(A) Diverse functionality of vitamin B6 and its involvement in bodily functions. The inner ring shows three of the vitamin B6 vitamers where the chemical entity at the 4′ position can be an aldehyde, an alcohol or an amine. R1 can either be a hydrogen or a phosphate group, thereby representing the vitamers shown or their phosphorylated derivatives respectively. The second and third rings indicate biochemical and physiological functions respectively in humans. (B) The three pathways of vitamin B6 biosynthesis. Pase*, the apparently unspecific phosphatases involved in dephosphorylating the phosphorylated B6 vitamers; Tase*, transaminase.
Figure 1Comparison of the overall architecture of PdxJ and Pdx1
(A) Ribbon representation of a PdxJ monomer (PDB code 1IXP). (B) Ribbon representation of a Pdx1 monomer (PDB code 2NV2). (C) The main-chain atoms of B. subtilis Pdx1 (PDB code 2NV2) and E. coli PdxJ (PDB code 1IXP) were superimposed and the root mean square deviation mapped on the three-dimensional structure of B. subtilis Pdx1. The increase in distance between aligned main-chain atoms is indicated by a shift in colour from blue to red. A total of 188 Cα atoms were aligned with an average root mean square deviation of 2.5 Å. (D) A ribbon representation of a monomer of B. subtilis Pdx1 from the ternary PLP synthase complex (PDB code 2NV2), coloured according to the B-factor values, which indicate an increase in thermal motion by a shift in colour from blue to red. An interactive three-dimensional version of this Figure is available at http://www.BiochemJ.org/bj/407/0001/bj4070001add.htm
(A) View of the active site of the E. coli PdxJ structure in the absence of any ligand (PDB code 1HO1). The flexible loop 4 that includes Thr102 and Thr103 is shown in yellow. (B) View of E. coli PdxJ as in (A), but with 1-deoxy-D-xylulose-5-phosphate (pale blue) and inorganic phosphate (orange) bound (PDB code 1M5W). The PA and PB phosphate-binding sites are indicated as transparent orange spheres. The projection of Arg20 into the active site, which comes from a neighbouring monomer, is shown in pale green. (C) Pdx1 from the T. maritima PLP synthase complex with Ru5P bound (pale blue) via an imine bond and inorganic phosphate (orange) (PDB code 2ISS). The P1 and P2 phosphate-binding sites are indicated as transparent red spheres. In all cases, observed phosphate ions and bound substrates are shown in ball-and-stick representation. Residues involved in phosphate binding and potential catalytic residues are highlighted. Note that the numbering of Pdx1 is for T. maritima and differs from that of B. subtilis by +1.
Stereo representation of structurally superimposed T. maritima Pdx1 (PDB code 2ISS) with Pdx1 from B. subtilis (PDB code 2NV2). Secondary structures of Pdx1 from T. maritima and B. subtilis are coloured in orange and yellow respectively. Covalently bound Ru5P and bound phosphate in T. maritima Pdx1 are depicted in ball-and-stick representation, whereas the bound chloride ion of B. subtilis Pdx1 is shown as a green sphere.
Stereo representation of a structural superposition of the active site of T. maritima Pdx1 with Ru5P bound (gold) (PDB code 2ISS) on the active site of E. coli PdxJ with deoxyxylulose-5-phosphate bound (PDB code 1M5W) (green). Note the overlap between the phosphate-binding sites P1 and PA, whereas P2 and PB are disparate.
Mechanisms proposed for the DXP-independent and DXP-dependent pathways of vitamin B6 biosynthesis. On the left is shown one of the two recently proposed mechanisms for the Pdx1-catalysed reaction involving 2′-hydroxypyridoxine 5′-phosphate as an intermediate. The panel on the right shows the proposed mechanism for the PdxJ-catalysed reaction. The green inset depicts the mechanism proposed by Ian Spenser and colleagues for the conversion of 2′-hydroxypyridoxine 5′-phosphate into PLP .
The structural homology search was performed with DALI using B. subtilis Pdx1 (PDB code 2NV2, chain A) as a query. The matched structures are sorted by the Z-score (i.e. the strength of structural similarity in S.D.s above expected). RMSD, positional root mean square deviation of superimposed Cα atoms in Å; LALI, total number of equivalenced residues; LSEQ2, length of the entire chain of the equivalenced structure; IDE, percentage of sequence identity over equivalenced positions.