1PP5 | pdb_00001pp5

Structure of Antibacterial Peptide Microcin J25: a 21-Residue Lariat Protoknot

• PDB DOI: https://doi.org/10.2210/pdb1PP5/pdb
• BMRB: 5859

• Classification: ANTIBIOTIC
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2003-06-16 Released: 2003-10-28 
• Deposition Author(s): Bayro, M.J., Swapna, G.V.T., Huang, J.Y., Ma, L.-C., Mukhopadhyay, J., Ebright, R.H., Montelione, G.T., Northeast Structural Genomics Consortium (NESG)

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 60 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

Literature

Structure of Antibacterial Peptide Microcin J25: A 21-Residue Lariat Protoknot.

Bayro, M.J., Mukhopadhyay, J., Swapna, G.V.T., Huang, J.Y., Ma, L.-C., Sineva, E., Dawson, P.E., Montelione, G.T., Ebright, R.H.

(2003) J Am Chem Soc 125: 12382-12383

• PubMed: 14531661 
• DOI: https://doi.org/10.1021/ja036677e
• Primary Citation Related Structures: 
  1PP5


• PubMed Abstract: 
  

  The antibacterial peptide microcin J25 (MccJ25) inhibits bacterial transcription by binding within, and obstructing, the nucleotide-uptake channel of bacterial RNA polymerase. Published covalent and three-dimensional structures indicate that MccJ25 is a 21-residue cycle. Here, we show that the published covalent and three-dimensional structures are incorrect, and that MccJ25 in fact is a 21-residue "lariat protoknot", consisting of an 8-residue cyclic segment followed by a 13-residue linear segment that loops back and threads through the cyclic segment. MccJ25 is the first example of a lariat protoknot involving a backbone-side chain amide linkage.

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Organizational Affiliation: 
• Department of Molecular Biology and Biochemistry, Waksman Institute, and Howard Hughes Medical Institute, Rutgers University, Piscataway, New Jersey 08854, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 2.13 kDa 
• Atom Count: 150 
• Modeled Residue Count: 21 
• Deposited Residue Count: 21 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
microcin J25	A	21	Escherichia coli	Mutation(s): 0  Gene Names: MCJA
UniProt
Find proteins for Q9X2V7 (Escherichia coli) Explore Q9X2V7  Go to UniProtKB:  Q9X2V7

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 1
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000184	A	Microcin J25	Polypeptide / Inhibitor

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 60 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-10-28 
Deposition Author(s): Bayro, M.J., Swapna, G.V.T., Huang, J.Y., Ma, L.-C., Mukhopadhyay, J., Ebright, R.H., Montelione, G.T., Northeast Structural Genomics Consortium (NESG)

Revision History  

• Version 1.0: 2003-10-28
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2011-07-27
  Changes: Non-polymer description, Structure summary
• Version 1.4: 2012-12-12
  Changes: Other
• Version 1.5: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary