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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 aerobic and anaerobic pathways of cobalamin synthesis. CobL in the aerobic pathway is colored red. CbiE and CbiT, which are equivalent to CobL, are colored blue and red with a boxed label, respectively, in the anaerobic pathway. The chemical structures of cobalt-precorrin-6B, 7 and 8, which are the substrates and products of CbiE and CbiT, are shown at the bottom of the figure.
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Figure 1: The aerobic and anaerobic pathways of cobalamin synthesis. CobL in the aerobic pathway is colored red. CbiE and CbiT, which are equivalent to CobL, are colored blue and red with a boxed label, respectively, in the anaerobic pathway. The chemical structures of cobalt-precorrin-6B, 7 and 8, which are the substrates and products of CbiE and CbiT, are shown at the bottom of the figure.

Mentions: The de novo synthesis of vitamin B12 (cobalamin) occurs via a complex biochemical pathway involving more than 30 enzyme-mediated steps [1,2]. Therefore, many organisms do not use cobalamin as a coenzyme, and neither synthesize nor require the vitamin in their metabolism. Interestingly, only certain eubacteria and archaea synthesize cobalamin, and the pathway apparently never made the transition to eukaryotes [3]. Although they are genetically distinct, two related pathways are involved in cobalamin biosynthesis in prokaryotes: the aerobic and anaerobic pathways [4]. The aerobic pathway requires molecular oxygen and is characterized by the comparatively late chelation of cobalt into the corrin ring [2,5-8]. In contrast, the anaerobic pathway does not require molecular oxygen, and the cobalt is inserted at an early synthetic stage [4,9,10]. For example, the pathway in Pseudomonas denitrificans, an aerobe, incorporates molecular oxygen into the precorrin-3 macrocycle as a prerequisite to ring contraction, and hence is classified as an aerobic pathway. The pathway in Salmonella typhimurium synthesizes cobalamin only in the absence of molecular oxygen. This pathway utilizes cobalt ion chelated into precorrin-2 (or Factor II) to set the stage for ring contraction, and hence is classified as anaerobic. The biosynthesis of precorrin-2 is common to both the aerobic and anaerobic pathways. At this stage, the two pathways divide, rejoining only after the synthesis of Cob(II)yrinate a,c diamide (Figure 1) [1].


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 aerobic and anaerobic pathways of cobalamin synthesis. CobL in the aerobic pathway is colored red. CbiE and CbiT, which are equivalent to CobL, are colored blue and red with a boxed label, respectively, in the anaerobic pathway. The chemical structures of cobalt-precorrin-6B, 7 and 8, which are the substrates and products of CbiE and CbiT, are shown at the bottom of the figure.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 1: The aerobic and anaerobic pathways of cobalamin synthesis. CobL in the aerobic pathway is colored red. CbiE and CbiT, which are equivalent to CobL, are colored blue and red with a boxed label, respectively, in the anaerobic pathway. The chemical structures of cobalt-precorrin-6B, 7 and 8, which are the substrates and products of CbiE and CbiT, are shown at the bottom of the figure.
Mentions: The de novo synthesis of vitamin B12 (cobalamin) occurs via a complex biochemical pathway involving more than 30 enzyme-mediated steps [1,2]. Therefore, many organisms do not use cobalamin as a coenzyme, and neither synthesize nor require the vitamin in their metabolism. Interestingly, only certain eubacteria and archaea synthesize cobalamin, and the pathway apparently never made the transition to eukaryotes [3]. Although they are genetically distinct, two related pathways are involved in cobalamin biosynthesis in prokaryotes: the aerobic and anaerobic pathways [4]. The aerobic pathway requires molecular oxygen and is characterized by the comparatively late chelation of cobalt into the corrin ring [2,5-8]. In contrast, the anaerobic pathway does not require molecular oxygen, and the cobalt is inserted at an early synthetic stage [4,9,10]. For example, the pathway in Pseudomonas denitrificans, an aerobe, incorporates molecular oxygen into the precorrin-3 macrocycle as a prerequisite to ring contraction, and hence is classified as an aerobic pathway. The pathway in Salmonella typhimurium synthesizes cobalamin only in the absence of molecular oxygen. This pathway utilizes cobalt ion chelated into precorrin-2 (or Factor II) to set the stage for ring contraction, and hence is classified as anaerobic. The biosynthesis of precorrin-2 is common to both the aerobic and anaerobic pathways. At this stage, the two pathways divide, rejoining only after the synthesis of Cob(II)yrinate a,c diamide (Figure 1) [1].

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