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The Open Protein Structure Annotation Network
PDB Keyword
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3f40

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

    Title Crystal structure of NTF2-like protein of unknown function (YP_677363.1) from CYTOPHAGA HUTCHINSONII ATCC 33406 at 1.27 A resolution. To be published
    Site JCSG
    PDB Id 3f40 Target Id 390727
    Molecular Characteristics
    Source Cytophaga hutchinsonii atcc 33406
    Alias Ids TPS14609,YP_677363.1, 3.10.450.50, 85500 Molecular Weight 13237.52 Da.
    Residues 113 Isoelectric Point 5.95
    Sequence mktqittrdlvlefihalntenfpaakkrlnenftfngpmghregserymndmekmkfkyvvhkmfeeg ndvcliydinmngktiaasglyhlekgeitslhvyfdprplfee
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 1.27 Rfree 0.199
    Matthews' coefficent 2.05 Rfactor 0.182
    Waters 150 Solvent Content 40.11

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3f40
    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
     

    Protein Summary

    Gene CHU_0736 from Cytophaga hutchinsonii (strain ATCC 33406 / NCIMB 9469), an abundant aerobic cellulolytic soil bacterium, encodes the YP_677363 protein.  C. hutchinsonii is a gram-negative bacterium that belongs to the phylum Bacteroidetes (also known as the Cytophaga-Flavobacterium-Bacteroides group). C. hutchinsonii utilizes very few substrates as sole carbon and energy sources.  Besides cellulose, its only known substrates are cellobiose and glucose. The sequence alignment results from NCBI BLAST server indicates that YP_677363 belongs to the NTF2-like superfamily. A search in Pfam with YP_677363 (residue 9-111) provides a weak hit with the Limonene Epoxide Hydrolase (LEH) group (Pfam 07858). Genome context analysis indicates a functional linkage (string score 0.822) with a putative flavoprotein (CHU_0735).

     

    Pre-SCOP classifies 3f40 in the alpha+beta class, NTF2-like superfamily, LEH-like family (?). DALI top hits with 3f40 are 3ff2 and the LEH-like structures 2bng (Z-scr=16) and 1nww (Z-scr=14). In the crystal packing of 3f40, there is one molecule in each asymmetric unit.  The interface interaction suggests that the biomolecule of 3f40 could be a dimer.

       

    390727_1.png

       

    Figure 1. The 3f40 molecule consists of α/β barrel mainly. 

       

       

    390727_3.png

       

    Figure 2. The likely biomolecule of 3f40 is a dimer based on interface interaction.

       

    390727_2.png

       

    Figure 3. 3f40 (green) is structurally similar to 2BNG (Zscr=16), 1TUH (Zscr=16), 1VZZ (Zscr=14) and 1SJW (Zscr=12). 

       

    References

       

    1.    Sultana A, Kallio P, Jansson A, Wang JS, Niemi J, Mantsala P, Schneider G; , EMBO J 2004;23:1911-1921.: Structure of the polyketide cyclase SnoaL reveals a novel mechanism for enzymatic aldol condensation. PUBMED:15071504 

    2.    Xie, G., Bruce, D.C., Challacombe, J.F., Chertkov, O., Detter, J.C., Gilna, P., Han, C.S., Lucas, S., Misra, M., Myers, G.L., Richardson, P., Tapia, R., Thayer, N., Thompson, L.S., Brettin, T.S., Henrissat, B., Wilson, D.B., and McBride, M.J. "Genome sequence of the cellulolytic gliding bacterium Cytophaga hutchinsonii." Appl. Environ. Microbiol. (2007) 73:3536-3546. 

    3.    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 1TUH)

    4.    Sultana, A.,  Kallio, P.,  Jansson, A.,  Wang, J.S.,  Niemi, J.,  Schneider, G.   (2004) Structure of the polyketide cyclase SnoaL reveals a novel mechanism for enzymatic aldol condensation.  Embo J.   23: 1911-1921   (PDB: 1SJW)

    5.    Johansson, P.,  Unge, T.,  Cronin, A.,  Arand, M.,  Bergfors, T.,  Jones, T.A.,  Mowbray, S.L.   (2005) Structure of an atypical epoxide hydrolase from Mycobacterium tuberculosis gives insights into its function.  J.Mol.Biol.   351: 1048-1056   (PDB: 2BNG)

    6.    Jang, D.S.,  Cha, H.J.,  Cha, S.S.,  Hong, B.H.,  Ha, N.C.,  Lee, J.Y.,  Oh, B.H.,  Lee, H.S.,  Choi, K.Y.  (2004) Structural double-mutant cycle analysis of a hydrogen bond network in ketosteroid isomerase from Pseudomonas putida biotype B.  Biochem.J.   382: 967-973  (PDB 1VZZ)

    Ligand Summary

    Reviews

    References

     

    No references found.

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