima at 2.40 A resolution. To be published
    Site JCSG
    PDB Id 1vjr Target Id 283597
    Molecular Characteristics
    Source Thermotoga maritima msb8
    Alias Ids TPS1312,TM1742, 89511 Molecular Weight 28803.82 Da.
    Residues 259 Isoelectric Point 5.58
    Sequence mldkielfildmdgtfylddsllpgslefletlkeknkrfvfftnnsslgaqdyvrklrnmgvdvpdda vvtsgeitaehmlkrfgrcrifllgtpqlkkvfeayghvideenpdfvvlgfdktltyerlkkacillr kgkfyiathpdincpskegpvpdagsimaaieastgrkpdliagkpnplvvdvisekfgvpkermamvg drlytdvklgknagivsilvltgettpedleraetkpdfvfknlgelakavq
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 2.40 Rfree 0.19427
    Matthews' coefficent 5.35 Rfactor 0.16381
    Waters 279 Solvent Content 76.82

    Access denied for user 'root'@'localhost' (using password: YES) (click for details)

    Ligand Information


    Google Scholar output for 1vjr
    1. Evolutionary genomics of the HAD superfamily: understanding the structural adaptations and catalytic diversity in a superfamily of phosphoesterases and allied
    AM Burroughs, KN Allen, D Dunaway-Mariano - Journal of molecular , 2006 - Elsevier
    2. The Buccaneer software for automated model building. 1. Tracing protein chains
    K Cowtan - Acta Crystallographica Section D: Biological , 2006 - scripts.iucr.org
    3. Leveraging enzyme structure-function relationships for functional inference and experimental design: the structure-function linkage database
    SCH Pegg, SD Brown, S Ojha, J Seffernick - Biochemistry, 2006 - ACS Publications
    4. 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
    5. On the combination of molecular replacement and single-wavelength anomalous diffraction phasing for automated structure determination
    S Panjikar, V Parthasarathy, VS Lamzin - Section D: Biological , 2009 - scripts.iucr.org
    6. Real-space protein-model completion: an inverse-kinematics approach
    H Van Den Bedem, I Lotan, JC Latombe - Section D: Biological , 2004 - scripts.iucr.org
    7. Shotgun crystallization strategy for structural genomics II: crystallization conditions that produce high resolution structures for T. maritima proteins
    R Page, AM Deacon, SA Lesley - Journal of structural and , 2005 - Springer
    8. Algorithms exploiting the chain structure of proteins
    I Lotan - 2004 - ai.stanford.edu
    9. Automated protein model completion: an inverse kinematics approach
    H van den Bedem, I Lotan, JC Latombe - Acta Cryst , 2004 - www-cs-students.stanford.edu

    Protein Summary

    The gene TM1742 from Thermotoga maritima encodes a 4-nitrophenylphosphatase EC:  The enzyme was previously crystallized 1PW5.  According to the fold type, the enzyme belongs to the family of NagD-like phosphohydrolase, a superfamily of haloalkanoic acid dehalogenases (HAD) PF00702 SCOP56783.  The enzyme catalyzes the hydrolysis of 4-nitrophenyl phosphate to form  4-nitrophenol.

    Putative Function: Uracil Monophophatase (UMPase)


    Not a pNPPase:


    When compared to E. coli(K-12 Strain) nagD protein (PDB 2C4N), TM1742 (PDB 1VJR) shares high structural and sequence similarity. The 3 important structural domains (Motif I, Motif II and the Cap Domain) are all conserved between both proteins, leading to the hypothesis that TM1742 is more correctly a nagD protein instead of a pNPPase protein. A NagD protein splits a ribonucleoside monophosphate into its respective ribonucleoside and a phosphate through the nucleophilic attack of phosphorus by water. Specifically, the Cap Domain may inhibit any enzymatic activity in relation to pNPP but promote enzymatic activity relating to ribonucleotide monophosphate (RMP) substrates, more specifically uridine monophosphate (UMP). This specificity should occur due to the hypothesized interaction between the Cap Domain and the aromatic moiety of the UMP molecule.


    When compared with E. coli class B acid phosphatase (PDB 2B82), TM1742 also shares a high degree of structural and sequence similarity. However, the Cap Domain is not conserved in the acid phosphatase protein, despite this protein showing specificity for adenosine monophosphate (AMP). Upon further examination of the interactions between the acid phosphatase active site and an AMP molecule, it is apparent that a non-conserved Cap Domain is used (F56 & Y193). This leads to the further hypothesis that the presence of a Cap Domain, in some capacity, allows for specificity of RMPs to occur in these types of phosphatase proteins. Thus, pNPP would not be able to undergo conversion to pNP in TM1742 due to a lack of the hypothesized interaction with the Cap Domain.


    BioLEd Contributors: Joseph Breheny, Kanishk Jain, Ryan Oliver, Justin Kim, Damian Njoku, Andaleeb Rahman, Tyler Skinner, Tsiga Solomon, Alison Underwood, Kristen Waterfield, Cameron Mura, Carol Price, Linda Columbus. Funded by NSF DUE 1044858.

    Ligand Summary





    No references found.

    Tag page

    Files (1)

    FileSizeDateAttached by 
     3 Sequence Alignments_final_2.png
    Sequence alignments with 3 homologs
    95.4 kB04:30, 17 Jul 2011kj3kvActions
    You must login to post a comment.
    All content on this site is licensed under a Creative Commons Attribution 3.0 License
    Powered by MindTouch