Structures of a non-ribosomal peptide synthetase condensation domain suggest the basis of substrate selectivity

Thierry Izoré; Y. T. Candace Ho; Joe A. Kaczmarski; Athina Gavriilidou; Ka Ho Chow; David L. Steer; Robert J.A. Goode; Ralf B. Schittenhelm; Julien Tailhades; Manuela Tosin; Gregory L. Challis; Elizabeth H. Krenske; Nadine Ziemert; Colin J. Jackson; Max J. Cryle

doi:10.1038/s41467-021-22623-0

Structures of a non-ribosomal peptide synthetase condensation domain suggest the basis of substrate selectivity

Thierry Izoré
, Y. T. Candace Ho
, Joe A. Kaczmarski
, Athina Gavriilidou
, Ka Ho Chow
, David L. Steer
, Robert J.A. Goode
, Ralf B. Schittenhelm
, Julien Tailhades
, Manuela Tosin
, Gregory L. Challis
, Elizabeth H. Krenske
, Nadine Ziemert
, Colin J. Jackson
, Max J. Cryle

Research output: Contribution to journal › Article › Research › peer-review

71 Citations (Scopus)

Abstract

Non-ribosomal peptide synthetases are important enzymes for the assembly of complex peptide natural products. Within these multi-modular assembly lines, condensation domains perform the central function of chain assembly, typically by forming a peptide bond between two peptidyl carrier protein (PCP)-bound substrates. In this work, we report structural snapshots of a condensation domain in complex with an aminoacyl-PCP acceptor substrate. These structures allow the identification of a mechanism that controls access of acceptor substrates to the active site in condensation domains. The structures of this complex also allow us to demonstrate that condensation domain active sites do not contain a distinct pocket to select the side chain of the acceptor substrate during peptide assembly but that residues within the active site motif can instead serve to tune the selectivity of these central biosynthetic domains.

Original language	English
Article number	2511
Number of pages	14
Journal	Nature Communications
Volume	12
Issue number	1
DOIs	https://doi.org/10.1038/s41467-021-22623-0
Publication status	Published - Dec 2021

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10.1038/s41467-021-22623-0Licence: CC BY

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Izoré, T., Candace Ho, Y. T., Kaczmarski, J. A., Gavriilidou, A., Chow, K. H., Steer, D. L., Goode, R. J. A., Schittenhelm, R. B., Tailhades, J., Tosin, M., Challis, G. L., Krenske, E. H., Ziemert, N., Jackson, C. J., & Cryle, M. J. (2021). Structures of a non-ribosomal peptide synthetase condensation domain suggest the basis of substrate selectivity. Nature Communications, 12(1), Article 2511. https://doi.org/10.1038/s41467-021-22623-0

@article{dd4ec603a8ba4e0e92daf9b699a5369e,

title = "Structures of a non-ribosomal peptide synthetase condensation domain suggest the basis of substrate selectivity",

abstract = "Non-ribosomal peptide synthetases are important enzymes for the assembly of complex peptide natural products. Within these multi-modular assembly lines, condensation domains perform the central function of chain assembly, typically by forming a peptide bond between two peptidyl carrier protein (PCP)-bound substrates. In this work, we report structural snapshots of a condensation domain in complex with an aminoacyl-PCP acceptor substrate. These structures allow the identification of a mechanism that controls access of acceptor substrates to the active site in condensation domains. The structures of this complex also allow us to demonstrate that condensation domain active sites do not contain a distinct pocket to select the side chain of the acceptor substrate during peptide assembly but that residues within the active site motif can instead serve to tune the selectivity of these central biosynthetic domains.",

author = "Thierry Izor{\'e} and \{Candace Ho\}, \{Y. T.\} and Kaczmarski, \{Joe A.\} and Athina Gavriilidou and Chow, \{Ka Ho\} and Steer, \{David L.\} and Goode, \{Robert J.A.\} and Schittenhelm, \{Ralf B.\} and Julien Tailhades and Manuela Tosin and Challis, \{Gregory L.\} and Krenske, \{Elizabeth H.\} and Nadine Ziemert and Jackson, \{Colin J.\} and Cryle, \{Max J.\}",

note = "Funding Information: J.Yin (University of Chicago) for the R4-4 Sfp expression plasmid; M. Kaniusaite (Monash) for assistance with cloning; T. Harshegyi, L. Scully, and S. Stamatis (Monash) for assistance with protein purification; D. Maksel and G. Kong (MMCF, Monash) for assistance with crystal screening experiments. This research was undertaken on the MX1 and MX2 beamlines at the Australian Synchrotron, part of ANSTO, and made use of the Australian Cancer Research Foundation (ACRF) detector. We would like to thank the beamline scientists at the Australian Synchrotron for their support during data collection. Computational resources were provided by the National Facility of the Australian National Computational Infrastructure through the National Computational Merit Allocation Scheme and by the University of Queensland Research Computing Centre. This work was supported by Monash University, EMBL Australia, the Australian Research Council (Discovery Project DP180103047, DP190101272, and DP210101752) and the National Health and Medical Research Council (APP1140619 to M.J.C.). T.I. is grateful for the support of the CASS foundation (grant \#8583). A.G. is grateful for the support of the Deutsche Forschungsgemeinschaft (DFG; Project ID \# 398967434-TRR 261). This research was conducted by the Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science (CE200100012) and funded by the Australian Government. Publisher Copyright: {\textcopyright} 2021, The Author(s). Copyright: Copyright 2021 Elsevier B.V., All rights reserved.",

year = "2021",

month = dec,

doi = "10.1038/s41467-021-22623-0",

language = "English",

volume = "12",

journal = "Nature Communications",

issn = "2041-1723",

publisher = "Nature Publishing Group",

number = "1",

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Izoré, T, Candace Ho, YT, Kaczmarski, JA, Gavriilidou, A, Chow, KH, Steer, DL, Goode, RJA, Schittenhelm, RB , Tailhades, J, Tosin, M, Challis, GL, Krenske, EH, Ziemert, N, Jackson, CJ & Cryle, MJ 2021, 'Structures of a non-ribosomal peptide synthetase condensation domain suggest the basis of substrate selectivity', Nature Communications, vol. 12, no. 1, 2511. https://doi.org/10.1038/s41467-021-22623-0

TY - JOUR

T1 - Structures of a non-ribosomal peptide synthetase condensation domain suggest the basis of substrate selectivity

AU - Izoré, Thierry

AU - Candace Ho, Y. T.

AU - Kaczmarski, Joe A.

AU - Gavriilidou, Athina

AU - Chow, Ka Ho

AU - Steer, David L.

AU - Goode, Robert J.A.

AU - Schittenhelm, Ralf B.

AU - Tailhades, Julien

AU - Tosin, Manuela

AU - Challis, Gregory L.

AU - Krenske, Elizabeth H.

AU - Ziemert, Nadine

AU - Jackson, Colin J.

AU - Cryle, Max J.

N1 - Funding Information: J.Yin (University of Chicago) for the R4-4 Sfp expression plasmid; M. Kaniusaite (Monash) for assistance with cloning; T. Harshegyi, L. Scully, and S. Stamatis (Monash) for assistance with protein purification; D. Maksel and G. Kong (MMCF, Monash) for assistance with crystal screening experiments. This research was undertaken on the MX1 and MX2 beamlines at the Australian Synchrotron, part of ANSTO, and made use of the Australian Cancer Research Foundation (ACRF) detector. We would like to thank the beamline scientists at the Australian Synchrotron for their support during data collection. Computational resources were provided by the National Facility of the Australian National Computational Infrastructure through the National Computational Merit Allocation Scheme and by the University of Queensland Research Computing Centre. This work was supported by Monash University, EMBL Australia, the Australian Research Council (Discovery Project DP180103047, DP190101272, and DP210101752) and the National Health and Medical Research Council (APP1140619 to M.J.C.). T.I. is grateful for the support of the CASS foundation (grant #8583). A.G. is grateful for the support of the Deutsche Forschungsgemeinschaft (DFG; Project ID # 398967434-TRR 261). This research was conducted by the Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science (CE200100012) and funded by the Australian Government. Publisher Copyright: © 2021, The Author(s). Copyright: Copyright 2021 Elsevier B.V., All rights reserved.

PY - 2021/12

Y1 - 2021/12

N2 - Non-ribosomal peptide synthetases are important enzymes for the assembly of complex peptide natural products. Within these multi-modular assembly lines, condensation domains perform the central function of chain assembly, typically by forming a peptide bond between two peptidyl carrier protein (PCP)-bound substrates. In this work, we report structural snapshots of a condensation domain in complex with an aminoacyl-PCP acceptor substrate. These structures allow the identification of a mechanism that controls access of acceptor substrates to the active site in condensation domains. The structures of this complex also allow us to demonstrate that condensation domain active sites do not contain a distinct pocket to select the side chain of the acceptor substrate during peptide assembly but that residues within the active site motif can instead serve to tune the selectivity of these central biosynthetic domains.

AB - Non-ribosomal peptide synthetases are important enzymes for the assembly of complex peptide natural products. Within these multi-modular assembly lines, condensation domains perform the central function of chain assembly, typically by forming a peptide bond between two peptidyl carrier protein (PCP)-bound substrates. In this work, we report structural snapshots of a condensation domain in complex with an aminoacyl-PCP acceptor substrate. These structures allow the identification of a mechanism that controls access of acceptor substrates to the active site in condensation domains. The structures of this complex also allow us to demonstrate that condensation domain active sites do not contain a distinct pocket to select the side chain of the acceptor substrate during peptide assembly but that residues within the active site motif can instead serve to tune the selectivity of these central biosynthetic domains.

UR - https://www.scopus.com/pages/publications/85105246468

U2 - 10.1038/s41467-021-22623-0

DO - 10.1038/s41467-021-22623-0

M3 - Article

C2 - 33947858

AN - SCOPUS:85105246468

SN - 2041-1723

VL - 12

JO - Nature Communications

JF - Nature Communications

IS - 1

M1 - 2511

ER -

Structures of a non-ribosomal peptide synthetase condensation domain suggest the basis of substrate selectivity

Abstract

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ARC Centre of Excellence for Innovations in Peptide and Protein Science

Understanding peptide bond formation in non-ribosomal peptide biosynthesis

Biosynthetic LEGO: enzymatic redesign to produce new vancomycin analogues

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Structures of a non-ribosomal peptide synthetase condensation domain suggest the basis of substrate selectivity

Abstract

Access to Document

Other files and links

Projects

ARC Centre of Excellence for Innovations in Peptide and Protein Science

Understanding peptide bond formation in non-ribosomal peptide biosynthesis

Biosynthetic LEGO: enzymatic redesign to produce new vancomycin analogues

Cite this