Structures of Nonribosomal Peptide Synthetases

Many Nonribosomal Peptide Synthetase (NRPS) proteins have been structurally characterized using a variety of techniques. These include free-standing proteins, truncated domains, fused proteins, and multidomain proteins caught in a different states of the structural cycle. In this list, we have tried to capture all NRPS proteins that have been structurally characterized, and deposited into the PDB. Proteins are sorted by domain, with Condensation, Adenylation, Thioesterase, Epimerase, and Reductase sections. Next, the table contains a separate section for multi-domain NRPS structures. There is some overlap with the adenylation domain list and the list of ANL Superfamily Members.

A question arises as to what we consider an NRPS protein. Currently (2023), strictly auxiliary proteins that are part of a NRPS biosynthetic pathway but not integrated into a multidomain protein are not included. Additionally, there is discussion in the field about multidomain proteins that do not make a peptide – should they be considered a nonribosomal peptide synthetase? While they may not be an NRPS in the strictest sense, multidomain proteins that include a catalytic domain that acts on a substrate that is loaded on a panthetheine-based carrier protein are included in the list because of the insights they provide.

A version of this table was featured in our 2023 review in Natural Product Reports. Our plan is to update the table regularly as new structures are published.

(Updated March 2024. Currently 184 structures of 80 different proteins.)

Condensation Domains

PDB Accession

Protein Name

Comments
1L5A VibH Free-standing condensation domain from vibriobactin biosynthesis
4JN3 4JN5 5DU9 CDA Condensation First condensation domain from the CDA Synthetase; 5DU9 contains a covalent substrate analog
4ZXW 4ZNM SgcC5 Structure of free-standing ester bond forming condensation domain from C-1027 (enediyne, PKS) biosynthesis
4TX2 Tcp12 Catalytically inactive, P450-recruiting X-domain from Teicoplanin synthetase
5T3E BmdB Cyclization domain from Bacilliamide E synthetase
5DIJ 5EGF 5DLK TqaA Fungal Terminating Condensation (CT) domain; PCP-CT in multidomains below
6AD3 MokA Condensation domain from polyketide Monacolin K (PKS) biosynthesis
7C1H 7C1K 7C1L 7C1P 7C1R 7C1S 7C1U RzmA Lipoinitiation domain of Rhizomide Synthetase
7JTJ 7JUA HMWP2 Crystal structure of the second cyclization domain of yersiniabactin synthetase
7R9X AmbE Crystal structure of a dehydrating condensation domain from AmbE
7RY6 HMWP2 NMR structure of the first cyclization domain of yersiniabactin synthetase
8F7F 8F7G 8F7H 8F7I SrfC Engineered Condensation domain from SrfC

Adenylation Domains

PDB Accession

Protein Name

Comments
1AMU PheA Truncated adenylation domain from Gramicidin biosynthesis, the face that launched a thousand ships
3DHV 3FCC 3FCE 3E7W 3E7X 4PZP DltA DltA, D-Ala-Ligase of cell wall biosynthesis. Not an NRPS, but loads a free-standing Carrier Protein
3O82 3O83 3O84 3U16 3U17 BasE Free-standing adenylation domain from acinetobactin biosynthesis, bound to inhibitors
3ITE SidN Third adenylation domain from a fungal NRPS
3WVN 3WV5 3WV4 VinN Adenylation domain from vicenistatin NRPS
4D4G 4D4H 4D4I 4D56 ApnA Adenylation domain with promiscuous activity from anabaenopeptin NRPS
4OXI AlmE NRPS-like Adenylation domain that is involved in glycyl transfer to lipopolysaccharide
5MSC 5MSD 5MST Car Adenylation domain from the NRPS-like Carboxylate Reductase. More structures below
5N9W 5N9X Thr1 Synthetase NRPS-like Adenylation domain that is involved in synthesis of 4-chlorothreonine in Streptomyces
5KEI MbtA Free-standing Adenylation domain of mycobactin NRPS pathway
5WM2 5WM3 5WM4 5WM5 5WM6 5WM7 CahJ Free-standing Adenylation domain of cahuitamycin NRPS pathway
6EA3 FscH Adenylation domain of fuscachelin NRPS pathway with MLP
6IYK 6IYL EntE Free-standing Adenylation domain of enterobactin NRPS pathway
6OZ1 GR01_22995 NRPS-like Adenylation domain of Carboxylic Acid Reductase (CAR)
6ULX 6ULY StsA Structures of a keto acid activating Adenylation domain; Didomain with KR below
6VHT 6VHU 6VHV 6VHW 6VHX 6VHZ NpsA Free-standing Adenylation domain of tilimycin/tilivalline biosynthesis; di-domain in multidomain structures
7VHV DltA Staphylococcus aureus DltA bound to ATP
7TYB 7TZ4 PchD Free-standing adenylation domain of pyochelin biosynthesis, bound to two AMS inhibitors
7WEW Pls-A Truncated adenylation domain from NRPS-like poly-e-Lys synthetase, bound to Lys-AMP
7XBS 7XBT 7XBU 7XBV CmnG Adenylation domain from Capreomycidine biosynthesis, bound to ATP, Capreomycidine, and AMPPNP
7YWK 7YWJ TycA Engineered Tyrocidine adenylation domains
8GJ4 8GIC 8GJP 8GKM 8GLC Tcp9 Ancestral NRPS
8G95 8G96 8G97 8G98 PosA Acore domain of a poly-delta-ornithine synthetase
8P5O GrsB1 Acore domain of a proline-activating GrsB1 synthetase

Thioesterase Domains

PDB Accession

Protein Name

Comments
1JMK SrfA-C Thioesterase domain from surfactin NRPS pathway
2CB9 FenTE Thioesterase domain from fengycin NRPS pathway
6ECB 6ECC 6ECD 6ECE 6ECF Vlm2 Thioesterase domain from valinomycin with engineered DAB nucleophile
6OJC NocB Thioesterase bound to a fluorophosphonate inhibitor
7CRN 7DXO Skyxy Bifunctional Thioesterase domain from skyllamycin NRPS pathway

Epimerase Domains

PDB Accession

Protein Name

Comments
2XHG TycA C-terminal epimerization domain from TycA
6TA8 TycB3(E) Epimerization domain from TycB3

Reductase Domains

PDB Accession

Protein Name

Comments
4DQV 4U5Q Mps2 Reductase domain from a glycopeptidolipid biosynthesic NRPS
4F6C 4F6L AusA Reductase domain from Aureusimine biosynthesis
4U7W 4W4T MxaA Reductase domain from myxalimid biosynthesis
5MSO 5MSU Car Reductase domain from NRPS-like Carboxylate Reductase

Multi-Domain Structures

We have included all multidomain structures here.
The Domain Architecture column describes the organization of the domain using standard condensation (C), adenylation (A), PCP (T), thioesterase (Te) descriptors as well as other less common supporting domains. These include MbtH-like proteins (MLP), epimerase (Ep), reductase (Red), methyltransferase (M), formyltransferase (F), and cyclization (Cy). When fused, the domains are reflected with a hyphen (-); when as a complex of indepedent proteins, we use a plus sign (+).

PDB Accession

Protein Name

Domain Architecture

Comments
2JGP TycC T-C PCP-Condensation from tyrocidine NRPS
2FQ1 EntB ICL-T Didomain isochorismatase-ArCP domain from enterobactin biosynthesis
2VSQ SrfA-C C-A-T-Te Termination module from Surfactin biosynthesis. A landmark structure from 2008
2ROQ 3TEJ EntF T-Te Structures by X-ray and NMR of the EntF PCP-TE
3RG2 4IZ6 EntE-EntB A-T Fusion construct of the Aden-ArCP domain from enterobactin biosynthesis
4DG8 4DG9 PA1221 A-T Didomain Aden-PCP domain from uncharacterized Pseudomonas NRPS
4GR4 4GR5 SlgN1 MLP-A Complex of an MLP with an Adenylation domain
4ZXI 4ZXH AB3403 C-A-T-Te Termination module from uncharacterized NRPS from Acinetobacter baumannii
5T3D 5JA1 5JA2 EntF MLP + C-A-T-Te Termination module from EntF from enterobactin pathway ± MLP
4R0M McyG A-T Didomain Aden-PCP domain from microcystin NRPS
5EJD TqaA T-CT Fungal Terminating didomain
5ES5 5ES6 5ES7 5ES8 5ES9 5JNF 6ULZ LgrA F-A-T Multidomain structures from linear gramicidin synthetase
5U89 DhbF MLP + ATC Cross-module structure of Bacillibactin NRPS, DhbF
5WMM TioS MLP + A-M Methyltransferase domain interrupting an adenylation domain, along with MLP
6MFW 6MFX 6MFY 6MFZ 6MG0 LgrA F-A-T-C-A-T Multimodular structures from linear gramicidin synthetase
5ISX GrsA T-Epim Complex between PCP and epimerization domains in gramicidin NRPS
5MSP 5MSS 5MST 5MSV 5MSW Car A-T and T-Red Didomain constructs from NRPS-like Carboxylate Reductase
5T7Z 5T81 EpoB Docking-Cy Docking domain with a cyclization NRPS
6LTA 6LTB 6LTC 6LTD FmoA3 Cy-A-T Tridomain NRPS for free-radical scavenging peptide; Cryo-EM structure reported also
6M01 HitB+HitD A + T Complex of freestanding Aden and PCP domain achieved with bromoacetamide pantetheine crosslinker
6M7L OxyA P450 + X-domain Complex of X-domain with OxyA oxidase in glycopeptide biosynthesis
6N8E BdObiF1 C-A-T-Te-MLP Terminating module of obafluorin biosynthesis, with MLP interacting upstream
6O6E PltF + PltL A + T Complex of adenylation domain with PCP in thioester-forming conformation
6OZV 6OYF 6P1J 6P3I 6P4U Txo1 and Txo2 C-A Condensation-adenylation proteins from modules 1 and 2 of teixobactin NRPS
6ULW StsA A-KR-T Structures of a keto acid activating Adenylation domain didomain with KR
6VHV NpsA-ThdA A-T Fused didomain adenylation domain and PCP in tilivalline biosynthesis
6VTJ Mru_0351 T-Red Didomain from Archaeal NRPS
7KVW 7KW0 7KW2 7KW3 FscG T-C Two didomain molecules in the asymmetric unit model the acceptor PCP position
7LY4 7LY5 7LY6 7LY7 BmdBC Cy-A-T + Ox Structures of the BmdB module in complex with the BmdC oxidase
7EMY 7EN1 7EN2 PchE ArCP-Cy-A-E-T CryoEM structures of the PchE module from Pseudomonas aeruginosa shows a dimeric complex
7X0E 7X0F 7X17 AmbB T-C Apo and holo structures of AmbB T-C didomain complexes, including loaded with Ala
7THN 7THQ PigI (or PltF) + PigG A + T Complex of adenylation domain with PCP in thioester-forming conformation
8HLK McbY C + Acore Condensation-Acore domain
8K4R VinM-VinL A + PCP Adenylation holo PCP complex

References to publications are available at the links at the Protein Data Bank.

Please contact me ( ) with updates or corrections.
Studies in the Gulick Lab on NRPSs and Related proteins are supported by NIH Grant R35-GM136235.