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(-) Description

Title :  CRYSTAL STRUCTURE OF THE CLASS A BETA-LACTAMASE SED-G238C MUTANT FROM CITROBACTER SEDLAKII
 
Authors :  L. Pernot, S. Petrella, W. Sougakoff
Date :  21 Nov 07  (Deposition) - 18 Dec 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Hydrolase, Beta-Lactamase, Class A, Sed-G238C Mutant (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  L. Pernot, S. Petrella, W. Sougakoff
Acyl-Intermediate Structures Of The Class A Beta-Lactamase Sed-G238C
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CLASS A BETA-LACTAMASE SED1
    ChainsA, B, C, D
    EC Number3.5.2.6
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21
    Expression System PlasmidPET29A
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    FragmentSED-G238C, UNP RESIDUES 33-295
    GeneBLA-SED-1
    MutationYES
    Organism ScientificCITROBACTER SEDLAKII
    Organism Taxid67826
    Strain2596

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)A   
Biological Unit 2 (1x) B  
Biological Unit 3 (1x)  C 
Biological Unit 4 (1x)   D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1CAC4Ligand/IonCACODYLATE ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1CAC1Ligand/IonCACODYLATE ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1CAC1Ligand/IonCACODYLATE ION
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1CAC1Ligand/IonCACODYLATE ION
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
1CAC1Ligand/IonCACODYLATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:70 , TRP A:105 , SER A:130 , ASN A:132 , ALA A:237 , HOH A:302 , HOH A:311 , HOH A:316 , HOH A:317BINDING SITE FOR RESIDUE CAC A 1
2AC2SOFTWARESER B:70 , TRP B:105 , SER B:130 , ASN B:132 , ALA B:237 , HOH B:300 , HOH B:302 , HOH B:317 , HOH B:401BINDING SITE FOR RESIDUE CAC B 2
3AC3SOFTWARESER C:70 , TRP C:105 , SER C:130 , ASN C:132 , ALA C:237 , HOH C:449 , HOH C:458 , HOH C:467 , HOH C:497BINDING SITE FOR RESIDUE CAC C 3
4AC4SOFTWARESER D:70 , TRP D:105 , SER D:130 , ALA D:237 , HOH D:473 , HOH D:475 , HOH D:483 , HOH D:515BINDING SITE FOR RESIDUE CAC D 4

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:69 -A:238
2B:69 -B:238
3C:69 -C:238
4D:69 -D:238

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Glu A:166 -Pro A:167
2Glu B:166 -Pro B:167
3Glu C:166 -Pro C:167
4Glu D:166 -Pro D:167

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3BFD)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3BFD)

(-) Exons   (0, 0)

(no "Exon" information available for 3BFD)

(-) 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:263
 aligned with Q93PQ0_9ENTR | Q93PQ0 from UniProtKB/TrEMBL  Length:295

    Alignment length:263
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292   
         Q93PQ0_9ENTR    33 DVQQVQKKLAALEKQSGGRLGVALINTADNSQVLYRADERFAMCSTSKVMTAAAVLKQSETHDGILQQKMTIKKADLTNWNPVTEKYVGNTMTLAELSAATLQYSDNTAMNKLLAHLGGPGNVTAFARSIGDTTFRLDRKEPELNTAIPGDERDTTSPLAMAKSLRKLTLGDALAGPQRAQLVDWLKGNTTGGQSIRAGLPAHWVVGDKTGAGDYGTTNDIAVIWPEDRAPLVLVTYFTQPQQDAKWRKDVLAAAAKIVTEGK 295
               SCOP domains d3bfda_ A: automated matches                                                                                                                                                                                                                                            SCOP domains
               CATH domains 3bfdA00 A:25-290 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                                                CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhh.eeeeeeee.....eeee.....ee...hhhhhhhhhhhhhh....hhhh.eeeehhhhh.....hhhhhh.eeeehhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhh........eehhhhhhhhhhhhhh....hhhhhhhhhhhhhh......hhhhhh....eeeeeeeee...eeeeeeeee......eeeeeeee........hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3bfd A  25 DVQQVQKKLAALEKQSGGRLGVALINTADNSQVLYRADERFAMCSTSKVMTAAAVLKQSETHDGILQQKMTIKKADLTNWNPVTEKYVGNTMTLAELSAATLQYSDNTAMNKLLAHLGGPGNVTAFARSIGDTTFRLDRKEPELNTAIPGDERDTTSPLAMAKSLRKLTLGDALAGPQRAQLVDWLKGNTTGGQSIRAGLPAHWVVGDKTGACDYGTTNDIAVIWPEDRAPLVLVTYFTQPQQDAKWRKDVLAAAAKIVTEGK 290
                                    34        44        54  ||    65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235  ||   246     ||257       267       277       287   
                                                           57|                                                                                                                                                                                238|         252|                                    
                                                            59                                                                                                                                                                                 240          254                                    

Chain B from PDB  Type:PROTEIN  Length:263
 aligned with Q93PQ0_9ENTR | Q93PQ0 from UniProtKB/TrEMBL  Length:295

    Alignment length:263
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292   
         Q93PQ0_9ENTR    33 DVQQVQKKLAALEKQSGGRLGVALINTADNSQVLYRADERFAMCSTSKVMTAAAVLKQSETHDGILQQKMTIKKADLTNWNPVTEKYVGNTMTLAELSAATLQYSDNTAMNKLLAHLGGPGNVTAFARSIGDTTFRLDRKEPELNTAIPGDERDTTSPLAMAKSLRKLTLGDALAGPQRAQLVDWLKGNTTGGQSIRAGLPAHWVVGDKTGAGDYGTTNDIAVIWPEDRAPLVLVTYFTQPQQDAKWRKDVLAAAAKIVTEGK 295
               SCOP domains d3bfdb_ B: automated matches                                                                                                                                                                                                                                            SCOP domains
               CATH domains 3bfdB00 B:25-290 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                                                CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhh.eeeeeeee.....eeee.....ee.hhhhhhhhhhhhhhhhh...hhhh.eee...........hhhhhh..eeehhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhh........eehhhhhhhhhhhhhh....hhhhhhhhhhhhhh......hhhhhh....eeeeeeeee...eeeeeeeee......eeeeeeee........hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3bfd B  25 DVQQVQKKLAALEKQSGGRLGVALINTADNSQVLYRADERFAMCSTSKVMTAAAVLKQSETHDGILQQKMTIKKADLTNWNPVTEKYVGNTMTLAELSAATLQYSDNTAMNKLLAHLGGPGNVTAFARSIGDTTFRLDRKEPELNTAIPGDERDTTSPLAMAKSLRKLTLGDALAGPQRAQLVDWLKGNTTGGQSIRAGLPAHWVVGDKTGACDYGTTNDIAVIWPEDRAPLVLVTYFTQPQQDAKWRKDVLAAAAKIVTEGK 290
                                    34        44        54  ||    65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235  ||   246     ||257       267       277       287   
                                                           57|                                                                                                                                                                                238|         252|                                    
                                                            59                                                                                                                                                                                 240          254                                    

Chain C from PDB  Type:PROTEIN  Length:263
 aligned with Q93PQ0_9ENTR | Q93PQ0 from UniProtKB/TrEMBL  Length:295

    Alignment length:263
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292   
         Q93PQ0_9ENTR    33 DVQQVQKKLAALEKQSGGRLGVALINTADNSQVLYRADERFAMCSTSKVMTAAAVLKQSETHDGILQQKMTIKKADLTNWNPVTEKYVGNTMTLAELSAATLQYSDNTAMNKLLAHLGGPGNVTAFARSIGDTTFRLDRKEPELNTAIPGDERDTTSPLAMAKSLRKLTLGDALAGPQRAQLVDWLKGNTTGGQSIRAGLPAHWVVGDKTGAGDYGTTNDIAVIWPEDRAPLVLVTYFTQPQQDAKWRKDVLAAAAKIVTEGK 295
               SCOP domains d3bfdc_ C: automated matches                                                                                                                                                                                                                                            SCOP domains
               CATH domains 3bfdC00 C:25-290 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                                                CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhh.eeeeeeee.....eeee.....ee.hhhhhhhhhhhhhhhh....hhhh.eeeehhhhh.....hhhhhh.eeeehhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhh........eehhhhhhhhhhhhhh....hhhhhhhhhhhhhh......hhhhhh....eeeeeeeee...eeeeeeeee......eeeeeeee........hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3bfd C  25 DVQQVQKKLAALEKQSGGRLGVALINTADNSQVLYRADERFAMCSTSKVMTAAAVLKQSETHDGILQQKMTIKKADLTNWNPVTEKYVGNTMTLAELSAATLQYSDNTAMNKLLAHLGGPGNVTAFARSIGDTTFRLDRKEPELNTAIPGDERDTTSPLAMAKSLRKLTLGDALAGPQRAQLVDWLKGNTTGGQSIRAGLPAHWVVGDKTGACDYGTTNDIAVIWPEDRAPLVLVTYFTQPQQDAKWRKDVLAAAAKIVTEGK 290
                                    34        44        54  ||    65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235  ||   246     ||257       267       277       287   
                                                           57|                                                                                                                                                                                238|         252|                                    
                                                            59                                                                                                                                                                                 240          254                                    

Chain D from PDB  Type:PROTEIN  Length:263
 aligned with Q93PQ0_9ENTR | Q93PQ0 from UniProtKB/TrEMBL  Length:295

    Alignment length:263
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292   
         Q93PQ0_9ENTR    33 DVQQVQKKLAALEKQSGGRLGVALINTADNSQVLYRADERFAMCSTSKVMTAAAVLKQSETHDGILQQKMTIKKADLTNWNPVTEKYVGNTMTLAELSAATLQYSDNTAMNKLLAHLGGPGNVTAFARSIGDTTFRLDRKEPELNTAIPGDERDTTSPLAMAKSLRKLTLGDALAGPQRAQLVDWLKGNTTGGQSIRAGLPAHWVVGDKTGAGDYGTTNDIAVIWPEDRAPLVLVTYFTQPQQDAKWRKDVLAAAAKIVTEGK 295
               SCOP domains d3bfdd_ D: automated matches                                                                                                                                                                                                                                            SCOP domains
               CATH domains 3bfdD00 D:25-290 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                                                CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh.eeeeeeee.....eeee.....ee...hhhhhhhhhhhhhh....hhhh.eeee..........hhhhh..eeeehhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhh........eehhhhhhhhhhhhhh....hhhhhhhhhhhhhh......hhhhhh....eeeeeeeee...eeeeeeeee......eeeeeeee........hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3bfd D  25 DVQQVQKKLAALEKQSGGRLGVALINTADNSQVLYRADERFAMCSTSKVMTAAAVLKQSETHDGILQQKMTIKKADLTNWNPVTEKYVGNTMTLAELSAATLQYSDNTAMNKLLAHLGGPGNVTAFARSIGDTTFRLDRKEPELNTAIPGDERDTTSPLAMAKSLRKLTLGDALAGPQRAQLVDWLKGNTTGGQSIRAGLPAHWVVGDKTGACDYGTTNDIAVIWPEDRAPLVLVTYFTQPQQDAKWRKDVLAAAAKIVTEGK 290
                                    34        44        54  ||    65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235  ||   246     ||257       267       277       287   
                                                           57|                                                                                                                                                                                238|         252|                                    
                                                            59                                                                                                                                                                                 240          254                                    

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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, 4)

Asymmetric Unit

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3BFD)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (Q93PQ0_9ENTR | Q93PQ0)
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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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/TrEMBL
        Q93PQ0_9ENTR | Q93PQ03bfc 3bfe 3bff 3bfg

(-) Related Entries Specified in the PDB File

3bfc CLASS A BETA-LACTAMASE SED-G238C COMPLEXED WITH IMIPENEM
3bfe CLASS A BETA-LACTAMASE SED-1
3bff CLASS A BETA-LACTAMASE SED-G238C COMPLEXED WITH FAROPENEM
3bfg CLASS A BETA-LACTAMASE SED-G238C COMPLEXED WITH MEROPENEM