5NJC

E. coli Microcin-processing metalloprotease TldD/E (TldD E263A mutant) with hexapeptide bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.145 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The Origins of Specificity in the Microcin-Processing Protease TldD/E.

Ghilarov, D.Serebryakova, M.Stevenson, C.E.M.Hearnshaw, S.J.Volkov, D.S.Maxwell, A.Lawson, D.M.Severinov, K.

(2017) Structure 25: 1549-1561.e5

  • DOI: 10.1016/j.str.2017.08.006
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • TldD and TldE proteins are involved in the biosynthesis of microcin B17 (MccB17), an Escherichia coli thiazole/oxazole-modified peptide toxin targeting DNA gyrase. Using a combination of biochemical and crystallographic methods we show that E. coli T ...

    TldD and TldE proteins are involved in the biosynthesis of microcin B17 (MccB17), an Escherichia coli thiazole/oxazole-modified peptide toxin targeting DNA gyrase. Using a combination of biochemical and crystallographic methods we show that E. coli TldD and TldE interact to form a heterodimeric metalloprotease. TldD/E cleaves the N-terminal leader sequence from the modified MccB17 precursor peptide, to yield mature antibiotic, while it has no effect on the unmodified peptide. Both proteins are essential for the activity; however, only the TldD subunit forms a novel metal-containing active site within the hollow core of the heterodimer. Peptide substrates are bound in a sequence-independent manner through β sheet interactions with TldD and are likely cleaved via a thermolysin-type mechanism. We suggest that TldD/E acts as a "molecular pencil sharpener": unfolded polypeptides are fed through a narrow channel into the active site and processively truncated through the cleavage of short peptides from the N-terminal end.


    Organizational Affiliation

    Centre for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, 143026 Moscow, Russia; Institute of Gene Biology of the Russian Academy of Sciences, 119334 Moscow, Russia; Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK. Electronic address: dmitry.gilyarov@uj.edu.pl.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Metalloprotease TldD
A, C
495Escherichia coli (strain K12)Mutation(s): 2 
Gene Names: tldD (yhdO)
EC: 3.4.-.-
Find proteins for P0AGG8 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AGG8
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Metalloprotease PmbA
B, D
450Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: pmbA (tldE)
EC: 3.4.-.-
Find proteins for P0AFK0 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AFK0
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
VAL-LEU-GLU-ASP-ARG-ILE
E, F
6N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, C
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download SDF File 
Download CCD File 
A, B, C, D
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, B, C, D
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
MES
Query on MES

Download SDF File 
Download CCD File 
A, B, C, D
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.145 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 65.290α = 90.00
b = 175.440β = 90.01
c = 84.330γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
REFMACphasing
PDB_EXTRACTdata extraction
REFMACrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Dynasty foundationRussian FederationPersonal fellowship
Russian Ministry of ScienceRussian FederationResearch and Scientific-Pedagogical Personnel of Innovative Russia in 2009-2013 grant 8591
Moscow State UniversityRussian FederationDevelopment Program PNG 5.13
European UnionPolandMarie Sklodowska-Curie grant agreement No. 665778
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/J016853/1
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/J004561/1 (MET)
John Innes FoundationUnited Kingdom--

Revision History 

  • Version 1.0: 2017-10-04
    Type: Initial release
  • Version 1.1: 2017-10-18
    Type: Database references