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The Open Protein Structure Annotation Network
PDB Keyword
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3cc8

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

    Title Crystal structure of putative methyltransferase from NDP-N-methyl-L-glucosamine biosynthetic pathway (NP_977653.1) from Bacillus cereus ATCC 10987 at 1.64 A resolution. To be published
    Site JCSG
    PDB Id 3cc8 Target Id 383436
    Molecular Characteristics
    Source Bacillus cereus atcc 10987
    Alias Ids TPS1772,NP_977653.1, 88895 Molecular Weight 26095.68 Da.
    Residues 229 Isoelectric Point 5.32
    Sequence mnspknslyeeksghyynavnpnllkhikkewkevldigcssgalgaaikengtrvsgieafpeaaeqa kekldhvvlgdietmdmpyeeeqfdcvifgdvlehlfdpwaviekvkpyikqngvilasipnvshisvl apllagnwtyteyglldkthirfftfnemlrmflkagysiskvdrvyvdhkmyeplieelygickkyrl gsgfmaetvvfqyiieaeksql
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 1.64 Rfree 0.200
    Matthews' coefficent 2.33 Rfactor 0.165
    Waters 177 Solvent Content 47.14

    Ligand Information
    Ligands
    Metals

    Jmol

     

    Protein Summary

    Gene BCE_1332 from Bacillus cereus atcc 10987 encodes the NP_977653 protein, a putative methyltransferase from the PF08241 group. Its genomic neighbor (BCE_1334; score 0.89) is likely to be involved in NDP-N-methyl-L-glucosamine biosynthesis (streptomycin biosynthesis pathway).

    Pre-SCOP classifies 3cc8 in the alpha/beta class, S-adenosyl-L-methionine-dependent methyltransferases superfamily, UbiE/COQ5-like family (?). DALI top hits are with the BH2331 protein 1VL5 (Z=18), the methyltransferases 3bus, 3dli, and 3l8d (Z=18). The 3cc8 structure contains residue 19 - 229, since the N-terminal residues 1-18 were not visible in the electron density map. Although in the crystal ASU 3cc8 is a monomer, the likely biological molecule is a dimer as shown here.

    The protein fold is also a homolog of Aclacinomycin-10-hydroxylase (RdmB) which lacks methyltransferase activity. RdmB is one of the tailoring enzymes in rhodomycin biosynthesis and catalyses hydroxylation of the C-10 carbon atom of the aklavinone skeleton. (see reference below).

    Functional associations identified using the STRING server indicate that NP_977653.1 has a role in streptomycin biosynthesis pathway. We could speculate (pkozbial) that this protein may be involved in NDP-N-methyl-L-glucosamine biosynthesis or alternatively in the modification of so far unknown component from this pathway. The pure speculation (prediction by functional associations analysis only) is that NP_977653.1 performs the following reaction:

    D-glucose 1-phosphate + nucleoside triphosphate + amino group donor + activated methyl group <=> NDP-N-methyl-L-glucosamine + orthophosphate

    Ligand Summary

    Two Ni atoms on the A subunit were found in the asu. The first Ni atom was coordinated to
    the side chain of His188, Glu192, and three waters. The other Ni atom was disordered and
    dual conformation were modeled. Dual Ni atoms were coordinated to the side chains of His 104, His 158, Gly 103 and four water molecules. Anomalous difference fouriers and X-ray fluorescence experiments support the assignment of the NI atoms. 


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