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 

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This is version 1.4 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.,Sect.D 58: 267


  • 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 clas ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CARBAPENEM-HYDROLYSING BETA-LACTAMASE SME-1
A, B
267Serratia marcescensGene Names: sme-2 (blaSME-2, blaSME-4, blaSME1)
EC: 3.5.2.6
Find proteins for Q54488 (Serratia marcescens)
Go to UniProtKB:  Q54488
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.13 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.184 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 81.500α = 90.00
b = 51.720β = 118.62
c = 71.690γ = 90.00
Software Package:
Software NamePurpose
MADNESSdata reduction
X-PLORphasing
Agrovatadata scaling
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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