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3ec4

    Table of contents
          1. 1.1.1.1. Protein Summary
    1. 2. Structural Comparisons
          1. 2.1.1.1. Ligand Summary

    Title Crystal structure of Putative Acetyltransferase from the GNAT family (YP_497011.1) from NOVOSPHINGOBIUM AROMATICIVORANS DSM 12444 at 1.80 A resolution. To be published
    Site JCSG
    PDB Id 3ec4 Target Id 379619
    Molecular Characteristics
    Source Novosphingobium aromaticivorans dsm 12444
    Alias Ids TPS7207,YP_497011.1, 87851 Molecular Weight 24101.06 Da.
    Residues 227 Isoelectric Point 5.30
    Sequence msedhpldrpvwnslggpqseldvasgnlrrldpaygpfaaaapgaeaglasllqgdadeiwlvepepv apppgtrvirvapllqmiadgpvpsfddpgivalgetdvpemtalalatepgpwasgtwrygqfygvri dgrlaamagermrpapnlaevsgvctwpeyrgrglaarlirkviagmaargevpylhsyasnasairly eslgfrarramtatllgkst
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 1.80 Rfree 0.215
    Matthews' coefficent 2.08 Rfactor 0.171
    Waters 500 Solvent Content 40.86

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3ec4
    1. Distributed structure determination at the JCSG
    H van den Bedem, G Wolf, Q Xu - Section D: Biological , 2011 - scripts.iucr.org
     

    Protein Summary

     Possible Structural Highlight-The structure of YP_497011.1 contains a unique N-terminal subdomain not observed in previously reported structures of GNAT-methyltransferases? This additional N-terminal domain is positioned to form interactions with substrates and or ligands in a large channel at the putative acetylCoA binding site.


        

    FOR LIGAND INFORMATION PLEASE SEE BELOW.

    The structure of YP_4970 11.1 has been determined to a resolution of 1.80 Angstroms by MAD. Amino acid residues 134-213 in this target belong to the Acetyltransf_1 (PF00583) Pfam group that includes the Acetyltransferase (GNAT) family of proteins. Many GNATs share several functional domains, including an N-terminal region of variable length, an acetyltransferase domain that encompasses the acetyltransferase Pfam group. The predominant oligomerization state of the protein in solution is most likely to be monomeric.

    monomer_YP_497011.1.bmp.png

    Shown above is a ribbon representation of the structure of  YP_497011.1. The N-terminal region of the protein is shown in blue and C-terminal region in red.

        

    The amino acid sequence and the correspoding secondary structure topology determined from the x-ray structure is shown below

    FN9311B_secondary_structure.bmp

        

    The protein structure can be described as consisting of two sub-domains. A smaller N-terminal domain extends from residue 1 to 64 and is comprised of three short alpha-helical elements and and two short beta strands. A much larger domain extends to the C-terminal region of the molecule. A seven strand twised beta sheet acts to bridges the N and C-terminal regions of the monomer.

        

        

    Shown below are least squares superimposed ribbon representations of the structures of  YP_4970 11.1 (green) and PDB ID 2cnm (blue). The structure in blue is the  Rimi- ribosomal s18 n-alpha-protein acetyltransferase in complex with a bisubstrate inhibitor (cterm-arg-arg-phe- tyr-arg-ala-n-alpha-acetyl-s-coa) (red). The most significant structural difference between the two proteins an additional N-terminal subdomain in the structure of YP_4970 11.1 (green) described here.

        

    overlap_FN9311B_2CNM.png

        

        

        

        

        

        

    The image below is a ribbon represenation of the least squares overlaped structures of  YP_4970 11.1 (green) with PDB  id 2CNT (blue). The protein structure shown in blue represents the Crystal Structure of Rimi from Salmonella Typhimurium Lt2, the Gnat Responsible for N{Alpha}-Acetylation of Ribosomal Protein S18 (the same protein shown as a blue ribbon representation in the preceding figure above). The red structure shown in red is a spherical representation of the acetyl CoA ligand from the x-ray coordinates a protein ligand complex. A similar acetyl coA ligand was not observed in the structure of YP_4970 11.1described here.

        

    overlap_FN9311B_to_2CNT.png

        

        

        

        

        

        

        

        

        

        

        

        

        

        

        

        

        

        

        


    Structural Comparisons

    The coordinates of  YP_497011.1 were used as a template to perform a seach for the Protein Data Bank for structurally similar targets. The results of this search are shown in the table below.

        

     RMSD (Angstroms)
     Sequence Identity(%)
     PDB Name
     Name
     1.82  25.2  2cnm Rimi- ribosomal s18 n-alpha-protein acetyltransferase in complex with a bisubstrate inhibitor (cterm-arg-arg-phe- tyr-arg-ala-n-alpha-acetyl-s-coa).
     1.98  17.4  2atr Acetyltransferase, gnat family protein sp0256 from streptococcus pneumoniae tigr4
     1.72  22.9  2pdo Crystal structure of the putative acetyltransferase of gnat family from shigella flexneri
     2.64  22.3  1sqh  X-ray structure of drosophila malonogaster protein q9vr51 northeast structural genomics consortium target fr87.
     2.18  15.8  1y7r 1.7 Ang crystal structure of protein of unknown function sa2161 from meticillin-resistant staphylococcus aureus, probable acetyltransferase
     1.79  25.2  2cns Rimi- ribosomal s18 n-alpha-protein acetyltransferase in complex with acetylcoa.
     1.80  25.2  2cnt Rimi- ribosomal s18 n-alpha-protein acetyltransferase in complex with coenzymea.
     2.03  19.0  3bln Crystal structure of acetyltransferase gnat family (np_981174.1) from bacillus cereus atcc 10987 at 1.31 a resolution
     2.06  20.1  2ob0 Human mak3 homolog in complex with acetyl-coa
    2.08
     20.4  1yvk

    Crystal structure of the bacillis subtilis acetyltransferase in complex with coa, northeast structural genomics target sr237. 

    Ligand Summary

    Acetate molecules from the crystallization solutions were modeled into the structure. No ligands of biological relevence were observed in the x-ray structure.

        

    acetyl_CoA_2cnt_ligplot.bmpTo the left is a plot of the interactions between the bound Acetyl-CoA and the  Rimi- ribosomal s18 n-alpha-protein acetyltransferase (PDB ID 2cnt), The C-terminal region of the structure of YP_4970 11.1 shows similarity to the structure represented by PDB ID 2CNT (see discussion above). Based on this similarity, the putative position of acetyl-CoA in the YP_498011.1 can be inferred from the structure of the 2CNT protein-ligand complex.

        

        

        

        

        

        

        

        

        

    overlap_acetylCoA_sidechains.bmp

        


    Reviews

    References

     

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