DOPA decarboxylase: Difference between revisions

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 tertiary structure (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). 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>

==Function==

===The Active Site===

The active site of DOPA decarboxylase is located in a cleft at the <scene name='DOPA_decarboxylase/Dimer_interface/2'>interface</scene> between the two subunits of the dimer, like all PLP-dependent enzymes of the aspartate aminotransferase family. Since it is at the interface, residues from both domains and both subunits are involved in cofactor binding, although the active site is composed of residues mainly from one monomer. The <scene name='DOPA_decarboxylase/Active_site/1'>active site</scene> is composed of several key residues. <scene name='DOPA_decarboxylase/Lysine2/1'>Lys303</scene> serves to bind PLP via a [http://en.wikipedia.org/wiki/Schiff_base Schiff base] linkage in the absence on substrate.

[[image:plp bound.png|thumb|center|400px|'''Schiff base linkage of PLP to Lys303 in the active site''']]

As well, a '''salt bridge''' exists between the carboxyl group of <scene name='DOPA_decarboxylase/Aspartic/1'>Asp271</scene> and the protonated pyridine nitrogen of PLP to further stabilize intermediate. Essentially, a salt bridge combines hydrogen bonding and electrostatic interactions (two common types non-covalent interactions). This interaction serves to provide an electron sink that can stabilize the carbanionic intermediates <ref name="jansonius">PMID:9914259  </ref> . PLP is further anchored to the protein by an extended '''hydrogen bond network''', as shown below.

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[[image:h-bonding.png|thumb|center|400px|'''H-bonding network of PLP in the active site''']]

The only two active site residues from the adjacent monomer, Ile-101 and Phe-103, are part of the substrate binding pocket.

 

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[[image:actsite.png|thumb|lcenter|400px|'''Key interactions between the active site residues, PLP, and carbiDOPA''']]

The inhibitor <scene name='Sandbox/Active_site3/1'>carbiDOPA</scene> binds to the enzyme by forming a hydrazone linkage with PLP through its hydrazine moiety. The catechol ring of carbiDOPA is deeply buried in the active site cleft and is stabilized by <scene name='DOPA_decarboxylase/Vanderwaals/1'>van der waals contact</scene> with Ile-101 and Phe-103. The 4' hydroxyl group of the catechol ring participates in hydrogen bonding with <scene name='DOPA_decarboxylase/Thr-82/1'>Thr-82</scene>, further stabilizing the inhibitor in the active site cleft. PLP is further involved in substrate binding by forming a hydrogen bond to the 3' of the catechol ring. <scene name='DOPA_decarboxylase/His192/1'>His-192</scene>, a highly conserved residue of PLP-dependent decarboxylases <ref name="ishii">PMID:8889823 </ref>  hydrogen bonds to the carboxylate group of carbiDOPA.

In all three crystal structures of DOPA decarboxylase solved to date, residues 328-339 are invisible in the electron density map. This is because these amino acids form a short mobile loop that is believed to be important to the catalytic mechanism of the enzyme <ref name="ishii">PMID:10082378 </ref>. During catalysis, this loop is proposed to lose its flexibility and extend toward the active site, both occluding the active site from solvent during catalysis and possibly even taking part in the catalytic mechanism. The mobile loop is found in other PLP-depended enzymes, such as glutamate 1-semialdehyde aminotransferase. The idea that this flexible loop plays an important role in catalysis is supported by the fact that it contains several highly conserved residues, Tyr-332 and Lys-334. The conformational change that occurs is thought to be a result of loop residues directly interacting with the inhbitor.

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===[http://scop.mrc-lmb.cam.ac.uk/scop/ SCOP]===

#'''Class''': alpha and beta proteins (α/β)

===[http://www.cathdb.info/ CATH]===