6TRP | pdb_00006trp

Solution Structure of Docking Domain Complex of Pax NRPS: PaxC NDD - PaxB CDD

PDB DOI: https://doi.org/10.2210/pdb6TRP/pdb
BMRB: 34469

Classification: PROTEIN BINDING
Organism(s): Xenorhabdus bovienii SS-2004
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2019-12-19 Released: 2020-08-12
Deposition Author(s): Watzel, J., Hacker, C., Duchardt-Ferner, E., Bode, H.B., Woehnert, J.

Experimental Data Snapshot

Method: SOLUTION NMR
Conformers Calculated: 20
Conformers Submitted: 20
Selection Criteria: structures with the least restraint violations

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

A New Docking Domain Type in the Peptide-Antimicrobial-Xenorhabdus Peptide Producing Nonribosomal Peptide Synthetase fromXenorhabdus bovienii.

Watzel, J., Hacker, C., Duchardt-Ferner, E., Bode, H.B., Wohnert, J.

(2020) ACS Chem Biol 15: 982-989

PubMed: 32167274 Search on PubMed
DOI: https://doi.org/10.1021/acschembio.9b01022
Primary Citation Related Structures:
6TRP

PubMed Abstract:
Nonribosomal peptide synthetases (NRPSs) produce a wide variety of different natural products from amino acid precursors. In contrast to single protein NRPS, the NRPS of the bacterium Xenorhabdus bovienii producing the peptide-antimicrobial-Xenorhabdus (PAX) peptide consists of three individual proteins (PaxA/B/C), which interact with each other noncovalently in a linear fashion. The specific interactions between the three different proteins in this NRPS system are mediated by short C- and N-terminal docking domains ( ^C/NDDs). Here, we investigate the structural basis for the specific interaction between the ^CDD from the protein PaxB and the ^NDD from PaxC. The isolated DD peptides feature transient α-helical conformations in the absence of the respective DD partner. Isothermal titration calorimetry (ITC) and nuclear magnetic resonance (NMR) titration experiments showed that the two isolated DDs bind to each other and form a structurally well-defined complex with a dissociation constant in the micromolar range as is typical for many DD interactions. Artificial linking of this DD pair via a flexible glycine-serine (GS) linker enabled us to solve the structure of the DD complex by NMR spectroscopy. In the complex, the two DDs interact with each other by forming a three helix bundle arranged in an overall coiled-coil motif. Key interacting residues were identified in mutagenesis experiments. Overall, our structure of the PaxB ^CDD/PaxC ^NDD complex represents an architecturally new type of DD interaction motif.

Organizational Affiliation

Molecular Biotechnology, Institute of Molecular Biosciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany.

Macromolecule Content

Total Structure Weight: 9.84 kDa
Atom Count: 687
Modeled Residue Count: 93
Deposited Residue Count: 93
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptide synthetase XpsB,Peptide synthetase XpsB	A	93	Xenorhabdus bovienii SS-2004	Mutation(s): 0 Gene Names: XBJ1_2151, XBJ1_2152 EC: 2.7.7.58 (PDB Primary Data), 5.1.1.12 (PDB Primary Data), 5.1.1.11 (PDB Primary Data), 6.2.1.26 (PDB Primary Data)
UniProt
Find proteins for D3V3G2 (Xenorhabdus bovienii (strain SS-2004)) Explore D3V3G2 Go to UniProtKB: D3V3G2
Find proteins for D3V3G3 (Xenorhabdus bovienii (strain SS-2004)) Explore D3V3G3 Go to UniProtKB: D3V3G3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Groups	D3V3G3 D3V3G2
Sequence Annotations Expand
Reference Sequence