Arginase

 

Arginase (L-arginine amidinohydrolase, E.C. 3.5.3.1) is a metal ion dependent enzyme that catalyzes the hydrolysis of L-arginine to L-ornithine and urea. The enzyme is widely distributed throughout the evolutionary spectrum in organisms as diverse as bacteria, yeast, plants and animals

Arginase catalyses the divalent cation-dependent hydrolysis of L-arginine to form the non-proteinogenic amino acid L-ornithine and urea.

Arginase is a manganese-dependent enzyme that catalyzes the hydrolysis of L-arginine to L-ornithine and urea. In ureotelic animals arginase is the final enzyme of the urea cycle, but in many species it has a wider role controlling the use of arginine for other metabolic purposes, including the production of creatine, polyamines, proline and nitric oxide. Arginase activity is regulated by various small molecules, including the product L-ornithine.

 

Reference Protein and Structure

Sequence
P53608 UniProt (3.5.3.1) IPR014033 (Sequence Homologues) (PDB Homologues)
Biological species
[Bacillus] caldovelox (Bacteria) Uniprot
PDB
1cev - ARGINASE FROM BACILLUS CALDOVELOX, NATIVE STRUCTURE AT PH 5.6 (2.4 Å) PDBe PDBsum 1cev
Catalytic CATH Domains
3.40.800.10 CATHdb (see all for 1cev)
Cofactors
Manganese(2+) (2)
Click To Show Structure

Enzyme Reaction (EC:3.5.3.1)

water
CHEBI:15377ChEBI
+
L-argininium(1+)
CHEBI:32682ChEBI
→
L-ornithinium(1+)
CHEBI:46911ChEBI
+
urea
CHEBI:16199ChEBI
Alternative enzyme names: L-arginase, Arginine amidinase, Arginine transamidinase, Canavanase,

Enzyme Mechanism

Introduction

The substrate L-arginine binds to the active site, but does not coordinate to the metal ion centres directly. The metal-bridging hydroxide then initiates a nucleophilic attack on the substrate's guanidinium group, which leads to the formation of a tetrahedral intermediate. Following a proton transfer to the leaving amino group mediated by Asp-128, the collapse of the tetrahedral intermediate yields products l-ornithine and urea. In the final step, to regenerate the active site and release the products, a water molecule enters to bridge the binuclear manganese cluster, causing the urea product to move to a terminal coordination site on manganese 1. The dissociation of the product facilitates ionisation of the metal-bridging water molecule to yield the catalytically active hydroxide ion. Proton transfer from metal-bridging water to bulk-solvent is mediated by the side chain of His-141.

Catalytic Residues Roles

UniProt PDB* (1cev)
Asp126 Asp126A Acts as the essential general acid/base. The combined effects of bridging two positive metal ions coupled with the proximity of this base favours the conversion of the bridging water to hydroxide. Further, in the substrate- and ornithine-bound complexes (PMID:10196128) this residue forms a a hydrogen bond to the N-eta atom of the arginine substrate and ornithine. As catalysis involves the protonation of this atom, it seems plausible that a proton is moved from the bridging water to N-eta via Asp126. modifies pKa, proton shuttle (general acid/base), metal ligand
Glu271 Glu271A Helps orientate the substrate and stabilise the positive charges present. electrostatic stabiliser, steric role
His99, Asp126, Asp122, Asp226 His99A, Asp126A, Asp122A, Asp226A Forms part of the Manganese 1 binding site. metal ligand
His124, Asp122, Asp226, Asp228 His124A, Asp122A, Asp226A, Asp228A Forms part of the Manganese 2 binding site. metal ligand
His139 His139A His139 helps to position the guanidine group of the substrate optimally for attack by the nucleophile.
This residue has also been suggested as a general acid/base in a later step in the reaction.		 proton shuttle (general acid/base), steric role
*PDB label guide - RESx(y)B(C) - RES: Residue Name; x: Residue ID in PDB file; y: Residue ID in PDB sequence if different from PDB file; B: PDB Chain; C: Biological Assembly Chain if different from PDB. If label is "Not Found" it means this residue is not found in the reference PDB.

Chemical Components

References

  1. Cox JD et al. (2001), Biochemistry, 40, 2689-2701. Mechanistic and metabolic inferences from the binding of substrate analogues and products to arginase. DOI:10.1021/bi002318+. PMID:11258880.
  2. García D et al. (2015), Biochimie, 108, 8-12. Mutagenic and kinetic support for an allosteric site in arginase from the extreme thermophile Bacillus caldovelox, which allows activation by arginine. DOI:10.1016/j.biochi.2014.10.017. PMID:25447142.
  3. Zhang X et al. (2013), Int J Biochem Cell Biol, 45, 995-1002. Structural, enzymatic and biochemical studies on Helicobacter pylori arginase. DOI:10.1016/j.biocel.2013.02.008. PMID:23454280.
  4. Stone EM et al. (2010), Biochemistry, 49, 10582-10588. The Second-Shell Metal Ligands of Human Arginase Affect Coordination of the Nucleophile and Substrate. DOI:10.1021/bi101542t. PMID:21053939.
  5. Leopoldini M et al. (2009), Chemistry, 15, 8026-8036. Determination of the Catalytic Pathway of a Manganese Arginase Enzyme Through Density Functional Investigation. DOI:10.1002/chem.200802252. PMID:19288480.
  6. Christianson DW (2005), Acc Chem Res, 38, 191-201. Arginase:  Structure, Mechanism, and Physiological Role in Male and Female Sexual Arousal. DOI:10.1021/ar040183k. PMID:15766238.
  7. Ash DE (2004), J Nutr, 134, 2760S-2764S; discussion 2765S. Structure and function of arginases. PMID:15465781.
  8. Kim NN et al. (2001), Biochemistry, 40, 2678-2688. Probing Erectile Function: S-(2-Boronoethyl)-l-Cysteine Binds to Arginase as a Transition State Analogue and Enhances Smooth Muscle Relaxation in Human Penile Corpus Cavernosum†,‡. DOI:10.1021/bi002317h. PMID:11258879.
  9. Ash DE et al. (2000), Met Ions Biol Syst, 37, 407-428. Arginase: a binuclear manganese metalloenzyme. PMID:10693141.
  10. Cox JD et al. (1999), Nat Struct Biol, 6, 1043-1047. Arginase-boronic acid complex highlights a physiological role in erectile function. DOI:10.1038/14929. PMID:10542097.
  11. Bewley MC et al. (1999), Structure, 7, 435-448. Crystal structures of Bacillus caldovelox arginase in complex with substrate and inhibitors reveal new insights into activation, inhibition and catalysis in the arginase superfamily. DOI:10.1016/s0969-2126(99)80056-2.
  12. Carvajal N et al. (1999), Arch Biochem Biophys, 371, 202-206. Chemical Modification and Site-Directed Mutagenesis of Human Liver Arginase: Evidence That the Imidazole Group of Histidine-141 Is Not Involved in Substrate Binding. DOI:10.1006/abbi.1999.1421. PMID:10545206.
  13. Carvajal N et al. (1999), Biochem Biophys Res Commun, 264, 196-200. Evidence That Histidine-163 Is Critical for Catalytic Activity, but Not for Substrate Binding to Escherichia coli Agmatinase. DOI:10.1006/bbrc.1999.1505. PMID:10527864.
  14. Khangulov SV et al. (1998), Biochemistry, 37, 8539-8550. l-Arginine Binding to Liver Arginase Requires Proton Transfer to Gateway Residue His141 and Coordination of the Guanidinium Group to the Dimanganese(II,II) Center†. DOI:10.1021/bi972874c. PMID:9622506.
  15. Scolnick LR et al. (1997), Biochemistry, 36, 10558-10565. Altering the Binuclear Manganese Cluster of Arginase Diminishes Thermostability and Catalytic Function†. DOI:10.1021/bi970800v. PMID:9265637.
  16. Kanyo ZF et al. (1996), Nature, 383, 554-557. Structure of a unique binuclear manganese cluster in arginase. DOI:10.1038/383554a0. PMID:8849731.
  17. Cavalli RC et al. (1994), Biochemistry, 33, 10652-10657. Mutagenesis of Rat Liver Arginase Expressed in Escherichia coli: Role of Conserved Histidines. DOI:10.1021/bi00201a012.

Step 1.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
His139A steric role
His99A metal ligand
Asp122A metal ligand
His124A metal ligand
Asp126A metal ligand, modifies pKa
Asp226A metal ligand
Asp228A metal ligand
Glu271A electrostatic stabiliser
His139A proton shuttle (general acid/base)
Asp126A proton shuttle (general acid/base)
Glu271A steric role

Chemical Components

Step 1.

Contributors

Gemma L. Holliday, Nozomi Nagano, Craig Porter