1DY6

Structure of the imipenem-hydrolyzing beta-lactamase SME-1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.13 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.184 

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This is version 1.5 of the entry. See complete history


Literature

Structure of the Imipenem-Hydrolyzing Class a Beta-Lactamase Sme-1 from Serratia Marcescens.

Sougakoff, W.L'Hermite, G.Billy, I.Pernot, L.Guillet, V.Naas, T.Nordmann, P.Jarlier, V.Delettre, J.

(2002) Acta Crystallogr D Biol Crystallogr 58: 267

  • DOI: 10.1107/s0907444901019606
  • Primary Citation of Related Structures:  
    1DY6

  • PubMed Abstract: 
  • The structure of the beta-lactamase SME-1 from Serratia marcescens, a class A enzyme characterized by its significant activity against imipenem, has been determined to 2.13 A resolution. The overall structure of SME-1 is similar to that of other class A beta-lactamases ...

    The structure of the beta-lactamase SME-1 from Serratia marcescens, a class A enzyme characterized by its significant activity against imipenem, has been determined to 2.13 A resolution. The overall structure of SME-1 is similar to that of other class A beta-lactamases. In the active-site cavity, most of the residues found in SME-1 are conserved among class A beta-lactamases, except at positions 104, 105 and 237, where a tyrosine, a histidine and a serine are found, respectively, and at position 238, which is occupied by a cysteine forming a disulfide bridge with the other cysteine residue located at position 69. The crucial role played by this disulfide bridge in SME-1 was confirmed by site-directed mutagenesis of Cys69 to Ala, which resulted in a mutant unable to confer resistance to imipenem and all other beta-lactam antibiotics tested. Another striking structural feature found in SME-1 was the short distance separating the side chains of the active serine residue at position 70 and the strictly conserved glutamate at position 166, which is up to 1.4 A shorter in SME-1 compared with other class A beta-lactamases. Consequently, the SME-1 structure cannot accommodate the essential catalytic water molecule found between Ser70 and Glu166 in the other class A beta-lactamases described so far, suggesting that a significant conformational change may be necessary in SME-1 to properly position the hydrolytic water molecule involved in the hydrolysis of the acyl-enzyme intermediate.


    Related Citations: 
    • Purification, Crystallization, and Preliminary X-Ray Diffraction Analysis of the Carbapenem-Hydrolyzing Class a Beta-Lactamase Sme-1 from Serratia Marcescens
      Sougakoff, W., Jarlier, V., Delettre, J., Colloc'H, N., L'Hermite, G., Nordmann, P., Naas, T.
      (1996) J Struct Biol 116: 313

    Organizational Affiliation

    Laboratoire de Recherche Moléculaire sur les Antibiotiques (LRMA), INSERM EMI0004, Faculté de Médecine Pitié-Salpêtrière, Université Pierre et Marie Curie, 75634 Paris CEDEX 13, France.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CARBAPENEM-HYDROLYSING BETA-LACTAMASE SME-1A, B267Serratia marcescensMutation(s): 0 
Gene Names: sme-2blaSME-1blaSME-4blaSME1SME12620_22
EC: 3.5.2.6
UniProt
Find proteins for Q54488 (Serratia marcescens)
Explore Q54488 
Go to UniProtKB:  Q54488
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ54488
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.13 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.184 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.5α = 90
b = 51.72β = 118.62
c = 71.69γ = 90
Software Package:
Software NamePurpose
X-PLORrefinement
MADNESSdata reduction
Agrovatadata scaling
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-01-26
    Type: Initial release
  • Version 1.1: 2011-05-07
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-07-05
    Changes: Data collection
  • Version 1.4: 2017-07-12
    Changes: Refinement description
  • Version 1.5: 2019-05-22
    Changes: Data collection, Refinement description