PDBsum entry 7csd

Oxidoreductase

PDB id: 7csd

Contents

Protein chains

309 a.a.

Ligands

GFU ×4

NDP ×4

Waters ×990

PDB id:

7csd

Name:

Oxidoreductase

Title:

Atprr1 with NADP+ and (+)lariciresinol

Structure:

Pinoresinol reductase 1. Chain: c, d, a, b. Synonym: atprr1,(+)-pinoresinol reductase,(-)-pinoresinol reductase, pinoresinol-lariciresinol reductase 1,atplr1. Engineered: yes

Source:

Arabidopsis thaliana. Mouse-ear cress. Organism_taxid: 3702. Gene: prr1, plr1, at1g32100, f3c3.10. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

1.80Å R-factor: 0.186 R-free: 0.222

Authors:

K.Shao,P.Zhang

Key ref:

Y.Xiao et al. (2021). Structure-based engineering of substrate specificity for pinoresinol-lariciresinol reductases. Nat Commun, 12, 2828. PubMed id: 33990581 DOI: 10.1038/s41467-021-23095-y

Date:

14-Aug-20 Release date: 09-Jun-21

Protein chains

Q9FVQ6  (PILR1_ARATH) -  Pinoresinol reductase 1 from Arabidopsis thaliana

Seq: 317 a.a.

Struc: 309 a.a.

Enzyme reactions

• Enzyme class 1: E.C.1.23.1.1 - (+)-pinoresinol reductase.
• Reaction: ⁺-lariciresinol + NADP⁺ = ⁺-pinoresinol + NADPH + H⁺

(+)-lariciresinol + NADP(+) (Bound ligand (Het Group name = NDP) corresponds exactly) = (+)-pinoresinol (Bound ligand (Het Group name = GFU) corresponds exactly) + NADPH + H(+)

• Enzyme class 2: E.C.1.23.1.3 - (-)-pinoresinol reductase.
• Reaction: ^--lariciresinol + NADP⁺ = ^--pinoresinol + NADPH + H⁺

(-)-lariciresinol (Bound ligand (Het Group name = GFU) corresponds exactly) + NADP(+) (Bound ligand (Het Group name = NDP) corresponds exactly) = (-)-pinoresinol + NADPH + H(+)

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1038/s41467-021-23095-y

Nat Commun 12:2828 (2021)

PubMed id: 33990581

Structure-based engineering of substrate specificity for pinoresinol-lariciresinol reductases.

Y.Xiao, K.Shao, J.Zhou, L.Wang, X.Ma, D.Wu, Y.Yang, J.Chen, J.Feng, S.Qiu, Z.Lv, L.Zhang, P.Zhang, W.Chen.

ABSTRACT

Pinoresinol-lariciresinol reductases (PLRs) are enzymes involved in the lignan biosynthesis after the initial dimerization of two monolignols, and this represents the entry point for the synthesis of 8-8' lignans and contributes greatly to their structural diversity. Of particular interest has been the determination of how differing substrate specificities are achieved with these enzymes. Here, we present crystal structures of IiPLR1 from Isatis indigotica and pinoresinol reductases (PrRs) AtPrR1 and AtPrR2 from Arabidopsis thaliana, in the apo, substrate-bound and product-bound states. Each structure contains a head-to-tail homodimer, and the catalytic pocket comprises structural elements from both monomers. β4 loop covers the top of the pocket, and residue 98 from the loop governs catalytic specificity. The substrate specificities of IiPLR1 and AtPrR2 can be switched via structure-guided mutagenesis. Our study provides insight into the molecular mechanism underlying the substrate specificity of PLRs/PrRs and suggests an efficient strategy for the large-scale commercial production of the pharmaceutically valuable compound lariciresinol.