Steve Ealick's Research Group

Thermotoga maritima YaaDE

PDB file:



Pyridoxal 5′-phosphate (PLP) is the biologically active form of vitamin B6 and is a cofactor for many enzymes involved in the metabolism of amino acids and carbohydrates. The pathway is well studied in E. coli and is distinct from that in Thermatoga maritima and a number of other organisms. The gene products that are responsible for PLP synthesis as part of the pathway are YaaD and YaaE, and are distinct from the genes in the E. coli pathway. Together YaaD and YaaE function as a PLP synthase. We had previously determined the structure of YaaE from Bacillus subtilis to whichYaaE from T. maritima is quite similar.

The structure of the YaaD monomer is based on a classic (βα)8 barrel fold, while the YaaE monomer is an α/β three layer sandwich that is characteristic of class I amidotransferases. In the pictures at right, TmYaaE is on the left and TmYaaD is on the middle and the YaaD/YaaE protomer on the right.


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The core of the PLP synthase complex is formed by a dodecamer of YaaD monomers. Each YaaD monomer has extensive interactions with a YaaE monomer, however the YaaE monomers have no interactions with each other.

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The formation of PLP requires that the ammonia molecule generated in the YaaE active site be channeled without exposure to bulk solvent to the active site of YaaD. The ribulose 5-phosphate binding site of YaaD is shown at the right.

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Zein F, Zhang Y, Kang Y-N, Burns K, Begley TP, and Ealick SE. Structural Insights into the Mechanism of the PLP Synthase Holoenzyme from Thermotoga maritima. Biochemistry 46:14609-14620 (2006)


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