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Crystal structure of putative CbiT from Methanocaldococcus jannaschii: an intermediate enzyme activity in cobalamin (vitamin B12) biosynthesis.

Padmanabhan B, Yokoyama S, Bessho Y - BMC Struct. Biol. (2013)

Bottom Line: The overall tertiary structure and the tetrameric arrangements are highly homologous to those found in MT0146/CbiT from Methanobacterium thermoautotrophicum.The conservation of functional residues in the binding site for the co-factor, AdoMet, and in the putative precorrin-7 binding pocket suggested that MJ0391 may also possess CbiT activity.The putative function of MJ0391 is discussed, based on structural homology.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biophysics, National Institute of Mental Health and Neuro Sciences (NIMHANS), Bangalore 560029, India. paddy@nimhans.kar.nic.in

ABSTRACT

Background: In the anaerobic pathway of cobalamin (vitamin B12) synthesis, the CbiT enzyme plays two roles, as a cobalt-precorrin-7 C15-methyltransferase and a C12-decarboxylase, to produce the intermediate, cobalt-precorrin 8.

Results: The primary structure of the hypothetical protein MJ0391, from Methanocaldococcus jannaschii, suggested that MJ0391 is a putative CbiT. Here, we report the crystal structure of MJ0391, solved by the MAD procedure and refined to final R-factor and R-free values of 19.8 & 27.3%, respectively, at 2.3 Å resolution. The asymmetric unit contains two NCS molecules, and the intact tetramer generated by crystallographic symmetry may be functionally important. The overall tertiary structure and the tetrameric arrangements are highly homologous to those found in MT0146/CbiT from Methanobacterium thermoautotrophicum.

Conclusions: The conservation of functional residues in the binding site for the co-factor, AdoMet, and in the putative precorrin-7 binding pocket suggested that MJ0391 may also possess CbiT activity. The putative function of MJ0391 is discussed, based on structural homology.

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The structure of MJ0391. (a) Ribbon diagram (stereo view) of the tertiary structure of MJ0391 (colored in a rainbow ramp from blue at the N-terminus to red at the C-terminus). (b) The ribbon diagram of the MJ0391 dimer in the asymmetric unit (shown in an arbitrary orientation). Subunit A is colored in a rainbow ramp as in (a), and subunit B is colored green. In the dimer, β6 of subunit A and β6’ of subunit B form an intermolecular antiparallel β-sheet. The MES molecule is shown as a stick model. All figures were produced with the PyMOL program (Schrödinger, LLC.), unless otherwise mentioned. (c) The quaternary structure of MJ0391. Stereo view of the intact tetramer arrangement of MJ0391, produced by the crystallographic 2-fold axis. The tetramer is shown in an arbitrary orientation. Subunits A-D are colored red, green, orange and blue, respectively. A few structural elements at the tetramer interface are labeled, for clarity.
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Figure 2: The structure of MJ0391. (a) Ribbon diagram (stereo view) of the tertiary structure of MJ0391 (colored in a rainbow ramp from blue at the N-terminus to red at the C-terminus). (b) The ribbon diagram of the MJ0391 dimer in the asymmetric unit (shown in an arbitrary orientation). Subunit A is colored in a rainbow ramp as in (a), and subunit B is colored green. In the dimer, β6 of subunit A and β6’ of subunit B form an intermolecular antiparallel β-sheet. The MES molecule is shown as a stick model. All figures were produced with the PyMOL program (Schrödinger, LLC.), unless otherwise mentioned. (c) The quaternary structure of MJ0391. Stereo view of the intact tetramer arrangement of MJ0391, produced by the crystallographic 2-fold axis. The tetramer is shown in an arbitrary orientation. Subunits A-D are colored red, green, orange and blue, respectively. A few structural elements at the tetramer interface are labeled, for clarity.

Mentions: The overall tertiary structure of the MJ0391 protein possesses the Rossmann-like “AdoMet-dependent methyltransferase” fold, comprising seven β-strands (Figure 2a). A long flexible stretch with a non-specific secondary structure conformation is observed at the N-terminal region, Met4 – Thr19. The methyltransferase fold is very similar to a canonical Rossmann fold, but it includes an antiparallel strand (β8) between the parallel strands, β5 and β6, at the C-terminal region. Furthermore, this fold is modified by the extension of the β6 strand, which forms a long irregular β hairpin with the β7 and β8 strands (Figure 2a). The canonical class I Rossmann-like methyltransferase fold consists of a central twisted seven-stranded β-sheet (β3-β2-β1-β4-β5-β8-β6), flanked by two bundles of helices on both sides. All of the strands are parallel except for the β8 strand, which is antiparallel to the other strands. Since the structure of MJ0391 is quite similar to that of MT0146/CbiT [22], the same nomenclature has been used for its description.


Crystal structure of putative CbiT from Methanocaldococcus jannaschii: an intermediate enzyme activity in cobalamin (vitamin B12) biosynthesis.

Padmanabhan B, Yokoyama S, Bessho Y - BMC Struct. Biol. (2013)

The structure of MJ0391. (a) Ribbon diagram (stereo view) of the tertiary structure of MJ0391 (colored in a rainbow ramp from blue at the N-terminus to red at the C-terminus). (b) The ribbon diagram of the MJ0391 dimer in the asymmetric unit (shown in an arbitrary orientation). Subunit A is colored in a rainbow ramp as in (a), and subunit B is colored green. In the dimer, β6 of subunit A and β6’ of subunit B form an intermolecular antiparallel β-sheet. The MES molecule is shown as a stick model. All figures were produced with the PyMOL program (Schrödinger, LLC.), unless otherwise mentioned. (c) The quaternary structure of MJ0391. Stereo view of the intact tetramer arrangement of MJ0391, produced by the crystallographic 2-fold axis. The tetramer is shown in an arbitrary orientation. Subunits A-D are colored red, green, orange and blue, respectively. A few structural elements at the tetramer interface are labeled, for clarity.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3672029&req=5

Figure 2: The structure of MJ0391. (a) Ribbon diagram (stereo view) of the tertiary structure of MJ0391 (colored in a rainbow ramp from blue at the N-terminus to red at the C-terminus). (b) The ribbon diagram of the MJ0391 dimer in the asymmetric unit (shown in an arbitrary orientation). Subunit A is colored in a rainbow ramp as in (a), and subunit B is colored green. In the dimer, β6 of subunit A and β6’ of subunit B form an intermolecular antiparallel β-sheet. The MES molecule is shown as a stick model. All figures were produced with the PyMOL program (Schrödinger, LLC.), unless otherwise mentioned. (c) The quaternary structure of MJ0391. Stereo view of the intact tetramer arrangement of MJ0391, produced by the crystallographic 2-fold axis. The tetramer is shown in an arbitrary orientation. Subunits A-D are colored red, green, orange and blue, respectively. A few structural elements at the tetramer interface are labeled, for clarity.
Mentions: The overall tertiary structure of the MJ0391 protein possesses the Rossmann-like “AdoMet-dependent methyltransferase” fold, comprising seven β-strands (Figure 2a). A long flexible stretch with a non-specific secondary structure conformation is observed at the N-terminal region, Met4 – Thr19. The methyltransferase fold is very similar to a canonical Rossmann fold, but it includes an antiparallel strand (β8) between the parallel strands, β5 and β6, at the C-terminal region. Furthermore, this fold is modified by the extension of the β6 strand, which forms a long irregular β hairpin with the β7 and β8 strands (Figure 2a). The canonical class I Rossmann-like methyltransferase fold consists of a central twisted seven-stranded β-sheet (β3-β2-β1-β4-β5-β8-β6), flanked by two bundles of helices on both sides. All of the strands are parallel except for the β8 strand, which is antiparallel to the other strands. Since the structure of MJ0391 is quite similar to that of MT0146/CbiT [22], the same nomenclature has been used for its description.

Bottom Line: The overall tertiary structure and the tetrameric arrangements are highly homologous to those found in MT0146/CbiT from Methanobacterium thermoautotrophicum.The conservation of functional residues in the binding site for the co-factor, AdoMet, and in the putative precorrin-7 binding pocket suggested that MJ0391 may also possess CbiT activity.The putative function of MJ0391 is discussed, based on structural homology.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biophysics, National Institute of Mental Health and Neuro Sciences (NIMHANS), Bangalore 560029, India. paddy@nimhans.kar.nic.in

ABSTRACT

Background: In the anaerobic pathway of cobalamin (vitamin B12) synthesis, the CbiT enzyme plays two roles, as a cobalt-precorrin-7 C15-methyltransferase and a C12-decarboxylase, to produce the intermediate, cobalt-precorrin 8.

Results: The primary structure of the hypothetical protein MJ0391, from Methanocaldococcus jannaschii, suggested that MJ0391 is a putative CbiT. Here, we report the crystal structure of MJ0391, solved by the MAD procedure and refined to final R-factor and R-free values of 19.8 & 27.3%, respectively, at 2.3 Å resolution. The asymmetric unit contains two NCS molecules, and the intact tetramer generated by crystallographic symmetry may be functionally important. The overall tertiary structure and the tetrameric arrangements are highly homologous to those found in MT0146/CbiT from Methanobacterium thermoautotrophicum.

Conclusions: The conservation of functional residues in the binding site for the co-factor, AdoMet, and in the putative precorrin-7 binding pocket suggested that MJ0391 may also possess CbiT activity. The putative function of MJ0391 is discussed, based on structural homology.

Show MeSH
Related in: MedlinePlus