DOPA decarboxylase: Difference between revisions
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====Tertiary Structure==== | ====Tertiary Structure==== | ||
This level of protein structure refers to the overall three-dimensional shape the polypeptide chain creates. Domains are the fundamental units that generate the tertiary structure, and DOPA decarboxylase is composed of three distinct domains. | This level of protein structure refers to the overall three-dimensional shape the polypeptide chain creates. Domains are the fundamental units that generate the tertiary structure, and DOPA decarboxylase is composed of three distinct domains. | ||
[[image:dopastructure.png|center|600px|'''large domain, small domain, and N-terminal domain''']] | |||
[[image:dopastructure.png | |||
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The <scene name='DOPA_decarboxylase/Large_domain/1'>large domain</scene> contains the PLP-binding site, and consists of a seven-stranded mixed β sheet that is surrounded by eight α helices, resulting in a typical α/β fold, the most regular and common of the protein structures (recall that α helices and β strands typically alternate in this fold, generating an outer layer of α helices and an inner layer of β sheets). This particular fold falls into the class of open twisted parallel or mixed β sheet with α helices on both sides of the sheet. The small <scene name='DOPA_decarboxylase/Small_domain/1'>C-terminal domain</scene> is comprised of a four-stranded anti-parallel β sheet that has three α helices packed against the face opposite to the large domain. Although the aforementioned domains exist in all members of this family of PLP-dependent enzymes, including bacterial [http://en.wikipedia.org/wiki/Ornithine_decarboxylase ''ornithine decarboxylase''] (OrnDC) and [http://en.wikipedia.org/wiki/2,2-dialkylglycine_decarboxylase_(pyruvate) ''dialkylglycine decarboxylase''] (DGD), the <scene name='Sandbox/N-terminal_domain/2'>N-terminal domain</scene> is unique to DOPA decarboxylase, and is a representative case of '''domain swapping'''. This domain is composed of two parallel helices linked by an extended strand, which essentially lies like a flap over the second subunit. As well, residues from the N-terminal domain and the small domain form a short <scene name='DOPA_decarboxylase/Two_domains/1'>two-stranded β sheet. </scene> | The <scene name='DOPA_decarboxylase/Large_domain/1'>large domain</scene> contains the PLP-binding site, and consists of a seven-stranded mixed β sheet that is surrounded by eight α helices, resulting in a typical α/β fold, the most regular and common of the protein structures (recall that α helices and β strands typically alternate in this fold, generating an outer layer of α helices and an inner layer of β sheets). This particular fold falls into the class of open twisted parallel or mixed β sheet with α helices on both sides of the sheet. The small <scene name='DOPA_decarboxylase/Small_domain/1'>C-terminal domain</scene> is comprised of a four-stranded anti-parallel β sheet that has three α helices packed against the face opposite to the large domain. Although the aforementioned domains exist in all members of this family of PLP-dependent enzymes, including bacterial [http://en.wikipedia.org/wiki/Ornithine_decarboxylase ''ornithine decarboxylase''] (OrnDC) and [http://en.wikipedia.org/wiki/2,2-dialkylglycine_decarboxylase_(pyruvate) ''dialkylglycine decarboxylase''] (DGD), the <scene name='Sandbox/N-terminal_domain/2'>N-terminal domain</scene> is unique to DOPA decarboxylase, and is a representative case of '''domain swapping'''. This domain is composed of two parallel helices linked by an extended strand, which essentially lies like a flap over the second subunit. As well, residues from the N-terminal domain and the small domain form a short <scene name='DOPA_decarboxylase/Two_domains/1'>two-stranded β sheet. </scene> | ||
