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(-) Description

Title :  STRUCTURE OF THE IMIPENEM-HYDROLYZING BETA-LACTAMASE SME-1
 
Authors :  W. Sougakoff, G. L'Hermite, I. Billy, V. Guillet, T. Naas, P. Nordman, V J. Delettre
Date :  27 Jan 00  (Deposition) - 26 Jan 01  (Release) - 12 Jul 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.13
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Hydrolase, Lactamase, Antibiotic, Carbapenem, Imipenem (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. Sougakoff, G. L'Hermite, I. Billy, L. Pernot, V. Guillet, T. Naas, P. Nordmann, V. Jarlier, J. Delettre
Structure Of The Imipenem-Hydrolyzing Class A Beta-Lactamas Sme-1 From Serratia Marcescens.
Acta Crystallogr. , Sect. D V. 58 267 2002
PubMed-ID: 11807251  |  Reference-DOI: 10.1107/S0907444901019606
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CARBAPENEM-HYDROLYSING BETA-LACTAMASE SME-1
    Chains: A, B
    EC Number: 3.5.2.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Gene: BLASME
    Expression System Plasmid: PPTN103
    Expression System Strain: JM109
    Expression System Taxid: 562
    Organism Scientific: SERRATIA MARCESCENS
    Organism Taxid: 615
    Other Details: APO FORM
    Strain: S6

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1DY6)

(-) Sites  (0, 0)

(no "Site" information available for 1DY6)

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:69 -A:238
2B:69 -B:238

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Glu A:166 -Leu A:167
2Glu B:166 -Leu B:167

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1DY6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1DY6)

(-) Exons   (0, 0)

(no "Exon" information available for 1DY6)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:267
 aligned with Q54488_SERMA | Q54488 from UniProtKB/TrEMBL  Length:294

    Alignment length:267
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       
        Q54488_SERMA     28 NKSDAAAKQIKKLEEDFDGRIGVFAIDTGSGNTFGYRSDERFPLCSSFKGFLAAAVLERVQQKKLDINQKVKYESRDLEYHSPITTKYKGSGMTLGDMASAALQYSDNGATNIIMERFLGGPEGMTKFMRSIGDNEFRLDRWELELNTAIPGDKRDTSTPKAVANSLNKLALGNVLNAKVKAIYQNWLKGNTTGDARIRASVPADWVVGDKTGSCGAYGTANDYAVIWPKNRAPLIVSIYTTRKSKDDKHSDKTIAEASRIAIQAID  294
               SCOP domains d1dy6a_ A: beta-Lactamase, class A                                                                                                                                                                                                                                          SCOP domains
               CATH domains 1dy6A00 A:24-291 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                                                    CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh.eeeeeeeee.....eeee.....ee.hhhhhhhhhhhhhhhhhh.......ee..........hhhhhhh....eehhhhhhhhhhh.hhhhhhhhhhhh.hhhhhhhhhhhhh...........hhhhh........eehhhhhhhhhhhhhh....hhhhhhhhhhhhhh......hhhhhh....eeeeeeee......eeeeeeee......eeeeeeeee.......hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1dy6 A   24 NKSDAAAKQIKKLEEDFDGRIGVFAIDTGSGNTFGYRSDERFPLCSSFKGFLAAAVLERVQQKKLDINQKVKYESRDLEYHSPITTKYKGSGMTLGDMASAALQYSDNGATNIIMERFLGGPEGMTKFMRSIGDNEFRLDRWELELNTAIPGDKRDTSTPKAVANSLNKLALGNVLNAKVKAIYQNWLKGNTTGDARIRASVPADWVVGDKTGSCGAYGTANDYAVIWPKNRAPLIVSIYTTRKSKDDKHSDKTIAEASRIAIQAID  291
                                    33        43        53   ||   64        74        84        94       104       114       124       134       143       153       163       173       183       193       203       213       223       233       243       254       264       274       284       
                                                            57|                                                                               141B                                                                                                            252|                                     
                                                             59                                                                                                                                                                                                254                                     


Chain B from PDB  Type:PROTEIN  Length:267
 aligned with Q54488_SERMA | Q54488 from UniProtKB/TrEMBL  Length:294

    Alignment length:267
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       
        Q54488_SERMA     28 NKSDAAAKQIKKLEEDFDGRIGVFAIDTGSGNTFGYRSDERFPLCSSFKGFLAAAVLERVQQKKLDINQKVKYESRDLEYHSPITTKYKGSGMTLGDMASAALQYSDNGATNIIMERFLGGPEGMTKFMRSIGDNEFRLDRWELELNTAIPGDKRDTSTPKAVANSLNKLALGNVLNAKVKAIYQNWLKGNTTGDARIRASVPADWVVGDKTGSCGAYGTANDYAVIWPKNRAPLIVSIYTTRKSKDDKHSDKTIAEASRIAIQAID  294
               SCOP domains d1dy6b_ B: beta-Lactamase, class A                                                                                                                                                                                                                                          SCOP domains
               CATH domains 1dy6B00 B:24-291 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                                                    CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh.eeeeeeeee.....eeee.....ee.hhhhhhhhhhhhhhhhhh.......ee..........hhhhhhh....eehhhhhhhhhhh.hhhhhhhhhhhh.hhhhhhhhhhhhh...........hhhhh........eehhhhhhhhhhhhhh....hhhhhhhhhhhhhh......hhhhhh....eeeeeeee......eeeeeeee......eeeeeeeee.......hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1dy6 B   24 NKSDAAAKQIKKLEEDFDGRIGVFAIDTGSGNTFGYRSDERFPLCSSFKGFLAAAVLERVQQKKLDINQKVKYESRDLEYHSPITTKYKGSGMTLGDMASAALQYSDNGATNIIMERFLGGPEGMTKFMRSIGDNEFRLDRWELELNTAIPGDKRDTSTPKAVANSLNKLALGNVLNAKVKAIYQNWLKGNTTGDARIRASVPADWVVGDKTGSCGAYGTANDYAVIWPKNRAPLIVSIYTTRKSKDDKHSDKTIAEASRIAIQAID  291
                                    33        43        53   ||   64        74        84        94       104       114       124       134       143       153       163       173       183       193       203       213       223       233       243       254       264       274       284       
                                                            57|                                                                               141B                                                                                                            252|                                     
                                                             59                                                                                                                                                                                                254
   Legend:   → Mismatch (orange background)
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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

Asymmetric Unit
(-)
Class: Multi-domain proteins (alpha and beta) (2421)

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1DY6)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q54488_SERMA | Q54488)
molecular function
    GO:0008800    beta-lactamase activity    Catalysis of the reaction: a beta-lactam + H2O = a substituted beta-amino acid.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
biological process
    GO:0030655    beta-lactam antibiotic catabolic process    The chemical reactions and pathways resulting in the breakdown of a beta-lactam antibiotic, any member of a class of natural or semisynthetic antibiotics whose characteristic feature is a strained, four-membered beta-lactam ring. They include the penicillins and many of the cephalosporins.
    GO:0046677    response to antibiotic    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms.

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    Glu A:166 - Leu A:167   [ RasMol ]  
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