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The Open Protein Structure Annotation Network
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3ggd

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

    Title Crystal structure of SAM-dependent methyltransferase (YP_325210.1) from ANABAENA VARIABILIS ATCC 29413 at 2.11 A resolution. To be published
    Site JCSG
    PDB Id 3ggd Target Id 379018
    Molecular Characteristics
    Source Anabaena variabilis atcc 29413
    Alias Ids TPS7140,YP_325210.1 Molecular Weight 27490.15 Da.
    Residues 244 Isoelectric Point 5.08
    Sequence meklsaikkpdinvadaweqywnktlvnstpvlwdanveravvvdlprfellfnpelplidfacgngtq tkflsqffprvigldvsksaleiaakentaanisyrlldglvpeqaaqihseigdaniymrtgfhhipv ekrellgqslrillgkqgamylielgtgcidffnsllekygqlpyelllvmehgirpgiftaedielyf pdfeilsqgeglfqsihklpdgnyatppafwavikhr
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 2.11 Rfree 0.175
    Matthews' coefficent Rfactor 0.162
    Waters 192 Solvent Content

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3ggd
    1. Juvenile hormone synthesis:esterify then epoxidize or epoxidize then esterify? Insights from the structural characterization of juvenile hormone acid
    LA Defelipe, E Dolghih, AE Roitberg, M Nouzova - Insect Biochemistry and , 2011 - Elsevier
     

    Protein Summary

     

    This protein is now in family PF08241.5 Methyltransf_11 CL0063, with other structures.

    YP_325210.1 is a gene from ANABAENA VARIABILIS ATCC 29413 and encodes 244 residues.  Sequence alignment from NCBI blast suggests this target belongs to the AdoMet_MTases superfamily.   SSM alignment suggests that protein YP_325210.1 is a structural homolog to 1CHM, 1KHH, 1XCJ, 2AZT, 2BZG and 2H11.  Similar to these structures, protein YP_325210.1 carries a conserved  binding site for SAM. SAM molecules are also applied as the additives during crystallization.  Interestingly, only SAH molecules are observed and modeled in the binding site during refinement. One creatine-like unknown ligand was modeled next the SAH molecule in this binding site.  One Co2+ cation from crystallization is modeled on the surface of the structure. One imidazole molecule presents the coordination to Co ion in addition to His 243 and Asp 209.  Even if the interface interaction calculation indicates the biomolecule of YP_325210.1 should be a monomer, the Glu 50 from another subunit in another asymmetric unit also complexes with the Co ion to achieve a stable geometry for Co-coordination.  There are two pieces of unknown electron density near to this metal binding site.
     
         
     
     
     
    There is one molecule in each asymmetric unit.  
     

    379018_1.png

     

    Figure 1. There is one molecule in each asymmetric unit.

     

     

    379018_2.png

     

    Figure 2.  Protein YP_325210.1 carries a conserved SAM/SAH binding site.

     

    379018_3.png

     

     

    Figure 3. In the conserved binding site, one creatine-like unknown ligand is modeled near the SAH ligand.

     

     

    379018_4.png

    Figure 4. One Co2+ cation from crystallization is modeled on the surface of this protein structure. One imidazole complexes with the Co. Two Sacrosine-like unknown ligands could also be modeled in the electron density  near to this metal-binding site.

     

     

    379018_5.png

     

    Figure 5. Protein YP_325210.1(green) is a structural homolog to 1XCJ(orange), 1KHH(blue), 2H11(cyan), 2BZG(yellow) and 2AZT(magenta). 

     

     

     

     

    References,

     

    1.    Komoto, J.,  Yamada, T.,  Takata, Y.,  Konishi, K.,  Ogawa, H.,  Gomi, T.,  Fujioka, M.,  Takusagawa, F.  (2004) Catalytic mechanism of guanidinoacetate methyltransferase: crystal structures of guanidinoacetate methyltransferase ternary complexes.  Biochemistry   43: 14385-14394   
     
    2.    Komoto, J.,  Huang, Y.,  Takata, Y.,  Yamada, T.,  Konishi, K.,  Ogawa, H.,  Gomi, T.,  Fujioka, M.,  Takusagawa, F.  (2002) Crystal structure of guanidinoacetate methyltransferase from rat liver: a model structure of protein arginine methyltransferase.  J.Mol.Biol.   320: 223-235   
     
    3.    Wu, H.,  Horton, J.R.,  Battaile, K.,  Allali-Hassani, A.,  Martin, F.,  Zeng, H.,  Loppnau, P.,  Vedadi, M.,  Bochkarev, A.,  Plotnikov, A.N.,  Cheng, X.   (2007) Structural basis of allele variation of human thiopurine-S-methyltransferase.  Proteins   67: 198-208   
     
    4.    Luka, Z.,  Pakhomova, S.,  Luka, Y.,  Newcomer, M.E.,  Wagner, C.   (2007) Destabilization of human glycine N-methyltransferase by H176N mutation.  Protein Sci.   16: 1957-1964   
     

    Ligand Summary

     

    SAH, Co, Imidazole, UNL.

    Reviews

    References

     

    No references found.

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