Arginine kinase

 

Arginine kinase and creatine kinase are members of the family of enzymes that catalyse the buffering of ATP in cells with fluctuating metabolic requirements.

 

Reference Protein and Structure

Sequence
P51541 UniProt (2.7.3.3) IPR000749 (Sequence Homologues) (PDB Homologues)
Biological species
Limulus polyphemus (Atlantic horseshoe crab) Uniprot
PDB
1bg0 - TRANSITION STATE STRUCTURE OF ARGININE KINASE (1.86 Å) PDBe PDBsum 1bg0
Catalytic CATH Domains
3.30.590.10 CATHdb (see all for 1bg0)
Cofactors
Magnesium(2+) (1), Water (1) Metal MACiE
Click To Show Structure

Enzyme Reaction (EC:2.7.3.3)

ATP(4-)
CHEBI:30616ChEBI
+
L-argininium(1+)
CHEBI:32682ChEBI
→
N(omega)-phosphonato-L-arginine
CHEBI:58477ChEBI
+
ADP(3-)
CHEBI:456216ChEBI
+
hydron
CHEBI:15378ChEBI
Alternative enzyme names: Adenosine 5'-triphosphate-arginine phosphotransferase, Adenosine 5'-triphosphate:L-arginine phosphotransferase, Arginine phosphokinase, ATP:L-arginine omega-N-phosphotransferase,

Enzyme Mechanism

Introduction

Glu225 acts as an acid/base catalyst. It is thought that the enzyme achieves much of its activity by bringing the substrates together and 'steering' their orbitals into the correct orientation for the reaction to proceed.

Catalytic Residues Roles

UniProt PDB* (1bg0)
Glu314 Glu314(313)A May act as a general acid/base, but more likely to be involved in substrate binding and stabilisation. electrostatic stabiliser
Cys271 Cys271(270)A Cys271 plays an important role in the conformational changes caused by the substrates and the transition-state analogues, and it thought to be located in the hinge region of the two domains of the protein, and involved in guiding conformational changes of the enzyme upon addition of substrates. hydrogen bond acceptor, electrostatic stabiliser, steric role
Thr273 Thr273(272)A Activates and stabilises the Cys271 thiolate anion. hydrogen bond donor, electrostatic stabiliser
Glu225 Glu225(224)A Functions as a general acid/base. hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor
Arg126, Arg229, Arg309, Arg280 Arg126(125)A, Arg229(228)A, Arg309(308)A, Arg280(279)A Involved in stabilisation of the transition states during the course of the reaction. hydrogen bond donor, electrostatic stabiliser
*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

proton transfer, bimolecular nucleophilic substitution, overall reactant used, intermediate formation, overall product formed, rate-determining step, intermediate terminated, proton relay, native state of enzyme regenerated, inferred reaction step

References

  1. Zhou G et al. (1998), Proc Natl Acad Sci U S A, 95, 8449-8454. Transition state structure of arginine kinase: Implications for catalysis of bimolecular reactions. DOI:10.1073/pnas.95.15.8449. PMID:9671698.
  2. Wu QY et al. (2014), Int J Biol Macromol, 63, 21-28. T273 plays an important role in the activity and structural stability of arginine kinase. DOI:10.1016/j.ijbiomac.2013.10.019. PMID:24157705.
  3. Wang WD et al. (2013), Int J Biol Macromol, 54, 238-243. Mutation of residue arginine 330 of arginine kinase results in the generation of the oxidized form more susceptible. DOI:10.1016/j.ijbiomac.2012.12.015. PMID:23262386.
  4. Clark SA et al. (2012), Biochem Biophys Res Commun, 427, 212-217. Crystal structures of arginine kinase in complex with ADP, nitrate, and various phosphagen analogs. DOI:10.1016/j.bbrc.2012.09.053. PMID:22995310.
  5. Liu N et al. (2011), Int J Biol Macromol, 49, 98-102. The role of Cys271 in conformational changes of arginine kinase. DOI:10.1016/j.ijbiomac.2011.04.002. PMID:21507330.
  6. Uda K et al. (2006), Comp Biochem Physiol Part D Genomics Proteomics, 1, 209-218. Evolution of the arginine kinase gene family. DOI:10.1016/j.cbd.2005.10.007. PMID:20483252.
  7. Jourden MJ et al. (2005), Biochim Biophys Acta, 1751, 178-183. Transition state stabilization by six arginines clustered in the active site of creatine kinase. DOI:10.1016/j.bbapap.2005.06.002. PMID:16005271.
  8. Gattis JL et al. (2004), Biochemistry, 43, 8680-8689. The Active Site Cysteine of Arginine Kinase:  Structural and Functional Analysis of Partially Active Mutants†,‡. DOI:10.1021/bi049793i. PMID:15236576.
  9. Pruett PS et al. (2003), J Biol Chem, 278, 26952-26957. The Putative Catalytic Bases Have, at Most, an Accessory Role in the Mechanism of Arginine Kinase. DOI:10.1074/jbc.m212931200. PMID:12732621.
  10. Yousef MS et al. (2002), Acta Crystallogr D Biol Crystallogr, 58, 2009-2017. Refinement of the arginine kinase transition-state analogue complex at 1.2 A resolution: mechanistic insights. PMID:12454458.
  11. Eder M et al. (2000), J Biol Chem, 275, 27094-27099. A conserved negatively charged cluster in the active site of creatine kinase is critical for enzymatic activity. DOI:10.1074/jbc.m004071200. PMID:10829032.
  12. Rao JK et al. (1998), FEBS Lett, 439, 133-137. Crystal structure of rabbit muscle creatine kinase1. DOI:10.1016/s0014-5793(98)01355-6. PMID:9849893.

Step 1. Glu225 deprotonates the amine of the guanidino group, initiating a nucleophilic attack on the gamma-phosphate of ATP in a substitution reaction eliminating ADP.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Thr273(272)A hydrogen bond donor, electrostatic stabiliser
Arg126(125)A hydrogen bond donor
Glu225(224)A hydrogen bond acceptor
Arg309(308)A electrostatic stabiliser, hydrogen bond donor
Arg229(228)A electrostatic stabiliser, hydrogen bond donor
Cys271(270)A hydrogen bond acceptor, electrostatic stabiliser, steric role
Arg280(279)A hydrogen bond donor
Glu314(313)A electrostatic stabiliser
Glu225(224)A proton acceptor

Chemical Components

proton transfer, ingold: bimolecular nucleophilic substitution, overall reactant used, intermediate formation, overall product formed, rate-determining step

Step 2. The beta-phosphate of ADP deprotonates water which deprotonates Glu225 in an inferred return step.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Thr273(272)A hydrogen bond donor, electrostatic stabiliser
Arg126(125)A hydrogen bond donor, electrostatic stabiliser
Glu225(224)A hydrogen bond donor
Arg309(308)A electrostatic stabiliser, hydrogen bond donor
Arg229(228)A electrostatic stabiliser, hydrogen bond donor
Cys271(270)A hydrogen bond acceptor, electrostatic stabiliser
Arg280(279)A hydrogen bond donor, electrostatic stabiliser
Glu314(313)A electrostatic stabiliser
Glu225(224)A proton donor

Chemical Components

proton transfer, intermediate terminated, overall product formed, proton relay, native state of enzyme regenerated, inferred reaction step
Download: Image, Marvin File

Step 1. Glu225 deprotonates the amine of the guanidino group, initiating a nucleophilic attack on the gamma-phosphate of ATP in a substitution reaction eliminating ADP.

Step 2. The beta-phosphate of ADP deprotonates water which deprotonates Glu225 in an inferred return step.

Products.

Contributors

Gemma L. Holliday, Daniel E. Almonacid, Gail J. Bartlett, Alex Gutteridge, Craig Porter