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3i0y

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

    Title Crystal structure of putative polyketide cyclase (NP_635776.1) from XANTHOMONAS CAMPESTRIS at 1.50 A resolution. To be published
    Site JCSG
    PDB Id 3i0y Target Id 391539
    Molecular Characteristics
    Source Xanthomonas campestris pv. campestris str. atcc 33913
    Alias Ids TPS20905,NP_635776.1, 3.10.450.50, 325214 Molecular Weight 15698.45 Da.
    Residues 139 Isoelectric Point 4.72
    Sequence msesnrqratglvqayyeafnrgdwdamlaflaedvahdlnqgpreigraafasflqrmndsyreqlrd ivvtandegtrvgaeyvvhgvyhttdeglpdangqtyvlpggaffdvrdgqitrvtnyynlqewiaqvsr
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 4
    Resolution (Å) 1.50 Rfree 0.206
    Matthews' coefficent 2.15 Rfactor 0.169
    Waters 543 Solvent Content 42.76

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3i0y

    Protein Summary

    Pfam update: This protein is now in family PF07366.5 SnoaL CL0051 along with other structures.

    Gene XCC0381 from Xanthomonas campestris pv. campestris str. ATCC 33913 encodes the NP_635776 sequence that folds into an alpha/beta protein which belongs to the NTF2_like Conserved Domain Superfamily. 

    This family includes members that perform a variety of diverse functions including delta-5-3-ketosteroid isomerases, scytalone dehydratases, ring hydroxylating dioxygenases, and nuclear transport factor 2 activity. The XCC0381 sequence belongs to the SnoaL-like polyketide cyclase Pfam family (PF07366). [1]

     

     two_dimer_asu (1).pngUNLall (2).png

    Fig 1. Two biological dimers in the asu of 3i0y. Each monomer contains one unidentified ligand (UNL; red dots) in the putative active site. The omit maps (1sigma) of UNLs are shown top of the UNLs.

     

     

     

    ActiveA.png

     

    Fig 2. The vicinity of the UNLs in the putative active site. From top, left to right, Tyr106, Glu65, Tyr85, Tyr16.

    From left to right of the 2nd row, Tyr133, Tyr128, Asn126 (dual confs).

     

     

    As shown below, a DALI search indicates that 3i0y is structurally similar to the following JCSG targets with TOPSAN entries available:

     

     

     

     

     

    No: Chain Z rmsd lali nres %id PDB Description  

    1. PDB:3f7x, 24.5 0.9 132 133 60 MOLECULE: PUTATIVE POLYKETIDE CYCLASE; TOPSAN

    2. PDB:3f8h, 23.3 1.2 134 136 51 MOLECULE: PUTATIVE POLYKETIDE CYCLASE; TOPSAN

    3. PDB:3ebt, 17.2 1.8 123 131 20 MOLECULE: UNCHARACTERIZED NTF2-LIKE PROTEIN; TOPSAN

    4. PDB:1tuh, 17.2 1.9 124 131 18 MOLECULE: HYPOTHETICAL PROTEIN EGC068;

    5. PDB:3ec9, 17.1 1.8 123 130 15 MOLECULE: UNCHARACTERIZED NTF2-LIKE PROTEIN; TOPSAN

     

    super_3f8h.png

     

    Fig 3. Superposition of 3i0y (red cartoon) and 3f8h (grey ribbon) highlighting the structural similarity. Notice that the dimerization mode is also very similar between two structures.

     

     

     

    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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