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2i9w

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

    Title Crystal structure of hypothetical protein (YP_265345.1) from Psychrobacter Arcticum 273-4 at 1.75 A resolution. To be published
    Site JCSG
    PDB Id 2i9w Target Id 368209
    Molecular Characteristics
    Source Psychrobacter arcticus 273-4
    Alias Ids TPS1537,YP_265345.1, BIG_389, 86235 Molecular Weight 20738.65 Da.
    Residues 183 Isoelectric Point 6.29
    Sequence mlfsiqtcpcqinpalnavstpllyqdccqpyhdglynqevedsdairadtaehlmrtrysafvlvkpe yivkttlpaqqdlldikaienwaketdwaglevvahtpklskrhaqvefkayfktpdglqahhelstfv kiknkansdaswyfldptvsmsvtqkqpcicgsgekfkrccgmyi
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 1.75 Rfree 0.238
    Matthews' coefficent 2.23 Rfactor 0.192
    Waters 128 Solvent Content 44.52

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 2i9w
    1. 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
     
    2. Ligands in PSI structures
    A Kumar, HJ Chiu, HL Axelrod, A Morse - Section F: Structural , 2010 - scripts.iucr.org
     
    3. Dimensionality reduction in computational demarcation of protein tertiary structures
    RR Joshi, PR Panigrahi, RN Patil - Journal of Molecular Modeling, 2011 - Springer
     
    4. Adaptation of Reference Frame into Bipartite Graph for protein tertiary structure recognition based on the backbone features
    F Othmana, R Abdullahb - Computer Technology and , 2010 - ieeexplore.ieee.org
     

    Protein Summary

    The Psyc_2064 gene from P. arcticum 273-4 encodes the YP_265345 protein that belongs to the SEC-C group (PF02810).

    SCOP divides 2i9w into three regions: the N-terminal belongs to the alpha+beta class, cystatin-like fold, NTF2-like superfamily, SEC-C associated NTF2-like domain family; the C-terminal region displays 2 Sec-C motif folds. A structural similarity search with DALI  provides a top hit with the SEC-C motif 2jq5 (Z=15). A weaker hit (Z=9) is observed with a putative NTF2-like transpeptidase 3k7c. DALI found several hits to the core of the 2i9w structure. But none of those hits contain a crystal structure with a cysteine rich cluster superimposed to that of 2i9w.

    Analysis of the crystallographic packing of 2i9w using the PQS server {Henrick, 1998 #73} indicates that a monomer is the biologically relevant form. In the 2i9w structure, two Zn cations are coordinated by cysteine side chains. N-terminal cysteine cluster is less conserved and contains the residues Cys8, Cys10, Cys28, and Cys29.  The C-terminal cluster of Zn-coordinating cysteines (Cys167, Cys169, Cys178, and Cys179) belongs to a putative active site with conserved together with residues Gly170, Ser171, Gly172, Lys174, Phe175, and Gly180.

    The C-terminal part of 2i9w is similar (both structurally and sequence) to chain "i" of otherwise not significantly similar subunit of Preprotein translocase secA (PDB structure PDB:1ozb, chain I).

    2i9w:A 161 VTQKQPCICGSGEKFKRCCGM
               :    || |||| |:|:| | 
    1ozb:I   2 IGRNEPCPCGSGKKYKHCHGS

    This similarity is too short to be significant by itself. But the rest of the protein is also similar to SecA Wing and Scaffold domain (Pfam07516). It is likely that the functions of YP_265345 are different from that of SecA, but have common mechanism involving the C-terminal cysteine-rich cluster. This C-terminal part has a similar fold to Sec-C motif [SCOP sunid 103641; Pfam02810], that is predicted to potentially to bind nucleic acids. It requires more analysis to see how the Gln163-Lys164 in YP_265345 (and Arg-Asn pair commonly found in other sequences) affects the functions of this motif.

    It is unknown if proteins with both cysteine-rich clusters from COG1312 have the same function as YP_265345.


     

    Ligand Summary



    References

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