5NJ5 | pdb_00005nj5

E. coli Microcin-processing metalloprotease TldD/E with phosphate bound

• PDB DOI: https://doi.org/10.2210/pdb5NJ5/pdb

• Classification: HYDROLASE
• Organism(s): Escherichia coli str. K-12 substr. MG1655
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2017-03-28 Released: 2017-10-04 
• Deposition Author(s): Ghilarov, D., Serebryakova, M., Stevenson, C.E.M., Hearnshaw, S.J., Volkov, D., Maxwell, A., Lawson, D.M., Severinov, K.
• Funding Organization(s): Dynasty foundation, Russian Ministry of Science, European Union, Biotechnology and Biological Sciences Research Council, John Innes Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.178 (Depositor), 0.183 (DCC) 
• R-Value Work: 
  0.139 (Depositor), 0.146 (DCC) 
• R-Value Observed: 
  0.141 (Depositor) 

Starting Model: experimental

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

• PubMed: 28943336 
• DOI: https://doi.org/10.1016/j.str.2017.08.006
• Primary Citation Related Structures: 
  5NJ5, 5NJ9, 5NJA, 5NJB, 5NJC, 5NJF


• 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 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.

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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: [e-mail].
Institute of Gene Biology of the Russian Academy of Sciences, 119334 Moscow, Russia; Lomonosov Moscow State University, Department of Chemistry, A.N. Belozersky Institute of Physico-Chemical Biology, 119992 Moscow, Russia.
Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK.
Lomonosov Moscow State University, Department of Chemistry, Analytical Chemistry Division, 119991 Moscow, Russia.
Centre for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, 143026 Moscow, Russia; Bionano Institute, Peter the Great Saint Petersburg State Polytechnical University, Saint Petersburg 195251, Russia; Waksman Institute for Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: native gel electrophoresis

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: native gel electrophoresis

Macromolecule Content 

• Total Structure Weight: 204.09 kDa 
• Atom Count: 16,162 
• Modeled Residue Count: 1,847 
• Deposited Residue Count: 1,890 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Metalloprotease TldD	A, C	495	Escherichia coli str. K-12 substr. MG1655	Mutation(s): 1  Gene Names: tldD, yhdO, b3244, JW3213 EC: 3.4
UniProt
Find proteins for P0AGG8 (Escherichia coli (strain K12)) Explore P0AGG8  Go to UniProtKB:  P0AGG8

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Metalloprotease PmbA	B, D	450	Escherichia coli str. K-12 substr. MG1655	Mutation(s): 0  Gene Names: pmbA, tldE, b4235, JW4194 EC: 3.4
UniProt
Find proteins for P0AFK0 (Escherichia coli (strain K12)) Explore P0AFK0  Go to UniProtKB:  P0AFK0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	F [auth A], N [auth C]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
ZN	E [auth A], M [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	G [auth A], H [auth A], I [auth A], J [auth A], K [auth B], L [auth B], O [auth C], P [auth C], Q [auth C], R [auth D], S [auth D], T [auth D]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.178 (Depositor), 0.183 (DCC) 
• R-Value Work:  0.139 (Depositor), 0.146 (DCC) 
• R-Value Observed: 0.141 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.77	α = 90
b = 173.99	β = 90
c = 83.52	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-10-04 
Deposition Author(s): Ghilarov, D., Serebryakova, M., Stevenson, C.E.M., Hearnshaw, S.J., Volkov, D., Maxwell, A., Lawson, D.M., Severinov, K.

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Funding Organization	Location	Grant Number
Dynasty foundation	Russian Federation	Personal fellowship
Russian Ministry of Science	Russian Federation	Research and Scientific-Pedagogical Personnel of Innovative Russia in 2009-2013 grant 8591
European Union	Poland	Marie Sklodowska-Curie grant agreement No. 665778
Biotechnology and Biological Sciences Research Council	United Kingdom	BB/J016853/1
Biotechnology and Biological Sciences Research Council	United Kingdom	BB/J004561/1 (MET)
John Innes Foundation	United Kingdom	--

Revision History  

• Version 1.0: 2017-10-04
  Type: Initial release
  
• Version 1.1: 2017-10-18
  Changes: Database references
• Version 1.2: 2024-01-17
  Changes: Data collection, Database references, Derived calculations, Refinement description