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PDB Keyword
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3mcq

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

    Title Crystal structure of Thiamine-monophosphate kinase (Mfla_0573) from METHYLOBACILLUS FLAGELLATUS KT at 1.91 A resolution. To be published
    Site JCSG
    PDB Id 3mcq Target Id
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    Molecular Characteristics
    Source
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    Alias Ids
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    TPS25777,YP_544684.1, _0097.001299_, 332992
    Molecular Weight
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    Da.
    Residues
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    Isoelectric Point
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    Sequence
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      BLAST   FFAS

    Structure Determination
    Method XRAY
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    Chains 1
    Resolution (Å)
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    Rfree
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    Matthews' coefficent 2.35 Rfactor 0.197
    Waters
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    Solvent Content 47.61

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    Ligand Information
    Ligands
    Metals

    Jmol

     
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    Google Scholar output for 3mcq

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    Protein Summary

    Gene Mfla_0573  (GenBank accession code YP_544684.1) encodes a 318-residue long protein from Methylobacillus flagellatus, a methylotrophic anaerobic bacteria found mainly in marine environments.   Methylobacillus bacteria play an important role as a carbon recyclers, utilizing carbon compounds such as methane and methanol as substrates for their energy needs.

    The N-terminal and C-terminal portions of YP_544684.1 belong to Pfam groups PF00586 and PF02769, respectively.   Both of these are families of AIR synthase related proteins, which include thiamine monophosphate kinase (ThiL), purine biosynthetic enzymes (PurM and PurL), [NiFe]-hydrogenase maturation protein (HypE), and selenophosphate synthase (SelD).

    YP_544684.1 is annotated as a thiamine monophosphate kinase (ThiL), an ATP-utilizing enzyme which plays an important role in the thiamine biosynthesis and salvage pathways.  Specifcially, it catalyzes the following reaction:

     

    ATP + thiamine phosphate \rightleftharpoons ADP + thiamine diphosphate

     

    The 3mcq structure, which was solved by the Se-MAD method to a resolution of 1.91 Angstroms, displays an alpha/beta fold with two structural domains: an N-terminal domain comprising residues 29-129 and a C-terminal domain from residues 132-296 (Figure 1).  The fold of each of these domains belongs to the PurM N-terminal domain-like and PurM C-terminal domain-like superfamilies, respectively, according to SCOP.

    Figure 1.  Monomer structure of 3mcq (a) gradiently colored from the N- (blue) to the C-terminus (red) and (b) showing the N-terminal (green) and C-terminal (purple) domains.

    (a)                                                                                       (b)

    MH15465B_gradient.png                MH15465B-domains.png

     

    Both crystallographic packing and PISA analyses suggest that the functional form of the protein is a dimer, which is consistent with the oligomeric state of other members in the PurM superfamily (Figure 2).

    Figure 2.  3mcq is most likely a dimer (monomer A in orange, monomer B in blue). Views (a) and (b) are orthogonal to each other about the horizontal axis.

    (a)                                                                                       (b)

    MH15465B-oligomer.png         MH15465B-oligomer-2.png

     

    A structural alignment search with DALI (Table 1) resulted in a number of matches with thiamine monophosphate kinases (ThiL) and the [NiFe] hydrogenase maturation protein (HypE).  Superposition of several of these top structural neighbors with 3mcq reveals similar overall folds (Figure 3).

     

    Table 1.  Structural neighbors of 3mcq as assessed by DALI.  Structures highlighed in blue and red have been superimposed with 3mcq (see Figure 3).

    N PDB Z-score RMSD LALI NRES %ID TITLE
    1 3c9u 30.8 2.1 256 308 27 THIAMINE MONOPHOSPHATE KINASE [Ref]
    2 3c9s 30.8 2.0 256 304 27 THIAMINE MONOPHOSPHATE KINASE
    3 3c9r 30.8 2.0 256 302 27 THIAMINE MONOPHOSPHATE KINASE
    4 3c9t 30.5 2.1 256 307 27 THIAMINE MONOPHOSPHATE KINASE
    5 1vqv 29.0 2.2 254 295 28 THIAMINE MONOPHOSPHATE KINASE
    6 2yxz 28.8 2.1 258 305 26 THIAMIN-MONOPHOSPHATE KINASE
    7 2rb9 27.3 2.6 274 322 21 HYPE PROTEIN [Ref]
    8 2i6r 27.2 2.5 273 321 21 HYPE PROTEIN
    9 2z1t 26.9 2.7 272 321 22 HYDROGENASE EXPRESSION/FORMATION PROTEIN HYPE [Ref]
    10 2z1u 26.6 3.0 277 335 22 HYDROGENASE EXPRESSION/FORMATION PROTEIN HYPE

     

    Figure 3.  Superposition of 3mcq (yellow) with the structures of A. aeolicus thiamine monophosphate kinase ThiL (blue, PDB id 3c9u, [Ref]) and E. coli hydrogenase maturation protein HypE (red, PDB id 2rb9, [Ref]).

    MH15465B-superpose.png

     

    Comparison of the active site of ThiL in which the product thiamin pyrophosphate (TPP) and adenosine-5'-diphosphate (ADP) are bound (PDB id 3c9u) with the corresponding site in 3mcq shows that the residues lining the site are similar in both structures (Figure 4).  A significant difference, however, is that residues 9-18 of 3mcq are situated where the substrate and product are bound in 3c9u.  If 3mcq binds the same molecules, it seems necessary for this region to flip out of the way before binding of these molecules could occur.

     

    Figure 4.  Comparison of active site of ThiL(blue), in which ADP and TPP are bound, to the corresponding site in 3mcq (yellow).

    MH15465B-superpose-activesite-labeled.png

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    Ligand Summary

    Reviews

    References

     

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