User:Brian Hernandez/DOPA Decarboxylase

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Revision as of 07:01, 29 November 2011

1 Introduction
2 Structure
3 Function
- 3.1 The Active Site
- 3.2 Flexible Loop
4 DDC and Parkinson's Disease
- 4.1 Treatment
- 4.2 Inhibitor Binding

Introduction

DOPA decarboxylase (Aromatic L-Amino Acid Decarboxylase, tryptophan decarboxylase, 5-hydroxytryptophan decarboxylase, AAAD, or DDC) is an essential lyase enzyme responsible for the conversion (via decarboxylation) of L-3,4-dihydroxyphenylalanine (L-DOPA) and L-5-hydroxytryptophan (5-HTP) to dopamine and serotonin^[1]. This 104 kDa protein is a tightly associated α₂-dimer that belongs to the aspartate aminotransferase family (fold type 1) of PLP-dependent (vitamin B6-dependent) enzymes, with the catalytically active form of the enzyme existing as the homodimer^[2]. DDC can be found in abundance in the nervous system, as well as the kidney. Because of its role in the biosynthesis of dopamine, DDC has been utilized in the treatment of Parksinon's disease- a chronic, progressively neurological disorder, thought to be the result of degeneration of dopamine-producing cells in the substantia nigra pars compacta (brain structure in the mesencephalon that plays an important role in reward, addiction, and movement) of the brain.

Structure

DDC consists of two monomers, each with three distinct domains: the large domain, the C-terminal small domain, and the N-terminal domain ^[3]. The consists of the cofactor (PLP- pyridoxal phosphate) binding site and is comprised of a central, seven-stranded mixed β-sheet surrounded by eight α-helices in a typical α/β fold. The small consists of a four-stranded antiparallel β-sheet with three helices packed against the face opposite the large domain. The (characteristic of all α-family enzymes) is composed of two parallel helices linked by an extended strand. This structure flaps over the top of the second subunit and vice versa, with the first helix of one subunit aligning parallel to the equivalent helix of the other subunit, thereby forming the extended dimer interface. Although it is unlikely that this domain represents an autonomous folding unit, it is most likely stable only in the context of the dimer by extending the interface between the two monomers.

Function

The Active Site

DDC's active site is located in a between the two monomer subunits, but is composed mainly of residues from one monomer.The is composed of several key residues, including Lys-303, Asp-271, His-192, Thr-82, Ile-101, and Phe-103. In the ligand free form, PLP binds to Lys 303 via a Schiff base linkage. A salt bridge forms between the carboxylate group of Asp 271 and the protonated pyridine nitrogen of PLP yielding a strong electron sink capable of stabilizing the carbanionic intermediates. The only two active site residues from the adjacent monomer, Ile-101 and Phe-103, are part of the substrate binding pocket.

Schiff base linkage of PLP to Lys303 in the active site

Flexible Loop

Residues 328-338 are a stretch of 11 amino acids that comprise a mobile loop (located near the dimer interface), thought to be significant in the catalytic mechanism^[4]. During catalysis, the loop is expected to adhere to a less solvent- and protease-exposed conformation, whereby it loses flexibility and extends toward the active site. Tyr-332 and Lys-334 are highly conserved residues indicative of the flexible loop's possible role in catalysis. The conformational change that occurs is thought to be a result of loop residues directly interacting with the inhibitor. Finally, with such a conformational change, the Tyr-332 residue could then be located closer to the substrate to possibly act as a proton donor for the quinonoid Cα.

DDC and Parkinson's Disease

Treatment

Parkinson's disease, a neurological disorder, can be characterized by tremor, bradykinesia, rigidity, and postural instability. With it's possible relation to degenerative dopamine-producing cells in the brain, administration of L-DOPA can increase the amount of synthesized dopamine in the nerve cell; direct treatment with dopamine is not sufficient as dopamine itself cannot pass the blood-brain barrier. However, only a small percentage of the dose actually reaches the nervous system, with the remaining majority being rapidly converted to dopamine in the blood stream. This dopamine-rich blood causes side effects of nausea, daytime sleepiness, orthostatic hypotension, involuntary movements, decreased appetite, insomnia, and cramping. Addition of a DDC inhibitor would block peripheral conversion to dopamine and allow a greater percentage of L-DOPA to reach the brain, causing an increase in brain dopamine levels, and diminishing the side effects of dopamine-rich blood.

Inhibitor Binding

The inhibitor binds to the enzyme by forming a hydrazone linkage with the PLP cofactor through its hydrazine moiety ^[3].

carbiDOPA

The catechol ring buries itself deep within the active site cleft, with the 4' hydroxyl of the catechol ring hydrogen bonded to the hydroxyl group of Thr 82. Additionally, the highly conserved His 192 residue forms a hydrogen bond to the carboxylate group of carbiDOPA (with the carboxylate group of L-DOPA being even closer in binding range). Thus, His 192 is most likely a key residue in the enzyme's catalytic activity because a H192A mutation can cause complete loss of activity.

3D structures of DOPA decarboxylase

1js3, resolution 2.25Å ()

Ligands:

, ,

Activity:

Aromatic-L-amino-acid decarboxylase, with EC number 4.1.1.28

Related:

1js6

Structural annotation:
Resources:	CATH : 1Js3A01, 1Js3A03, 1Js3A02, 1Js3B03, 1Js3B02, 1Js3B01 InterPro : Ipr010977, Ipr002129, Ipr015421, Ipr015424, Ipr015422 Pfam : PF00282 SCOP : d1js3a_, d1js3b_ UniProt : P80041

Functional annotation:
Biological process:	carboxylic acid metabolic process amino acid and derivative metabolic process catecholamine biosynthetic process
Molecular function:	lyase activity carboxy-lyase activity catalytic activity pyridoxal phosphate binding aromatic-L-amino-acid decarboxylase activity

Evolutionary conservation:

Toggle Conservation Colors:	Rows = identical sequences:
Further Information:	Caveats, Explanation, Complete Results at ConSurfDB

Resources:

FirstGlance, OCA, RCSB, PDBsum

Coordinates:

save as pdb, mmCIF, xml

3k40 – DDC – Drosophila melanogaster
1js3 – pDDC + inhibitor – pig
1js6 - pDDC
3rbf, 3rbl – hDDC – human
3rch – hDDC + vitamin B6 phosphate + pyridoxal phosphate

References

↑ Christenson JG, Dairman W, Udenfriend S. On the identity of DOPA decarboxylase and 5-hydroxytryptophan decarboxylase (immunological titration-aromatic L-amino acid decarboxylase-serotonin-dopamine-norepinephrine). Proc Natl Acad Sci U S A. 1972 Feb;69(2):343-7. PMID:4536745
↑ Schneider G, Kack H, Lindqvist Y. The manifold of vitamin B6 dependent enzymes. Structure. 2000 Jan 15;8(1):R1-6. PMID:10673430
↑ ^3.0 ^3.1 Burkhard P, Dominici P, Borri-Voltattorni C, Jansonius JN, Malashkevich VN. Structural insight into Parkinson's disease treatment from drug-inhibited DOPA decarboxylase. Nat Struct Biol. 2001 Nov;8(11):963-7. PMID:11685243 doi:http://dx.doi.org/10.1038/nsb1101-963
↑ Ishii S, Mizuguchi H, Nishino J, Hayashi H, Kagamiyama H. Functionally important residues of aromatic L-amino acid decarboxylase probed by sequence alignment and site-directed mutagenesis. J Biochem. 1996 Aug;120(2):369-76. PMID:8889823

Proteopedia Page Contributors and Editors (what is this?)

Brian Hernandez

Retrieved from "http://52.214.119.220/wiki/index.php/User:Brian_Hernandez/DOPA_Decarboxylase"

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 ==Structure==
 ----
-DDC consists of two monomers, each with three distinct domains: the large domain, the C-terminal small domain, and the N-terminal domain <ref name=Burkhard>PMID: 11685243 </ref>. The <scene name='DOPA_decarboxylase/Large_domain/1'>large domain</scene> consists of the cofactor (PLP- pyridoxal phosphate) binding site and is comprised of a central, seven-stranded mixed β-sheet surrounded by eight α-helices in a typical α/β fold. The small <scene name='DOPA_decarboxylase/Small_domain/1'>C-terminal domain</scene> consists of a four-stranded antiparallel β-sheet with three helices packed against the face opposite the large domain. The <scene name='Sandbox/N-terminal_domain/2'>N-terminal domain</scene> (characteristic of all α-family enzymes) is composed of two parallel helices linked by an extended strand. This structure flaps over the top of the second subunit and vice versa, with the first helix of one subunit aligning parallel to the equivalent helix of the other subunit, thereby forming the extended dimer interface. Although it is unlikely that this domain represents an autonomous folding unit, it is most likely stable only in the context of the dimer by extending the interface between the two monomers.
+DDC consists of two monomers, each with three distinct domains: the large domain, the C-terminal small domain, and the N-terminal domain <ref name=Burkhard>PMID: 11685243 </ref>. The <scene name='DOPA_decarboxylase/Large_domain/1'>large domain</scene> consists of the cofactor (PLP- pyridoxal phosphate) binding site and is comprised of a central, seven-stranded mixed β-sheet surrounded by eight α-helices in a typical α/β fold. The small <scene name='DOPA_decarboxylase/Small_domain/1'>C-terminal domain</scene> consists of a four-stranded antiparallel β-sheet with three helices packed against the face opposite the large domain. The <scene name='Sandbox/N-terminal_domain/2'>N-terminal domain</scene> (characteristic of all α-family enzymes) is composed of two parallel helices linked by an extended strand. This structure flaps over the top of the second subunit and vice versa, with the first helix of one subunit aligning parallel to the equivalent helix of the other subunit, thereby forming the '''extended dimer interface'''. Although it is unlikely that this domain represents an autonomous folding unit, it is most likely stable only in the context of the dimer by extending the interface between the two monomers.
 ==Function==