6KGV

Crystal structure of Penicillin binding protein 3 (PBP3) from Mycobacterium tuerculosis, complexed with amoxicillin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 

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Literature

Structures ofMycobacterium tuberculosisPenicillin-Binding Protein 3 in Complex with Fivebeta-Lactam Antibiotics Reveal Mechanism of Inactivation.

Lu, Z.Wang, H.Zhang, A.Liu, X.Zhou, W.Yang, C.Guddat, L.Yang, H.Schofield, C.J.Rao, Z.

(2020) Mol Pharmacol 97: 287-294

  • DOI: 10.1124/mol.119.118042
  • Primary Citation of Related Structures:  
    6KGH, 6KGS, 6KGU, 6KGT, 6KGW, 6KGV

  • PubMed Abstract: 
  • Because of β -lactamase-mediated resistance, β -lactam antibiotics were long considered ineffective drugs for tuberculosis (TB) treatment. However, some β -lactams, including meropenem and faropenem, are being re-evaluated in patients infected with TB ...

    Because of β -lactamase-mediated resistance, β -lactam antibiotics were long considered ineffective drugs for tuberculosis (TB) treatment. However, some β -lactams, including meropenem and faropenem, are being re-evaluated in patients infected with TB. Penicillin-binding protein (PBP) 3, or ftsI, is an essential transpeptidase in Mycobacterium tuberculosis (Mtb) required for cell division, and thus it is an important drug target. Structures of apo Mtb PBP3 and of complexes with five β -lactams, including meropenem and faropenem, reveal how they cause inactivation via formation of hydrolytically stable acyl-enzyme complexes. The structures reveal unique features of the antibiotic interactions, both in terms of differences in their binding to Mtb PBP3 and in comparison with structures of other PBPs and serine β -lactamases, including the tautomerization status of the carbapenem-derived acyl-enzyme complexes. The results suggest that rather than hoping PBP inhibitors developed for other infections will work against TB, work should focus on developing PBP inhibitors specialized for treating TB. SIGNIFICANCE STATEMENT: The structures of Mycobacterium tuberculosis penicillin-binding protein 3, an essential protein in M. tuberculosis , in complex with a number of widely used β -lactam antibiotics (e.g., meropenem, aztreonam, and amoxicillin) were solved. These data provide new insights for next-generation rational approaches to design tuberculosis (TB)-specific β -lactam or nonlactam antibiotics. This manuscript is a seminal article in the field of anti-TB drug discovery and suitable for the broad readership.


    Organizational Affiliation

    Key Laboratory of Biomarker Based Rapid-detection Technology for Food Safety of Henan Province, Xuchang University, Xuchang, Henan, China (Z.L., A.Z.); College of Life Sciences (Z.L., H.W., W.Z. and Z.R.) and College of Pharmacy (X.L., C.Y.), Nankai University, Tianjin, China; School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Queensland, Australia (L.G.); School of Life Sciences, Tianjin University, Tianjin, China (H.Y.); University of Oxford, Chemistry Research Laboratory, Oxford, United Kingdom (C.J.S.); National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Science, Beijing, China (Z.R.); and Laboratory of Structural Biology, School of Medicine, Tsinghua University, Beijing, China (Z.R.) raozh@mail.tsinghua.edu.cn.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Penicillin-binding protein PbpBA562Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: pbpBftsIpbp3Rv2163c
UniProt
Find proteins for L0T911 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore L0T911 
Go to UniProtKB:  L0T911
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AXL (Subject of Investigation/LOI)
Query on AXL

Download Ideal Coordinates CCD File 
F [auth A]2-{1-[2-AMINO-2-(4-HYDROXY-PHENYL)-ACETYLAMINO]-2-OXO-ETHYL}-5,5-DIMETHYL-THIAZOLIDINE-4-CARBOXYLIC ACID
C16 H21 N3 O5 S
SMLJDSWXGVMNTH-NRWUCQMLSA-N
 Ligand Interaction
CO
Query on CO

Download Ideal Coordinates CCD File 
B [auth A], C [auth A], D [auth A], E [auth A]COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.63α = 90
b = 83.8β = 111.71
c = 90.13γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (China)China15 2017YFC0840300
Chinese Academy of SciencesChinaXDB08020200
National Natural Science Foundation of ChinaChina81520108019

Revision History  (Full details and data files)

  • Version 1.0: 2020-03-11
    Type: Initial release