UDP-sulfoquinovose synthase

 

The SQD1 enzyme from Arabidopsis thaliana catalyses the addition of sulphite to UDP-glucose to form UDP-6-sulphoquinovose and a molecule of water. This is involved in the biosynthesis of the unique sulpholipid SQDG, found in plants and many photosynthetic bacteria.

 

Reference Protein and Structure

Sequence
O48917 UniProt (3.13.1.1) IPR016040 (Sequence Homologues) (PDB Homologues)
Biological species
Arabidopsis thaliana (Thale cress) Uniprot
PDB
1qrr - CRYSTAL STRUCTURE OF SQD1 PROTEIN COMPLEX WITH NAD AND UDP-GLUCOSE (1.6 Å) PDBe PDBsum 1qrr
Catalytic CATH Domains
3.40.50.720 CATHdb (see all for 1qrr)
Cofactors
Nadph(4-) (1), Water (1)
Click To Show Structure

Enzyme Reaction (EC:3.13.1.1)

UDP-alpha-D-glucose(2-)
CHEBI:58885ChEBI
+
sulfite
CHEBI:17359ChEBI
+
hydron
CHEBI:15378ChEBI
→
UDP-6-sulfoquinovose(3-)
CHEBI:60009ChEBI
+
water
CHEBI:15377ChEBI
Alternative enzyme names: UDPsulfoquinovose synthase, Sulfite:UDP-glucose sulfotransferase,

Enzyme Mechanism

Introduction

The 4' hydroxyl is deprotonated by the negatively charged tyrosinate 182. Tyr 182 is stabilised by Lys 186. NAD+ accepts a hydride from the C4' atom, reducing the hydroxyl group to a ketone. This intermediate is stabilised by low barrier hydrogen bonds to Thr 145, which also promote the removal of the O6' hydroxyl, along with a deprotonation of C5' by His 183, to form a water molecule. This forms the UPD-4'-keto-glucose-5-ene intermediate. The sulphur donor then transfers SO3- to the intermediate by electrophilic addition across the C5'=C6' double bond, and the C5' atom is re-protonated by the protonated His 183 residue. The 4'-keto group is then reduced back to a hydroxyl by the O4' protonation by Tyr 182 and the hydride transfer from NADH to the C4' atom.

Catalytic Residues Roles

UniProt PDB* (1qrr)
Ser263 Ser180A Ser180 holds the His183 in the correct conformation. hydrogen bond acceptor, steric role
Tyr265 Tyr182A The Tyr 182 residue exists as the negatively charged tyrosinate, and acts as a general base by abstracting a proton from the 4' hydroxyl. In the regeneration of the 4' hydroxyl, Tyr 182 acts as a general acid by donating a proton to the 4' O atom. hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, steric role
Lys269 Lys186A The positive charge of the Lys 186 sidechain substantially lowers the pKa of Tyr 182. hydrogen bond donor, electrostatic stabiliser, increase acidity
Thr228 Thr145A Thr 145 stablilizes the reaction intermediates by hydrogen bonding to the 4' hydroxyl/ketone and the 6' hydroxyl. These 'low barrier hydrogen bonds' also promote the removal of the O6' hydroxyl. hydrogen bond acceptor, hydrogen bond donor, steric role, electrostatic stabiliser
His266 His183A His 183 acts as a general acid by deprotonating the C5' atom of the substrate. In the subsequent step, the protonated His 183 then acts as a general acid to protonate the C5' atom on addition of sulphur. hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor
*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, hydride transfer, bimolecular elimination, bimolecular nucleophilic addition, cofactor used, intermediate formation, overall reactant used, dehydration, proton relay, overall product formed, bimolecular electrophilic addition, unimolecular elimination by the conjugate base, native state of cofactor regenerated, native state of enzyme regenerated, intermediate terminated

References

  1. Mulichak AM et al. (1999), Proc Natl Acad Sci U S A, 96, 13097-13102. Crystal structure of SQD1, an enzyme involved in the biosynthesis of the plant sulfolipid headgroup donor UDP-sulfoquinovose. DOI:10.1073/pnas.96.23.13097. PMID:10557279.
  2. Zolghadr B et al. (2015), Extremophiles, 19, 451-467. UDP-sulfoquinovose formation by Sulfolobus acidocaldarius. DOI:10.1007/s00792-015-0730-9. PMID:25605538.
  3. Cleland WW et al. (1998), J Biol Chem, 273, 1-17. The low-barrier hydrogen bond in enzymic catalysis. DOI:10.1016/s0065-3160(08)44001-7. PMID:9748211.
  4. Liu Y et al. (1997), Biochemistry, 36, 10675-10684. Mechanistic Roles of Tyrosine 149 and Serine 124 in UDP-galactose 4-Epimerase fromEscherichia coli†. DOI:10.1021/bi970430a. PMID:9271498.

Step 1. Tyr182 deprotonates the 4'-hydroxyl of UDP-glucose causing the formation of a ketone with concomitant hydride transfer from C4' of the substrate to C4 of NAD+.

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Catalytic Residues Roles

Residue Roles
Thr145A hydrogen bond acceptor, hydrogen bond donor, steric role
His183A hydrogen bond donor
Ser180A hydrogen bond acceptor, steric role
Tyr182A hydrogen bond acceptor
Lys186A hydrogen bond donor, electrostatic stabiliser
Tyr182A proton acceptor

Chemical Components

proton transfer, hydride transfer, ingold: bimolecular elimination, ingold: bimolecular nucleophilic addition, cofactor used, intermediate formation, overall reactant used

Step 2. His183 deprotonates C5' of the intermediate and causes the elimination of the O6' hydroxyl group to form a C5'=C6' double bond. Due to lack of evidence it has been inferred that protonated water acts as the proton donor for the O6' hydroxyl leaving group.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Ser180A hydrogen bond acceptor, steric role
Thr145A electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, steric role
Lys186A hydrogen bond donor
Tyr182A hydrogen bond acceptor, hydrogen bond donor, steric role
His183A hydrogen bond acceptor, hydrogen bond donor, proton acceptor

Chemical Components

proton transfer, ingold: bimolecular elimination, dehydration, proton relay, intermediate formation, overall product formed

Step 3. Sulfite is added across the double bond by electrophilic addition with His183 protonating the C5' position.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
His183A hydrogen bond donor
Tyr182A hydrogen bond acceptor, hydrogen bond donor
Lys186A hydrogen bond donor
Thr145A hydrogen bond acceptor, hydrogen bond donor, steric role
Ser180A hydrogen bond acceptor, steric role
His183A proton donor

Chemical Components

ingold: bimolecular electrophilic addition, proton transfer, intermediate formation, overall reactant used

Step 4. NADH transfers a hydride from C4 of NADH to C4' of the intermediate. The resulting alkoxide is protonated by Tyr182.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Ser180A hydrogen bond acceptor, steric role
His183A hydrogen bond donor
Thr145A hydrogen bond acceptor, hydrogen bond donor, steric role
Lys186A hydrogen bond donor, increase acidity
Tyr182A hydrogen bond acceptor, hydrogen bond donor
Tyr182A proton donor

Chemical Components

hydride transfer, ingold: unimolecular elimination by the conjugate base, ingold: bimolecular nucleophilic addition, proton transfer, native state of cofactor regenerated, native state of enzyme regenerated, intermediate terminated, overall product formed
Download: Image, Marvin File

Step 1. Tyr182 deprotonates the 4'-hydroxyl of UDP-glucose causing the formation of a ketone with concomitant hydride transfer from C4' of the substrate to C4 of NAD+.

Step 2. His183 deprotonates C5' of the intermediate and causes the elimination of the O6' hydroxyl group to form a C5'=C6' double bond. Due to lack of evidence it has been inferred that protonated water acts as the proton donor for the O6' hydroxyl leaving group.

Step 3. Sulfite is added across the double bond by electrophilic addition with His183 protonating the C5' position.

Step 4. NADH transfers a hydride from C4 of NADH to C4' of the intermediate. The resulting alkoxide is protonated by Tyr182.

Products.

Contributors

Judith A. Reeks, Gemma L. Holliday, Ellie Wright, Charity Hornby