Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 59295.73 
• Atom Count: 4184 
• Residue Count: 520 
• Unique protein chains: 1

2JGP

Structure of the TycC5-6 PCP-C bidomain of the tyrocidine synthetase TycC

• DOI: 10.2210/pdb2JGP/pdb

• Classification: LIGASE
• Organism(s): Brevibacillus parabrevis
• Expression System: Escherichia coli


• Deposited: 2007-02-13 Released: 2007-10-30 
• Deposition Author(s): Samel, S.A., Schoenafinger, G., Knappe, T.A., Marahiel, M.A., Essen, L.-O.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.238 
• R-Value Work: 0.208 

Literature

Structural and Functional Insights Into a Peptide Bond-Forming Bidomain from a Nonribosomal Peptide Synthetase.

Samel, S.A., Schoenafinger, G., Knappe, T.A., Marahiel, M.A., Essen, L.-O.

(2007) Structure 15: 781

• PubMed: 17637339 
• DOI: 10.1016/j.str.2007.05.008


• PubMed Abstract: 
  

The crystal structure of the bidomain PCP-C from modules 5 and 6 of the nonribosomal tyrocidine synthetase TycC was determined at 1.8 A resolution. The bidomain structure reveals a V-shaped condensation domain, the canyon-like active site groove of which is associated with the preceding peptidyl carrier protein (PCP) domain at its donor side. The relative arrangement of the PCP and the peptide bond-forming condensation (C) domain places the active sites approximately 50 A apart. Accordingly, this PCP-C structure represents a conformational state prior to peptide transfer from the donor-PCP to the acceptor-PCP domain, implying the existence of additional states of PCP-C domain interaction during catalysis. Additionally, PCP-C exerts a mode of cyclization activity that mimics peptide bond formation catalyzed by C domains. Based on mutational data and pK value analysis of active site residues, it is suggested that nonribosomal peptide bond formation depends on electrostatic interactions rather than on general acid/base catalysis.

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Organizational Affiliation: 

Department of Chemistry/Biochemistry, Philipps-Universität, Hans-Meerwein-Strasse, D-35032 Marburg, Germany.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
TYROCIDINE SYNTHETASE 3	A	520	Brevibacillus parabrevis	Mutation(s): 0  Gene Names: tycC
Find proteins for O30409 (Brevibacillus parabrevis) Go to UniProtKB:  O30409

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
NA	A	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N
SO4	A	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
DIO	A	1,4-DIETHYLENE DIOXIDE C4 H8 O2 RYHBNJHYFVUHQT-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.238 
• R-Value Work: 0.208 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length (Å)	Angle (°)
a = 84.973	α = 90.00
b = 84.973	β = 90.00
c = 164.969	γ = 90.00

Software Package:

Software Name	Purpose
SHARP	phasing
SHELX	phasing
MOSFLM	data reduction
SCALA	data scaling
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-02-13 
• Released Date: 2007-10-30 
• Deposition Author(s): Samel, S.A., Schoenafinger, G., Knappe, T.A., Marahiel, M.A., Essen, L.-O.

Revision History 

• Version 1.0: 2007-10-30
  Type: Initial release
• Version 1.1: 2011-07-13
  Type: Advisory, Version format compliance
• Version 1.2: 2012-06-13
  Type: Other
• Version 1.3: 2019-07-24
  Type: Advisory, Data collection