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Dimethylarginine Dimethylaminohydrolase

1 Introduction
2 General Structure
- 2.1 Lid Region
- 2.2 Active Site
  - 2.2.1 Zn2+ Bound to the Active Site

Introduction

Dimethylarginine Dimethyaminohydrolase (commonly known as DDAH) is a member of the hydrolase family of enzymes which use water to break down molecules ^[1]. Specifically, DDAH is a nitric oxide synthase (NOS) regulator. Its metabolizes free arginine derivatives, namely NѠ,NѠ-dimethyl-L-arginine (ADMA) and NѠ-methyl-L-arginine (MMA) which competitively inhibit NOS ^[2]. DDAH converts MMA and ADMA to L-citrulline and monoamine or dimethylamine ^[3]. DDAH is expressed in the cytosol of cells in humans, mice, rates, sheep, cattle, and bacteria ^[1]. DDAH activity has been localized mainly to the brain, kidney, pancreas, and liver in these organisms. If DDAH is overexpressed, NOS can be activated ^[3]. ADMA and MMA can inhibit the synthesis of NO by competitively inhibiting all three kinds of NOS (endothelial, neuronal, and inducible) ^[3]. Underexpression or inhibition of DDAH decreases NOS activity and NO levels will decrease. Because of nitric oxide’s (NO) role in signaling and defense, NO levels in an organism must be regulated to reduce damage to cells ^[4]. NO is made by NOS creating L-citrulline from L-arginine ^[3]. In humans, many diseases can come from improper control of NO levels including diabetes mellitus and hypertension. Current research has identified several inhibitors of DDAH which could be important in fighting diseases involving irregular NO levels ^[3].

General Structure

DDAH’s structure has a propeller-like fold which is characteristic of the superfamily of L-arginine/glycine amidinotransferases ^[5]. This five-stranded propeller contains five repeats of a ββαβ motif ^[3]. This motif consists of two beta-sheets that are anti-parallel, an alpha helix, and another beta-sheet that is parallel to the second beta-sheet in the motif. These motifs in DDAH form a channel in the center of the protein structure. Lys174 and Glu77 form a salt bridge in the channel that forms the bottom of the active site for the protein. One side of the channel is a water-filled pore, whereas the other side is the active site cleft that is defined by a short loop region and alpha helical structures ^[3].

Lid Region

Amino acids 25-36 of DDAH constitute the loop region of the protein ^[3]. This is more commonly known as the lid region. The lid is what allows the active site to be exposed to substate binding or not. Studies have shown crystal structures of the lid at open and closed conformations. In the open conformation, the lid forms an alpha helix and the amino acid Leu29 is moved so it does not interact with the active site. This allows the active site to be vulnerable to attack. This lid region is very flexible. This open conformation has been shown when DDAH had been crystalized when Zn2+ was bound at pH 6.3. There is a closed form which has been observed with Zn2+ binding at pH 9.0 and in the unliganded enzyme. When the lid is closed, a specific hydrogen bond can form between the Leu29 carbonyl and the amino group on bound molecule. This stabilizes this complex. The Leu29 is then blocking the active site entrance ^[3]. Opening and closing the lid takes place faster than the actual reaction in the active site ^[6]. This suggests that the rate-limiting step of this reaction is not the lid movement but is the actual chemistry happening to the substrate in the active site of DDAH ^[6]. The specific residues in the lid region are different in different organisms ^[3]. The only consistent similarity is a conserved leucine residue in this lid that function to hydrogen bond with the ligand bound to the active site ^[6]. Different isoforms from the same species can have differences in lid regions as well ^[3]. DDAH-2 has a negatively charged lid while DDAH-1 has a positively charged lid ^[3].

Active Site

The normal DDAH regulation mechanism depends on the presence of Cys249 in the active site that acts as a nucleophile in the mechanism ^[7]. The Cys249 is used to attack the guanidinium carbon on the substrate that is held in the active site via hydrogen bonds. This is followed by collapsing the tetrahedral product to get rid of the alkylamine leaving group. A thiouronium intermediate is then formed with sp2 hybridization. This intermediate is hydrolyzed to form citrulline. The His162 protonates the leaving group in this reaction and generates hydroxide to hydrolyze the intermediate formed in the reaction. Studies suggest that Cys249 is neutral until binding of guanidinium near Cys249 decreases Cys249’s pKa and deprotonates the thiolate to activate the nucleophile. Other studies suggest that the Cys249 and an active site Histidine162 form an ion pair to deprotonate the thiolate. Cys249 and His162 can also form a binding site for inhibitors to bind to which stabilizes the thiolate. This is important in regulating NO activity in organisms and designing drugs to inhibit this enzyme ^[7].

There is a channel in the center of the protein that is closed by a salt bridge connecting Glu77 and Lys174 ^[3]. This salt bridge constitutes the bottom of the active site. There is a pore containing water on one side of the channel. This pore is delineated by the first β strand of each of the five propeller blades. The water in the water-filled pore forms hydrogen bonds to His172 and Ser175. The other side of the channel is the active site. Short loop regions and a helical structure define the outward boundaries of this site. Active sites of DDAH from different organisms is similar. Amino acids involved in the chemical mechanism of creating products are also conserved. Amino acids in the lid region are not conserved except for a Leucine amino acid. When MMA or ADMA bind in the active site, they are broken down into L-citrulline and amines (Figure 1). L-citrulline leaves the active site when the lid opens. The amines can either leave through the entrance to the active site or through a pore made by movement of Glu77 and Lys174 ^[3].

Zn2+ Bound to the Active Site

In DDAH, Zinc (Zn2+) acts as an endogenous inhibitor and prevents normal NOS activity ^[3]. The Zn(II)-binding site is located inside the protein’s active site, which makes it a competitive inhibitor. When bound, Zn(II) blocks the entrance of any other substrate. It was found that Cys273, His172, Glu77, Asp78, and Asp 268 all play a role in the binding of Zn(II). Cys273 directly coordinates with the Zn(II) ion in the active site while the other significant residues stabilize the ion via hydrogen bonding interactions with water molecules in the active site. Depending on pH, His172 can change conformations and use the imidazole group to directly coordinate the Zn(II) ion. Cys273, which is conserved between bovine and humans, is the key active site residue that coordinates Zn(II) ^[3]. Zinc-cysteine complexes have been found to be important mediators of protein catalysis, regulation, and structure ^[8]

References

↑ ^1.0 ^1.1 [Palm F, Onozato ML, Luo Z, Wilcox CS. Dimethylarginine dimethylaminohydrolase (DDAH): expression, regulation, and function in the cardiovascular and renal systems. American Journal of Physiology. 2007 Dec 1;293(6):3227-3245. PMID:17933965 doi:10.1152/ajpheart.00998.2007
↑ [Tran CTL, Leiper JM, Vallance P. The DDAH/ADMA/NOS pathway. Atherosclerosis Supplements. 2003 Dec;4(4):33-40. PMID:14664901 doi:10.1016/S1567-5688(03)00032-1]
↑ ^3.00 ^3.01 ^3.02 ^3.03 ^3.04 ^3.05 ^3.06 ^3.07 ^3.08 ^3.09 ^3.10 ^3.11 ^3.12 ^3.13 ^3.14 ^3.15 [Frey D, Braun O, Briand C, Vasak M, Grutter MG. Structure of the mammalian NOS regulator dimethylarginine dimethylaminohydrolase: a basis for the design of specific inhibitors. Structure. 2006 May;14(5):901-911. PMID:16698551 doi:10.1016/j.str.2006.03.006]
↑ [Janssen W, Pullamsetti SS, Cooke J, Weissmann N, Guenther A, Schermuly RT. The role of dimethylarginine dimethylaminohydrolase (DDAH) in pulmonary fibrosis. The Journal of Pathology. 2012 Dec 12;229(2):242-249. Epub 2013 Jan. PMID: 23097221 doi:10.1002/path.4127/full]
↑ [Humm A, Fritsche E, Mann K, Göhl M, Huber R. Recombinant expression and isolation of human L-arginine:glycine amidinotransferase and identification of its active-site cysteine residue. Biochemical Journal. 1997 March 15;322(3):771-776. PMID: 9148748 doi:10.1042/bj3220771]
↑ ^6.0 ^6.1 ^6.2 [Rasheed M, Richter C, Chisty LT, Kirkpatrick J, Blackledge M, Webb MR, Driscoll PC. Ligand-dependent dynamics of the active site lid in bacterial Dimethyarginine Dimethylaminohydrolase. Biochemistry. 2014 Feb 18;53:1092-1104. PMCID:PMC3945819 doi:10.1021/bi4015924]
↑ ^7.0 ^7.1 [Stone EM, Costello AL, Tierney DL, Fast W. Substrate-assisted cysteine deprotonation in the mechanism of Dimethylargininase (DDAH) from Pseudomonas aeruginosa. Biochemistry. 2006 May 2;45(17):5618-5630. PMID:16634643 doi:10.1021/bi052595m]
↑ [Pace NJ, Weerpana E. Zinc-binding cysteines: diverse functions and structural motifs. Biomolecules. 2014 June;4(2):419-434. PMCID:4101490 doi:10.3390/biom4020419] <ref></ref>. Cys273 and the water molecules stabilize the Zn(II) ion in a tetrahedral environment. The Zn(II) dissociation constant is 4.2 nM which is consistent with the nanomolar concentrations of Zn(II) in the cells, thus provides more evidence for the regulatory use of Zn(II) by DDAH <ref></ref>.

Figure Legend

Inhibitors

L-homocysteine and L-citrulline bind in the active site in the same orientation to create the same intermolecular bonds between it and DDAH <ref></ref>. L-citrulline is a product of DDAH hydrolyzing ADMA and MMA, suggesting DDAH activity creates a negative feedback look on itself. Both molecules enter the active site and cause DDAH to be in its closed lid formation. The αC on either molecule creates three salt bridges with DDAH: two with the guanidine group of Arg144 and one with the guanidine group Arg97. Another salt bridge is formed between the ligand and Asp72. The molecules are stabilized in the active site by H-bonds: αC-amino group of the ligand to main chain carbonyls of Val267 and Leu29. Hydrogen bonds also form between the side chains of Asp78 and Glu77 with the ureido group of L-citrulline.
Like L-homocysteine and L-citrulline, S-nitroso-L-homocysteine binds and the lid region of DDAH is closed. When DDAH reacts with S-nitroso-L-homocysteine, a covalent product, N-thiosulfximide exist in the active site because of its binding to Cys273. N-thiosulfximide is stabilized by several salt bridges and H-bonds. Arg144 and Arg97 stabilize the αC-carbonyl group via salt bridges, and Leu29, Val267, and Asp72 stabilize the Cα-amino group by forming Hydrogen bonds <ref></ref>.

Different Isoforms

DDAH has two main isoforms <ref></ref>. DDAH-1 colocalizes with nNOS (neuronal NOS). This enzyme is found mainly in the brain and kidney of organisms <ref></ref>. DDAH-2 is found in tissues with eNOS (endothelial NOS) <ref></ref>. DDAH-2 localization has been found in the heart, kidney, and placenta <ref></ref>. Additionally, studies show that DDAH-2 is expressed in iNOS containing immune tissues (inducible NOS) <ref></ref>. Both of the isoforms have conserved residues that are involved in the catalytic mechanism of DDAH (Cys, Asp, and His). The differences between the isoforms is in the substrate binding residues and the lid region residues. DDAH-1 has a positively charged lid region while DDAH-2 has negatively charged lid. In total, three salt bridge differ between DDAH-1 and DDAH-2 isoforms. Researchers can take advantage of the fact that there are two different isoforms of this enzyme and create drugs that target one isoform over another to control NO levels in specific tissues in the body <ref></ref>.

Medical Relevancy

DDAH works to hydrolyze MMA and ADMA <ref></ref>. Both MMA and ADMA competitively inhibit NO synthesis by inhibiting Nitric Oxide Synthase (NOS). NO is an important signaling and effector molecule in neurotransmission, bacterial defense, and regulation of vascular tone <ref>[Colasanti M, Suzuki H. The dual personality of NO. ScienceDirect. 2000 Jul 1;21(7):249-252. PMID:10979862 doi: 10.1016/S0165-6147(00)01499-1]<ref/>. Because NO is highly toxic, freely diffusible across membranes, and its radical form is fairly reactive, cells must maintain a large control on concentrations by regulating NOS activity and the activity of enzymes such as DDAH that have an indirect effect of the concentration of NO <ref name="rassaf">[Rassaf T, Feelisch M, Kelm M. Circulating NO pool: assessment of nitrite and nitroso species in blood and tissues. Free Rad. Biol. Med. 2004 Feb 15;36(4):413-422. PMID:14975444 doi:10.1016/j.freeradbiomed.2003.11.011]<ref/>. An imbalance of NO contributes to several diseases. Low NO levels, potentially caused by low DDAH activity and therefore high MMA and ADMA concentrations, have been implicated with diseases such as uremia, chronic heart failure, atherosclerosis, and hyperhomocysteinemia <ref name="tsao">[Tsao PS, Cooke JP. Endothelial alterations in hypercholesterolemia: more than simply vasodilator dysfunction. Journal of Cardiovascular Pharmacology. 1998;32(3):48-53. PMID:9883748]<ref/>. High levels of NO have been involved with diseases such as septic shock, migraine, inflammation, and neurodegenerative disorders <ref name="vallance">[Vallance P, Leiper J. Blocking NO synthesis: how, where and why? Nat. Rev. Drug Discov. 2002 Dec;1(12):939-950. PMD:12461516 doi:10.1038/nrd960]<ref/>. Because of the effects on NO levels and known inhibitors to DDAH, regulation of DDAH may be an effective way to regulate NO levels therefore treating the diseases <ref name="frey" />.
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