Crystal structure of Mycobacterium tuberculosis D,D-peptidase Rv3330 in complex with meropenem

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.186 

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Subfamily-specific adaptations in the structures of two penicillin-binding proteins from Mycobacterium tuberculosis.

Prigozhin, D.M.Krieger, I.V.Huizar, J.P.Mavrici, D.Waldo, G.S.Hung, L.W.Sacchettini, J.C.Terwilliger, T.C.Alber, T.

(2014) PLoS One 9: e116249-e116249

  • DOI: https://doi.org/10.1371/journal.pone.0116249
  • Primary Citation of Related Structures:  
    4P0M, 4PPR

  • PubMed Abstract: 

    Beta-lactam antibiotics target penicillin-binding proteins including several enzyme classes essential for bacterial cell-wall homeostasis. To better understand the functional and inhibitor-binding specificities of penicillin-binding proteins from the pathogen, Mycobacterium tuberculosis, we carried out structural and phylogenetic analysis of two predicted D,D-carboxypeptidases, Rv2911 and Rv3330. Optimization of Rv2911 for crystallization using directed evolution and the GFP folding reporter method yielded a soluble quadruple mutant. Structures of optimized Rv2911 bound to phenylmethylsulfonyl fluoride and Rv3330 bound to meropenem show that, in contrast to the nonspecific inhibitor, meropenem forms an extended interaction with the enzyme along a conserved surface. Phylogenetic analysis shows that Rv2911 and Rv3330 belong to different clades that emerged in Actinobacteria and are not represented in model organisms such as Escherichia coli and Bacillus subtilis. Clade-specific adaptations allow these enzymes to fulfill distinct physiological roles despite strict conservation of core catalytic residues. The characteristic differences include potential protein-protein interaction surfaces and specificity-determining residues surrounding the catalytic site. Overall, these structural insights lay the groundwork to develop improved beta-lactam therapeutics for tuberculosis.

  • Organizational Affiliation

    Los Alamos National Laboratory, Los Alamos, New Mexico, 87545, United States of America; Department of Biochemistry and Biophysics, Texas A & M University, College Station, Texas, 77843, United States of America.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Penicillin-binding protein DacB1334Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: Rv3330RVBD_3330dacB1
EC: 3.4.16
Find proteins for O53380 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore O53380 
Go to UniProtKB:  O53380
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO53380
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on MER

Download Ideal Coordinates CCD File 
B [auth A](4R,5S)-3-{[(3S,5S)-5-(dimethylcarbamoyl)pyrrolidin-3-yl]sulfanyl}-5-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-4-methyl-4,5-d ihydro-1H-pyrrole-2-carboxylic acid
C17 H27 N3 O5 S
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.186 
  • Space Group: P 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.291α = 90
b = 76.291β = 90
c = 99.978γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-11-05
    Type: Initial release
  • Version 1.1: 2015-03-04
    Changes: Database references
  • Version 1.2: 2015-03-11
    Changes: Database references
  • Version 1.3: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary