Hydroxymethylglutaryl-CoA reductase (NADPH)

 

Hydroxymethylglutaryl-CoA reductase catalyses the committed step in the biosynthesis of isoprenoids, compounds involved in diverse cellular functions such as sterol synthesis and growth control. The precursor of such products is melvalonic acid and concentrations of mevalonate are tightly controlled within cells. This is achieved through the activity of 3-hydroxy-3-methylglutaryl-CoA reductase which catalyses the four electron reduction reduction of 3-hydroxy-3-methylglutaryl-CoA to mevalonate. The activity of 3-hydroxy-3-methylglutaryl-CoA reductase is controlled physiologically through synthesis, degradation and phosphorylation as well as clinically, being the target of several high cholesterol drugs.

 

Reference Protein and Structure

Sequence
P04035 UniProt (1.1.1.34) IPR004816 (Sequence Homologues) (PDB Homologues)
Biological species
Homo sapiens (Human) Uniprot
PDB
1dqa - COMPLEX OF THE CATALYTIC PORTION OF HUMAN HMG-COA REDUCTASE WITH HMG, COA, AND NADP+ (2.0 Å) PDBe PDBsum 1dqa
Catalytic CATH Domains
3.90.770.10 CATHdb 3.30.70.420 CATHdb (see all for 1dqa)
Click To Show Structure

Enzyme Reaction (EC:1.1.1.34)

(3S)-3-hydroxy-3-methylglutaryl-CoA(5-)
CHEBI:43074ChEBI
+
NADPH(4-)
CHEBI:57783ChEBI
+
hydron
CHEBI:15378ChEBI
→
coenzyme A(4-)
CHEBI:57287ChEBI
+
(R)-mevalonate
CHEBI:36464ChEBI
+
NADP(3-)
CHEBI:58349ChEBI
Alternative enzyme names: 3-hydroxy-3-methylglutaryl CoA reductase (NADPH), 3-hydroxy-3-methylglutaryl-CoA reductase, S-3-hydroxy-3-methylglutaryl-CoA reductase, Beta-hydroxy-beta-methylglutaryl coenzyme A reductase, HMGCoA reductase-mevalonate:NADP-oxidoreductase (acetylating-CoA), NADPH-hydroxymethylglutaryl-CoA reductase, Hydroxymethylglutaryl CoA reductase (NADPH), Hydroxymethylglutaryl coenzyme A reductase (reduced nicotinamide adenine dinucleotide phosphate), HMG-CoA reductase, 3-hydroxy-3-methylglutaryl-coenzyme A reductase, Hydroxymethylglutaryl-CoA reductase (NADPH(2)),

Enzyme Mechanism

Introduction

The first reduction step to mevaldyl-CoA, with concomittant deprotonation of Glu559. In the second step Glu559 deprotonates the hydroxide formed in step one, and the eliminated thiolate deprotonates His866. In the third step several residues are involved in the reduction of mevaldehyde. Glu559 is thought to be the proton donor for mevaldehyde.

Catalytic Residues Roles

UniProt PDB* (1dqa)
Glu559, His866 Glu559(138)B, His866(445)B Acts as a general acid/base. hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, electrostatic stabiliser
Lys691, Asp767 Lys691(270)A, Asp767(346)A Acts to stabilise the reactive intermediates in the active site. 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

aromatic unimolecular elimination by the conjugate base, hydride transfer, bimolecular nucleophilic addition, proton transfer, bimolecular elimination, native state of enzyme regenerated, inferred reaction step

References

  1. Haines BE et al. (2012), Biochemistry, 51, 7983-7995. Molecular Modeling of the Reaction Pathway and Hydride Transfer Reactions of HMG-CoA Reductase. DOI:10.1021/bi3008593. PMID:22971202.
  2. Oliveira EF et al. (2016), Catal Sci Technol, 6, 7172-7185. QM/MM study of the mechanism of reduction of 3-hydroxy-3-methylglutaryl coenzyme A catalyzed by human HMG-CoA reductase. DOI:10.1039/c6cy00356g.
  3. Haines BE et al. (2013), Acc Chem Res, 46, 2416-2426. The Increasingly Complex Mechanism of HMG-CoA Reductase. DOI:10.1021/ar3003267. PMID:23898905.

Step 1. NADP eliminates a hydride, which adds to the carbonyl carbon adjacent to the CoA moiety.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Lys691(270)A hydrogen bond donor
Glu559(138)B hydrogen bond donor
Asp767(346)A hydrogen bond acceptor, electrostatic stabiliser
Glu559(138)B proton donor

Chemical Components

ingold: aromatic unimolecular elimination by the conjugate base, hydride transfer, ingold: bimolecular nucleophilic addition, proton transfer

Step 2. The oxyanion collapses, eliminating CoA, which deprotonates His866B.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
His866(445)B hydrogen bond donor
Lys691(270)A electrostatic stabiliser, hydrogen bond donor
Glu559(138)B hydrogen bond donor, electrostatic stabiliser
Asp767(346)A hydrogen bond acceptor, electrostatic stabiliser
Glu559(138)B proton acceptor
His866(445)B proton donor

Chemical Components

proton transfer, ingold: bimolecular elimination

Step 3. A second molecule of NADP eliminates a hydride, which adds to the terminal carbonyl carbon, which deprotonates Glu559B.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Lys691(270)A hydrogen bond donor
Glu559(138)B hydrogen bond donor
Asp767(346)A hydrogen bond acceptor, electrostatic stabiliser
Glu559(138)B proton donor

Chemical Components

proton transfer, hydride transfer, ingold: bimolecular nucleophilic addition, ingold: aromatic unimolecular elimination by the conjugate base

Step 4. Glu559B deprotonates water in an inferred return step.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
His866(445)B hydrogen bond acceptor
Glu559(138)B hydrogen bond acceptor
Asp767(346)A hydrogen bond acceptor, activator
His866(445)B proton acceptor
Glu559(138)B proton acceptor

Chemical Components

proton transfer, native state of enzyme regenerated, inferred reaction step
Download: Image, Marvin File

Step 1. NADP eliminates a hydride, which adds to the carbonyl carbon adjacent to the CoA moiety.

Step 2. The oxyanion collapses, eliminating CoA, which deprotonates His866B.

Step 3. A second molecule of NADP eliminates a hydride, which adds to the terminal carbonyl carbon, which deprotonates Glu559B.

Step 4. Glu559B deprotonates water in an inferred return step.

Products.

Introduction

The first reduction step to mevaldyl-CoA leaves a negatively charged oxygen which is stabilised by Lys691. In the second step His866 is proposed as a proton donor to the thioanion. In the third step several residues are involved in the reduction of mevaldehyde. Glu559, its pKa raised by the close proximity of Asp767, is thought to be the proton donor for mevaldehyde.

Catalytic Residues Roles

UniProt PDB* (1dqa)
Glu559, His866 Glu559(138)B, His866(445)B Acts as a general acid/base. hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, electrostatic stabiliser
Lys691, Asp767 Lys691(270)A, Asp767(346)A Acts as an electrostatic stabiliser. 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

aromatic unimolecular elimination by the conjugate base, hydride transfer, bimolecular nucleophilic addition, proton transfer, unimolecular elimination by the conjugate base, native state of enzyme regenerated, inferred reaction step

References

  1. Istvan ES et al. (2000), EMBO J, 19, 819-830. Crystal structure of the catalytic portion of human HMG-CoA reductase: insights into regulation of activity and catalysis. DOI:10.1093/emboj/19.5.819. PMID:10698924.
  2. Oliveira EF et al. (2016), Catal Sci Technol, 6, 7172-7185. QM/MM study of the mechanism of reduction of 3-hydroxy-3-methylglutaryl coenzyme A catalyzed by human HMG-CoA reductase. DOI:10.1039/c6cy00356g.
  3. Leichner GS et al. (2009), Mol Biol Cell, 20, 3330-3341. Dislocation of HMG-CoA Reductase and Insig-1, Two Polytopic Endoplasmic Reticulum Proteins, En Route to Proteasomal Degradation. DOI:10.1091/mbc.e08-09-0953. PMID:19458199.
  4. Friesen JA et al. (2004), Genome Biol, 5, 248-. The 3-hydroxy-3-methylglutaryl coenzyme-A (HMG-CoA) reductases. DOI:10.1186/gb-2004-5-11-248. PMID:15535874.
  5. Istvan ES et al. (2000), Biochim Biophys Acta, 1529, 9-18. The structure of the catalytic portion of human HMG-CoA reductase. DOI:10.1016/s1388-1981(00)00134-7. PMID:11111074.

Step 1. NADP eliminates a hydride, which adds to the carbonyl carbon adjacent to the CoA moiety.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Lys691(270)A hydrogen bond donor
Glu559(138)B hydrogen bond donor
Asp767(346)A hydrogen bond acceptor, electrostatic stabiliser
Lys691(270)A electrostatic stabiliser

Chemical Components

ingold: aromatic unimolecular elimination by the conjugate base, hydride transfer, ingold: bimolecular nucleophilic addition

Step 2. The oxyanion collapses, eliminating CoA, which deprotonates His866B.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
His866(445)B hydrogen bond donor
Lys691(270)A electrostatic stabiliser, hydrogen bond donor
Glu559(138)B hydrogen bond donor, electrostatic stabiliser
Asp767(346)A hydrogen bond acceptor, electrostatic stabiliser
His866(445)B proton donor

Chemical Components

proton transfer, ingold: unimolecular elimination by the conjugate base

Step 3. A second molecule of NADP eliminates a hydride, which adds to the terminal carbonyl carbon, which deprotonates Glu559B.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Lys691(270)A hydrogen bond donor
Glu559(138)B hydrogen bond donor
Asp767(346)A hydrogen bond acceptor, electrostatic stabiliser
Lys691(270)A electrostatic stabiliser
Glu559(138)B proton donor

Chemical Components

proton transfer, hydride transfer, ingold: bimolecular nucleophilic addition, ingold: aromatic unimolecular elimination by the conjugate base

Step 4. Glu559B deprotonates water in an inferred return step.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
His866(445)B hydrogen bond acceptor
Glu559(138)B hydrogen bond acceptor
Asp767(346)A hydrogen bond acceptor, activator
Glu559(138)B proton acceptor
His866(445)B proton acceptor

Chemical Components

proton transfer, native state of enzyme regenerated, inferred reaction step
Download: Image, Marvin File

Step 1. NADP eliminates a hydride, which adds to the carbonyl carbon adjacent to the CoA moiety.

Step 2. The oxyanion collapses, eliminating CoA, which deprotonates His866B.

Step 3. A second molecule of NADP eliminates a hydride, which adds to the terminal carbonyl carbon, which deprotonates Glu559B.

Step 4. Glu559B deprotonates water in an inferred return step.

Products.

Introduction

The first reduction step to mevaldyl-CoA leaves a negatively charged oxygen which is stabilised by Lys691. In the second step His866 is proposed as a proton donor to the thioanion. In the third step several residues are involved in the reduction of mevaldehyde. Lys691 is thought to be the proton donor for mevaldehyde.

Catalytic Residues Roles

UniProt PDB* (1dqa)
His866, Lys691 His866(445)B, Lys691(270)A Acts as a general acid/base. hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor
Glu559, Asp767 Glu559(138)B, Asp767(346)A Acts to stabilise the reactive intermediates in the active site. hydrogen bond acceptor, 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

aromatic unimolecular elimination by the conjugate base, hydride transfer, bimolecular nucleophilic addition, proton transfer, unimolecular elimination by the conjugate base, overall product formed, native state of enzyme regenerated, inferred reaction step

References

  1. Tabernero L et al. (1999), Proc Natl Acad Sci U S A, 96, 7167-7171. Substrate-induced closure of the flap domain in the ternary complex structures provides insights into the mechanism of catalysis by 3-hydroxy-3-methylglutaryl-CoA reductase. DOI:10.1073/pnas.96.13.7167.
  2. Oliveira EF et al. (2016), Catal Sci Technol, 6, 7172-7185. QM/MM study of the mechanism of reduction of 3-hydroxy-3-methylglutaryl coenzyme A catalyzed by human HMG-CoA reductase. DOI:10.1039/c6cy00356g.

Step 1. NADP eliminates a hydride, which adds to the carbonyl carbon adjacent to the CoA moiety.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Lys691(270)A hydrogen bond donor
Glu559(138)B hydrogen bond donor
Asp767(346)A hydrogen bond acceptor, electrostatic stabiliser

Chemical Components

ingold: aromatic unimolecular elimination by the conjugate base, hydride transfer, ingold: bimolecular nucleophilic addition

Step 2. The oxyanion collapses, eliminating CoA, which deprotonates His866B.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
His866(445)B hydrogen bond donor
Lys691(270)A electrostatic stabiliser, hydrogen bond donor
Glu559(138)B hydrogen bond donor, electrostatic stabiliser
Asp767(346)A hydrogen bond acceptor, electrostatic stabiliser
His866(445)B proton donor

Chemical Components

proton transfer, ingold: unimolecular elimination by the conjugate base, overall product formed

Step 3. A second molecule of NADP eliminates a hydride, which adds to the terminal carbonyl carbon, which deprotonates Lys691.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Lys691(270)A hydrogen bond donor
Glu559(138)B hydrogen bond donor
Asp767(346)A hydrogen bond acceptor, electrostatic stabiliser
Glu559(138)B electrostatic stabiliser
Lys691(270)A proton donor

Chemical Components

proton transfer, hydride transfer, ingold: bimolecular nucleophilic addition, ingold: aromatic unimolecular elimination by the conjugate base

Step 4. Lys691 and His866B deprotonate water in an inferred return step.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
His866(445)B hydrogen bond acceptor
Glu559(138)B hydrogen bond acceptor
Asp767(346)A hydrogen bond acceptor, activator
His866(445)B proton acceptor
Lys691(270)A proton acceptor

Chemical Components

proton transfer, native state of enzyme regenerated, inferred reaction step
Download: Image, Marvin File

Step 1. NADP eliminates a hydride, which adds to the carbonyl carbon adjacent to the CoA moiety.

Step 2. The oxyanion collapses, eliminating CoA, which deprotonates His866B.

Step 3. A second molecule of NADP eliminates a hydride, which adds to the terminal carbonyl carbon, which deprotonates Lys691.

Step 4. Lys691 and His866B deprotonate water in an inferred return step.

Products.

Contributors

Gemma L. Holliday, Daniel E. Almonacid, Gail J. Bartlett, James W. Murray, Craig Porter