The Open Protein Structure Annotation Network
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    Table of contents
    1. 1. Protein Summary
    2. 2. Ligand Summary
    3. 3. References

    Title Crystal structure of predicted acetamidase/formamidase (YP_546212.1) from Methylobacillus flagellatus KT at 1.58 A resolution. To be published
    Site JCSG
    PDB Id 3b9t Target Id 374794
    Molecular Characteristics
    Source Methylobacillus flagellatus kt
    Alias Ids TPS1634,YP_546212.1, PF03069, 104417 Molecular Weight 52825.76 Da.
    Residues 483 Isoelectric Point 5.78
    Sequence msdhvcqegcrhhshgedspeiqqefqegrrdfmrdfavggvlasaaslgisssafgqtmpktgltsgh athyyipasdktvswgffskslkpvvelesgdfatietlthhsnddaslmvkgdpgaesvfywdskrkn vdrrgmgpmdhklgagggmgvhiltgpvaikgaepgdvlevrivdvalrpsanpefkgktfgsnvaanw gfhynelieepkkrevvtiyeldatgernwarafynyrwtpqkdpfgvvhpivdypgvpvdhstiskny nvlknirvpvrphfgtmglapkeadlvnsvppshfggnidnwrigkgatmyypvsvagglfsvgdphas qgdsemcgtaiecsltgtfqfilhkkadlpgtpladlqyplletqdewvlhgfsyanylaelgpdaqns ifskssldlalkdafrkmrhflmqtqnltedeavslmsigvdfgitqvvdgnwgvhavvkkgifpgrdv
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 4
    Resolution (Å) 1.58 Rfree 0.177
    Matthews' coefficent 1.80 Rfactor 0.138
    Waters 1710 Solvent Content 31.83

    Ligand Information


    Google Scholar output for 3b9t
    1. Distributed structure determination at the JCSG
    H van den Bedem, G Wolf, Q Xu - Section D: Biological , 2011 - scripts.iucr.org
    2. Crystal Structure Analysis of a Recombinant Predicted Acetamidase/Formamidase from the Thermophile Thermoanaerobacter tengcongensis
    M Qian, Q Huang, G Wu, L Lai, Y Tang, J Pei - The Protein , 2012 - Springer

    Protein Summary

    This structure (red) is a homolog of TM0119 (green) and TB0119A (blue). The core of the structure as well as the active site are conserved (27% seq id). This indicates that PJ03069C is also likely to function as acetamidase/formamidase. The active site residues are N314, D316, D341, H343, E350, E357.

    Beyond the conservation of the structure core, PJ03069C has several long insertions,  110-161, 186-198, 240-281. TB0119A also have a insertion at the loop of 110-116, but it adopts a completely different conformation. Due to these insertions (orange), the active site of PJ03069C (green) are a lot less solvent exposed. There is only one small chanel leading to the active site. As a result, the role for these loop insertions are to protect the active site as well as to increase substrate specificity. This may be important since PJ03069C is likely to function in periplasm due to presence of twin-arginine translocation signal peptide at the N-terminus (TM0119 and other sequence homologs lack the signal peptide and thus likely to function in cytoplasm instead).

    The first 0-63 is absent in the crystal structure. Sequence analysis by TATP server (http://www.cbs.dtu.dk/services/TatP/) indicated that the  first  60  residues are likely to be twin arginine translocation signal peptide with putative cleavage site between 57-58. As a result, it is possible that the first ~60 residues in present in the crystal but completely disordered or a truncated form of the PJ03069C was crystallized. Sequence analysis indicated that the putative signal peptide is unique, all other homologous sequences do not have leading sequences. It is interesting to note some of the homologs are fused to DNA binding protein, indicating some of enzymes are involved in transcription regulation. The physiological role of PJ03069C is not clear, it is found via STRING server (http://string.embl.de) to be neighbour to TerC (tellurite resistence) and co-occur extracellular solute-binding protein (Mfla_2313), and a hybrid histide kinase (Mfla_2587). This may hint that it may be a component of two cmponent signal transduction system which regulates cellular response to a unknown extracellular signal/condition.

    SLS/SEC data suggests that PJ03069C is likely to form  dimers in solutions. The dimer of PJ03069C is arranged similar to TM0119. In the crystal structure, the asu contains 2 dimers which form a pseudo "tetramer". The Dimer-Dimer interaction is much weaker than intra-dimer interactions, the tetramer is likely an artifact of crystallization.

    There are two ethylene glycol molecules in the active besides two magnesium ions in the active site. The magnesium ions are located in similar positions compared to TM0119 and TB0119A. One of the ethylene glycol molecule  (tentative assignment) seems to interacts with both metals. Since the ethylene glycol is similar to potential ligand such as formides and actemides, it could be substrate analog (may be a reaction mechanism can be proposed based on this?).

    Ligand Summary





    No references found.

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