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3kkg

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

    Title Crystal structure of Putative SnoaL-like polyketide cyclase (YP_509242.1) from Jannaschia Sp. CCS1 at 1.40 A resolution. To be published
    Site JCSG
    PDB Id 3kkg Target Id 396293
    Molecular Characteristics
    Source Jannaschia sp. ccs1
    Alias Ids TPS29550,YP_509242.1, 3.10.450.50, 326171 Molecular Weight 15994.16 Da.
    Residues 145 Isoelectric Point 4.12
    Sequence qdrspietqnvetvlrlfdegwgaqdgwrdvwretmtpgfrsifhsnqavegieqaiafnavlfegfpr levvvenvtvegdnvvvqarltgaqdgpflgvppsgqmvdvpdvtlftladgqviemryftdllavmta isappen
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 1.40 Rfree 0.198
    Matthews' coefficent 2.62 Rfactor 0.181
    Waters 212 Solvent Content 53.00

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3kkg
    1. Insights from the sea: Structural biology of marine polyketide synthases
    DL Akey, JJ Gehret, D Khare, JL Smith - Natural Product Reports, 2012 - pubs.rsc.org
     

    Protein Summary

    Pfam update: SnoaL family

    Gene Jann_1300 from Jannaschia sp. ccs1 encodes the YP_509242.1 prtoein that belongs to the SnoaL-like polyketide cyclase Pfam family (PF07366) , consisting of several hypothetical bacterial proteins of around 125 residues in length. The function of this family is unknown.

    SCOP classifies 3kkg in the alpha+beta class, NTF2-like superfamily, SnoaL-like polyketide cyclase family. 3kkg crystal structure contains one protomer in the asu. The likely biological molecule is a dimer.

    mol.png 

    Fig1. The monomer found in the asu of 3kkg

     

     

     

    dimer.png

    Fig2. Biological dimer of 3kkg

     

    The 3kkg structure is similar to many JCSG targets. Among them, the best DALI hit (3I0Y) is shown superimposed to 3kkg below.

     

    DALI hits:

        No:  Chain   Z    rmsd lali nres  %id PDB  Description
    1: 3i0y-A 18.5 1.8 135 138 14 PDB MOLECULE: PUTATIVE POLYKETIDE CYCLASE; 2: 3i0y-C 18.1 1.8 133 136 14 PDB MOLECULE: PUTATIVE POLYKETIDE CYCLASE; 3: 3i0y-B 18.1 1.7 132 135 14 PDB MOLECULE: PUTATIVE POLYKETIDE CYCLASE; 4: 3i0y-D 17.7 1.8 133 136 14 PDB MOLECULE: PUTATIVE POLYKETIDE CYCLASE; 5: 3f7x-A 17.2 1.8 129 133 12 PDB MOLECULE: PUTATIVE POLYKETIDE CYCLASE; 6: 3f8h-B 17.2 2.1 133 136 16 PDB MOLECULE: PUTATIVE POLYKETIDE CYCLASE; 7: 2gey-A 16.8 2.2 131 157 20 PDB MOLECULE: ACLR PROTEIN; 8: 2gey-B 16.8 2.2 131 133 19 PDB MOLECULE: ACLR PROTEIN; 9: 1tuh-A 16.6 2.0 124 131 21 PDB MOLECULE: HYPOTHETICAL PROTEIN EGC068; 10: 2gey-D 16.6 2.2 130 132 19 PDB MOLECULE: ACLR PROTEIN; 11: 3f8h-A 16.4 2.1 134 137 16 PDB MOLECULE: PUTATIVE POLYKETIDE CYCLASE; 12: 3f9s-B 16.2 2.2 134 142 16 PDB MOLECULE: PUTATIVE POLYKETIDE CYCLASE; 13: 3f9s-A 16.0 2.2 134 143 16 PDB MOLECULE: PUTATIVE POLYKETIDE CYCLASE; 14: 3grd-A 16.0 1.9 123 133 13 PDB MOLECULE: UNCHARACTERIZED NTF2-SUPERFAMILY PROTEIN; 15: 2f99-C 16.0 2.6 131 140 17 PDB MOLECULE: AKLANONIC ACID METHYL ESTER CYCLASE, AKNH; 16: 2f99-B 15.9 2.7 132 141 17 PDB MOLECULE: AKLANONIC ACID METHYL ESTER CYCLASE, AKNH; 17: 2f98-D 15.9 2.7 133 140 17 PDB MOLECULE: AKLANONIC ACID METHYL ESTER CYCLASE, AKNH; 18: 2f99-D 15.8 2.6 132 143 17 PDB MOLECULE: AKLANONIC ACID METHYL ESTER CYCLASE, AKNH; 19: 2f99-A 15.8 2.7 131 141 17 PDB MOLECULE: AKLANONIC ACID METHYL ESTER CYCLASE, AKNH; 20: 2f98-A 15.8 2.7 133 141 17 PDB MOLECULE: AKLANONIC ACID METHYL ESTER CYCLASE, AKNH;

     

     

     

    super_3i0y.png

     

    Fig 3. Superposition of 3kkg (green) with 3i0y (blue). PEG (red) of 3kkg is located near the UNL of 3i0y.

     

     

     

    References

    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  

    Beinker, P.,  Lohkamp, B.,  Peltonen, T.,  Niemi, J.,  Mantsala, P.,  Schneider, G. (2006) Crystal structures of SnoaL2 and AclR: two putative hydroxylases in the biosynthesis of aromatic polyketide antibiotics J.Mol.Biol. 359: 728-740 

    Ligand Summary

    Reviews

    References

     

    No references found.

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    203.9 kB03:31, 19 Sep 2009gyewonActions
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    170.93 kB03:31, 19 Sep 2009gyewonActions
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