3LO7

Crystal structure of PBPA from Mycobacterium tuberculosis

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.217 

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This is version 1.2 of the entry. See complete history. 


Literature

Unusual conformation of the SxN motif in the crystal structure of penicillin-binding protein A from Mycobacterium tuberculosis.

Fedarovich, A., Nicholas, R.A., Davies, C.

(2010) J Mol Biol 398: 54-65

  • DOI: 10.1016/j.jmb.2010.02.046
  • Primary Citation of Related Structures:  
    3LO7

  • PubMed Abstract: 

    • PBPA from Mycobacterium tuberculosis is a class B-like penicillin-binding protein (PBP) that is not essential for cell growth in M. tuberculosis, but is important for proper cell division in Mycobacterium smegmatis. We have determined the crystal structu ...

    PBPA from Mycobacterium tuberculosis is a class B-like penicillin-binding protein (PBP) that is not essential for cell growth in M. tuberculosis, but is important for proper cell division in Mycobacterium smegmatis. We have determined the crystal structure of PBPA at 2.05 A resolution, the first published structure of a PBP from this important pathogen. Compared to other PBPs, PBPA has a relatively small N-terminal domain, and conservation of a cluster of charged residues within this domain suggests that PBPA is more related to class B PBPs than previously inferred from sequence analysis. The C-terminal domain is a typical transpeptidase fold and contains the three conserved active-site motifs characteristic of penicillin-interacting enzymes. Whilst the arrangement of the SxxK and KTG motifs is similar to that observed in other PBPs, the SxN motif is markedly displaced away from the active site, such that its serine (Ser281) is not involved in hydrogen bonding with residues of the other two motifs. A disulfide bridge between Cys282 (the "x" of the SxN motif) and Cys266, which resides on an adjacent loop, may be responsible for this unusual conformation. Another interesting feature of the structure is a relatively long connection between beta 5 and alpha 11, which restricts the space available in the active site of PBPA and suggests that conformational changes would be required to accommodate peptide substrate or beta-lactam antibiotics during acylation. Finally, the structure shows that one of the two threonines postulated to be targets for phosphorylation is inaccessible (Thr362), whereas the other (Thr437) is well placed on a surface loop near the active site.

    Organizational Affiliation: 

    Department of Biochemistry and Molecular Biology, Medical University of South Carolina, 173 Ashley Avenue, Charleston, SC 29425, USA.



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Penicillin-binding protein A A, B483Mycobacterium tuberculosisMutation(s): 0 
Gene Names: MT0019, MTCY10H4.16c, pbpA, Rv0016c
EC: 3.4.16.4
Find proteins for P9WKD1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WKD1 
Go to UniProtKB:  P9WKD1
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.217 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 120.6α = 90
b = 120.6β = 90
c = 92.2γ = 120
Software Package:
Software NamePurpose
MAR345data collection
SOLVEphasing
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-03-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description