PDBsum entry: 1dy6

Hydrolase

PDB-id: 1dy6

Contents

Description

Header details

Header records

References

PROCHECK

Protein chains

267 a.a. *

Waters ×397

* Residue conservation analysis

Tools

Clefts Calculation

PDB id:

1dy6

Name:

Hydrolase

Title:

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

Structure:

Carbapenem-hydrolysing beta-lactamase sme-1. Chain: a, b. Engineered: yes. Other_details: apo form

Source:

Serratia marcescens. Organism_taxid: 615. Strain: s6. Expressed in: escherichia coli. Expression_system_taxid: 562.

UniProt:

Chains A, B: Q54488 (Q54488_SERMA)

Seq:

Struc:

Seq:

294 a.a.

Struc:

267 a.a.

Key:	PfamA domain
Secondary structure	CATH domain

Resolution:

2.1Å

R-factor:

0.184

R-free:

0.244

Authors:

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

Key ref:

W.Sougakoff et al. (2002). Structure of the imipenem-hydrolyzing class A beta-lactamase SME-1 from Serratia marcescens.. Acta Crystallogr D Biol Crystallogr, 58, 267-274. [PubMed id: 11807251] [DOI: 10.1107/S0907444901019606]

Date:

27-Jan-00

Release date:

26-Jan-01

Quick_links

Procheck

Clefts

Surface

Key reference

DOI no: 10.1107/S0907444901019606

Acta Crystallogr D Biol Crystallogr 58:267-274 (2002)

PubMed id: 11807251

Structure of the imipenem-hydrolyzing class A beta-lactamase SME-1 from Serratia marcescens.

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

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. 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.

Selected figure(s)

Figure 3.
Figure 3 (a) Stereoview of the ribbon diagram of the SME-1 -lactamase. The helices are coloured red and the -sheets are green. The conserved amino-acid residues interacting with one another in the tertiary structure by hydrogen bonds or salt-bridge interactions are also represented. Dashed lines indicate the hydrogen-bonding interactions. (b) Stereoview of the active-site region in SME-1: -helices are in red, -strands in green. Hydrogen bonds are depicted by green dotted lines. The disulfide bridge between Cys69 and Cys238 is indicated in yellow. O atoms are coloured red, C atoms grey and N atoms blue.

Figure 5.
Figure 5 Antibiotic susceptibility testing of E. coli producing SME-1 (a) and the C69A mutant (b). The antibiotics used were imipenem (1), amoxicillin (2), ticarcillin (3), kanamycin (4), cefoxitin (5) and aztreonam (6).

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2002, 58, 267-274) copyright 2002.

Figures were selected by an automated process.