5NJF

E. coli Microcin-processing metalloprotease TldD/E (TldD H262A mutant) with pentapeptide bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.42 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.139 
  • R-Value Observed: 0.140 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 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: https://doi.org/10.1016/j.str.2017.08.006
  • Primary Citation of 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.


  • 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Metalloprotease TldD
A, C
495Escherichia coli K-12Mutation(s): 2 
Gene Names: tldDyhdOb3244JW3213
EC: 3.4
UniProt
Find proteins for P0AGG8 (Escherichia coli (strain K12))
Explore P0AGG8 
Go to UniProtKB:  P0AGG8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AGG8
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Metalloprotease PmbA
B, D
450Escherichia coli K-12Mutation(s): 0 
Gene Names: pmbAtldEb4235JW4194
EC: 3.4
UniProt
Find proteins for P0AFK0 (Escherichia coli (strain K12))
Explore P0AFK0 
Go to UniProtKB:  P0AFK0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AFK0
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
ALA-ALA-ALA-ALA-ALA
E, F
5Escherichia coli str. K-12 substr. MG1655Mutation(s): 0 
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MES
Query on MES

Download Ideal Coordinates CCD File 
H [auth A],
I [auth A],
M [auth B],
S [auth C],
V [auth D]
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
G [auth A],
R [auth C]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
J [auth A]
L [auth A]
N [auth B]
O [auth B]
P [auth B]
J [auth A],
L [auth A],
N [auth B],
O [auth B],
P [auth B],
T [auth C],
W [auth D],
X [auth D],
Y [auth D],
Z [auth D]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
AA [auth D],
K [auth A],
Q [auth B],
U [auth C]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.42 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.139 
  • R-Value Observed: 0.140 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.16α = 90
b = 174.48β = 90.04
c = 83.65γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing

Structure Validation

View Full Validation Report



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  (Full details and data files)

  • 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