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3f14

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

    Title Crystal structure of NTF2-like protein of unknown function (YP_680363.1) from CYTOPHAGA HUTCHINSONII ATCC 33406 at 1.45 A resolution. To be published
    Site JCSG
    PDB Id 3f14 Target Id
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    Molecular Characteristics
    Source
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    Alias Ids
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    TPS14608,YP_680363.1, 3.10.450.50, 85535
    Molecular Weight
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    Da.
    Residues
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    Isoelectric Point
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    Sequence
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      BLAST   FFAS

    Structure Determination
    Method XRAY
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    Chains 1
    Resolution (Å)
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    Rfree
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    Matthews' coefficent 2.21 Rfactor 0.171
    Waters
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    Solvent Content 44.39

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    Ligand Information
    Ligands
    Metals

    Jmol

     
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    Google Scholar output for 3f14
    1. Modeling discrete heterogeneity in X-ray diffraction data by fitting multi-conformers
    H Van Den Bedem, A Dhanik, JC Latombe - Section D: Biological , 2009 - scripts.iucr.org
     

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    Protein Summary

    Gene CHU_3788 from Cytophaga hutchinsonii (strain ATCC 33406 / NCIMB 9469) encodes the YP_680363 protein. C. hutchinsonii is an aerobic Gram-negative bacterium that is commonly found in soil, and able to rapidly digests crystalline cellulose.  Cellulose is one of the most abundant biopolymers on earth with the common component of plant cell walls, which is insoluble and relatively resistant to degradation. As many of the bacteria in the Cytophaga-Flavobacterium branch of the eubacterial phylogenetic tree, C. hutchinsonii exhibits the ability to move rapidly over surfaces by a process known as gliding motility.  The results from NCBI sequence alignment can not provide a clear clue for the possible function annotation of protein YP_680363.1 other than hypothetic protein.  No function information can be found from Pfam for this protein. 

     

    The SSM comparison suggests the 3f14 structure shares a similar fold with those nuclear transport factor 2 (NTF2) protein, including structures 2PZV, 1GY5, 1AR0,  1JB4,  1TUH and 1A2K. Pre-SCOP classifies 3f14 in the alpha+beta class, NTF2-like superfamily, ketosteroid isomerase-like family (?). DALI top hits are with steroid isomerases 1ohp, 1ocv, 1qjg (Zscr=14). There is only one molecule in each asymmetric unit in the 3f14 crystal structure.  The interface interaction suggests that the likely biomolecule of 3f14 is a dimer.

       

       

    390726_1.png

     Figure 1. The 3f14 molecule carries an α/β-barrel.

       

    390726_2.png

     Figure 2. The biomolecule of 3f14 is a dimer based on interface interaction.

       

    390726_3.png

       

    Figure 3. 3f14 (green) is structurally similar to 2PZV (Zscr=14), 1GY5 (Zscr=13), 1AR0 (Zscr=13),  1JB4 (Zscr=13),  1TUH (Zscr=13) and 1A2K (Zscr=12). 

     

    References 

    1.    Kraut, D.A.,  Sigala, P.A.,  Pybus, B.,  Liu, C.W.,  Ringe, D.,  Petsko, G.A.,  Herschlag, D.   (2006) Testing Electrostatic complementarity in Enzyme Catalysis: Hydrogen Bonding in the Ketosteroid Isomerase Oxyanion Hole  PLoS Biol.   4: 501-519   (PDB ID: 2PZV)

    2.    Bayliss, R.,  Leung, S.W.,  Baker, R.P.,  Quimby, B.B.,  Corbett, A.H.,  Stewart, M.   (2002) Structural basis for the interaction between NTF2 and nucleoporin FxFG repeats.  EMBO J.   21: 2843-2853   (PDB ID: 1GY5)

    3.    Clarkson, W.D.,  Corbett, A.H.,  Paschal, B.M.,  Kent, H.M.,  McCoy, A.J.,  Gerace, L.,  Silver, P.A.,  Stewart, M.   (1997) Nuclear protein import is decreased by engineered mutants of nuclear transport factor 2 (NTF2) that do not bind GDP-Ran.  J.Mol.Biol.   272: 716-730   (PDB ID: 1AR0)

    4.    Chaillan-Huntington, C.,  Butler, P.J.,  Huntington, J.A.,  Akin, D.,  Feldherr, C.,  Stewart, M.   (2001) NTF2 monomer-dimer equilibrium.  J.Mol.Biol.   314: 465-477   (PDB ID: 1JB4)

    5.    Robinson, A.,  Wu, P.S.-C.,  Harrop, S.J.,  Schaeffer, P.M.,  Dosztanyi, Z.,  Gillings, M.R.,  Holmes, A.J.,  Nevalainen, K.M.H.,  Stokes, H.W.,  Otting, G.,  Dixon, N.E.,  Curmi, P.M.G.,  Mabbutt, B.C.  (2005) Integron-associated Mobile Gene Cassettes Code for Folded Proteins: The Structure of Bal32a, a New Member of the Adaptable alpha+beta Barrel Family  J.Mol.Biol.   346: 1229-1241  (PDB ID: 1TUH)

    6.    Stewart, M.,  Kent, H.M.,  McCoy, A.J.  (1998) Structural basis for molecular recognition between nuclear transport factor 2 (NTF2) and the GDP-bound form of the Ras-family GTPase Ran.  J.Mol.Biol.   277: 635-646   (PDB ID: 1A2K)

    Ligand Summary

    Tris, PEG

    Reviews

    References

     

    No references found.

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