PDBsum entry 5o3v

Hydrolase

PDB id: 5o3v

Contents

Protein chains

716 a.a.

14 a.a.

13 a.a.

Ligands

SO4 ×4

Metals

_MG ×2

Waters ×257

PDB id:

5o3v

Name:

Hydrolase

Title:

Structural characterization of the fast and promiscuous macrocyclase from plant - pcy1-s562a bound to presegetalin b1

Structure:

Peptide cyclase 1. Chain: a, b. Engineered: yes. Mutation: yes. Putative presegetalin b1. Chain: d, c. Engineered: yes

Source:

Vaccaria hispanica. Organism_taxid: 39387. Gene: pcy1. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Expression_system_taxid: 469008

Resolution:

2.17Å R-factor: 0.217 R-free: 0.248

Authors:

H.Ludewig,C.M.Czekster,A.F.Bent,J.H.Naismith

Key ref:

H.Ludewig et al. (2018). Characterization of the Fast and Promiscuous Macrocyclase from Plant PCY1 Enables the Use of Simple Substrates. ACS Chem Biol, 13, 801-811. PubMed id: 29377663 DOI: 10.1021/acschembio.8b00050

Date:

25-May-17 Release date: 07-Feb-18

Protein chains

R4P353  (R4P353_GYPVA) -  Prolyl endopeptidase from Gypsophila vaccaria

Seq: 724 a.a.

Struc: 716 a.a.*

Protein chain

F6LNL6  (F6LNL6_GYPVA) -  Putative presegetalin B1 from Gypsophila vaccaria

Seq: 31 a.a.

Struc: 14 a.a.

Protein chain

F6LNL6  (F6LNL6_GYPVA) -  Putative presegetalin B1 from Gypsophila vaccaria

Seq: 31 a.a.

Struc: 13 a.a.

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class 2: Chains A, B: E.C.3.4.21.- - ?????
• Enzyme class 3: Chains A, B: E.C.3.4.21.26 - prolyl oligopeptidase.
• Reaction: Hydrolysis of Pro-|-Xaa >> Ala-|-Xaa in oligopeptides.
• Enzyme class 4: Chains D, C: E.C.?

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.

DOI no: 10.1021/acschembio.8b00050

ACS Chem Biol 13:801-811 (2018)

PubMed id: 29377663

Characterization of the Fast and Promiscuous Macrocyclase from Plant PCY1 Enables the Use of Simple Substrates.

H.Ludewig, C.M.Czekster, E.Oueis, E.S.Munday, M.Arshad, S.A.Synowsky, A.F.Bent, J.H.Naismith.

ABSTRACT

Cyclic ribosomally derived peptides possess diverse bioactivities and are currently of major interest in drug development. However, it can be chemically challenging to synthesize these molecules, hindering the diversification and testing of cyclic peptide leads. Enzymes used in vitro offer a solution to this; however peptide macrocyclization remains the bottleneck. PCY1, involved in the biosynthesis of plant orbitides, belongs to the class of prolyl oligopeptidases and natively displays substrate promiscuity. PCY1 is a promising candidate for in vitro utilization, but its substrates require an 11 to 16 residue C-terminal recognition tail. We have characterized PCY1 both kinetically and structurally with multiple substrate complexes revealing the molecular basis of recognition and catalysis. Using these insights, we have identified a three residue C-terminal extension that replaces the natural recognition tail permitting PCY1 to operate on synthetic substrates. We demonstrate that PCY1 can macrocyclize a variety of substrates with this short tail, including unnatural amino acids and nonamino acids, highlighting PCY1's potential in biocatalysis.