Steve Ealick's Research Group


Oxalate Decarboxylase


PDB files:

1J58 (native)
1L3J (complexed with formate)

Description:

Oxalate decarboxylase (OXDC) is in the cupin family of proteins which is defined by a characteristic β-sandwich domain having one six-stranded β-sheet and one five-stranded β-sheet. Specifically OXDC is a bicupin since each 46 kD monomer has two β-barrel domains. Domain I of OXDC comprises a continuous stretch of amino acid residues from 56 to 233. Domain II comprises residues 234 to 379 plus residues 8 to 55, which contribute one β-strand of the second cupin barrel and two short helices. The domains are structurally similar, providing evidence of gene duplication.

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The quaternary structure of OXDC is a 264 kD homohexamer, which is made up of two trimeric layers packed face to face. A large solvent channel extends entirely through the hexamer along the three-fold axis. The trimeric layers of the hexamer are stabilized by interlocking claw-like a-helical protrusions of adjacent monomers.

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Each OXDC domain has a manganese binding site that is buried deep inside the β-barrel. Shown in the diagram are: (a) Manganese binding site of domain I. (b) Manganese binding site of domain II. (c) Unknown metal site at the protein surface. The metal was assigned as magnesium for the purposes of the X-ray refinement.

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Reference:

Anand R, Dorrestein PC, Kinsland C, Begley TP, and Ealick SE. Structure of Oxalate Decarboxylase from Bacillus subtilis at 1.75 Å Resolution. Biochemistry 41:7659-7669 (2002).



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