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(-) Description

Title :  CRYSTAL STRUCTURE OF FLUORESCEIN-LABELED CLASS A -BETA LACTAMASE PENP IN COMPLEX WITH CEFOTAXIME
 
Authors :  Y. X. Zhao, Y. C. Leung, W. T. Wong
Date :  07 Mar 10  (Deposition) - 16 Mar 11  (Release) - 24 Aug 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Beta-Lactamase, Fluorophore, Biosensor, Hydrolase, Cefotaxime, Antibiotic Resistance, Cell Membrane, Lipoprotein, Membrane, Palmitate (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. X. Zhao, Y. C. Leung, W. T. Wong
Crystal Structure Of Fluorescein-Labeled Class A -Beta Lactamase Penp In Complex With Cefotaxime
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - BETA-LACTAMASE
    ChainsA, B
    EC Number3.5.2.6
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPRSET
    Expression System StrainBL21(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentRESIDUES 47-301
    GenePENP
    MutationYES
    Organism ScientificBACILLUS LICHENIFORMIS
    Organism Taxid1402
    Strain749/C
    SynonymPENICILLINASE, LARGE EXOPENICILLINASE, SMALL EXOPENICILLINASE

 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  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1PCZ2Ligand/Ion(2R)-2-[(1R)-1-{[(2Z)-2-(2-AMINO-1,3-THIAZOL-4-YL)-2-(METHOXYIMINO)ACETYL]AMINO}-2-OXOETHYL]-5-METHYLIDENE-5,6-DIHYDRO-2H-1,3-THIAZINE-4-CARBOXYLIC ACID
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1PCZ1Ligand/Ion(2R)-2-[(1R)-1-{[(2Z)-2-(2-AMINO-1,3-THIAZOL-4-YL)-2-(METHOXYIMINO)ACETYL]AMINO}-2-OXOETHYL]-5-METHYLIDENE-5,6-DIHYDRO-2H-1,3-THIAZINE-4-CARBOXYLIC ACID
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1PCZ1Ligand/Ion(2R)-2-[(1R)-1-{[(2Z)-2-(2-AMINO-1,3-THIAZOL-4-YL)-2-(METHOXYIMINO)ACETYL]AMINO}-2-OXOETHYL]-5-METHYLIDENE-5,6-DIHYDRO-2H-1,3-THIAZINE-4-CARBOXYLIC ACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:70 , LYS A:73 , SER A:130 , ASN A:132 , THR A:235 , GLY A:236 , ALA A:237 , ARG A:244BINDING SITE FOR RESIDUE PCZ A 1
2AC2SOFTWAREALA B:69 , SER B:70 , ASN B:104 , SER B:130 , ASN B:132 , THR B:235 , GLY B:236 , ALA B:237 , SER B:240BINDING SITE FOR RESIDUE PCZ B 1

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3M2K)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3M2K)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3M2K)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BETA_LACTAMASE_APS00146 Beta-lactamase class-A active site.BLAC_BACLI82-97
 
  2A:66-81
B:66-81
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BETA_LACTAMASE_APS00146 Beta-lactamase class-A active site.BLAC_BACLI82-97
 
  1A:66-81
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BETA_LACTAMASE_APS00146 Beta-lactamase class-A active site.BLAC_BACLI82-97
 
  1-
B:66-81

(-) Exons   (0, 0)

(no "Exon" information available for 3M2K)

(-) 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:245
 aligned with BLAC_BACLI | P00808 from UniProtKB/Swiss-Prot  Length:307

    Alignment length:256
                                    57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297      
           BLAC_BACLI    48 DDFAKLEEQFDAKLGIFALDTGTNRTVAYRPDERFAFASTIKALTVGVLLQQKSIEDLNQRITYTRDDLVNYNPITEKHVDTGMTLKELADASLRYSDNAAQNLILKQIGGPESLKKELRKIGDEVTNPERFEPELNEVNPGETQDTSTARALVTSLRAFALEDKLPSEKRELLIDWMKRNTTGDALIRAGVPDGWEVADKTGAASYGTRNDIAIIWPPKGDPVVLAVLSSRDKKDAKYDDKLIAEATKVVMKALN 303
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhh....eeeeeeee.....eeee....eee...hhhhhhhhhhhhh...hhhh.ee............hhhhh....eehhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh.........-----------.....eeehhhhhhhhhhhhh....hhhhhhhhhhhhhh......hhhhh.....eeeeeeeee...eeeeeeeee......eeeeeeee.........hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------BETA_LACTAMASE_A-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3m2k A  31 DDFAKLEEQFDAKLGIFALDTGTNRTVAYRPDERFAFASTIKALTVGVLLQQKSIEDLNQRITYTRDDLVNYNPITEKHVDTGMTLKELADASLRYSDNAAQNLILKQIGGPESLKKELRKIGDEVTNPE-----------GETQDTSTARALVTSLRAFALEDKLPSEKRELLIDWMKRNTTGDALIRAGVPDGWEVADKTGAASYGTRNDIAIIWPPKGDPVVLAVLSSRDKKDAKYDDKLIAEATKVVMKALN 291
                                    40        50      ||61        71        81 ||     93       103       113       123       133       143       153       163         - |     183       193       203       213       223       233    || 244       255       265       275       285      
                                                     57|                      83|                                                                          163         175                                                            238|         252|                                     
                                                      59                       86                                                                                                                                                      240          254                                     

Chain B from PDB  Type:PROTEIN  Length:251
 aligned with BLAC_BACLI | P00808 from UniProtKB/Swiss-Prot  Length:307

    Alignment length:257
                                    56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       
           BLAC_BACLI    47 KDDFAKLEEQFDAKLGIFALDTGTNRTVAYRPDERFAFASTIKALTVGVLLQQKSIEDLNQRITYTRDDLVNYNPITEKHVDTGMTLKELADASLRYSDNAAQNLILKQIGGPESLKKELRKIGDEVTNPERFEPELNEVNPGETQDTSTARALVTSLRAFALEDKLPSEKRELLIDWMKRNTTGDALIRAGVPDGWEVADKTGAASYGTRNDIAIIWPPKGDPVVLAVLSSRDKKDAKYDDKLIAEATKVVMKALN 303
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---Beta-lactamase-3m2kB01 B:33-284                                                                                                                                                                                                                        ------- Pfam domains (1)
           Pfam domains (2) ---Beta-lactamase-3m2kB02 B:33-284                                                                                                                                                                                                                        ------- Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhh.eeeeeeee.....eeee....eee...hhhhhhhhhhhhh...hhhh.ee............hhhhh....eehhhhhhhhhhh.hhhhhhhhhhhh.hhhhhhhhhhh...........------........eeehhhhhhhhhhhhh....hhhhhhhhhhhhhh.......hhhhh....eeeeeeeee...eeeeeeeee......eeeeeeee.........hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------BETA_LACTAMASE_A-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3m2k B  30 KDDFAKLEEQFDAKLGIFALDTGTNRTVAYRPDERFAFASTIKALTVGVLLQQKSIEDLNQRITYTRDDLVNYNPITEKHVDTGMTLKELADASLRYSDNAAQNLILKQIGGPESLKKELRKIGDEVTNPERF------VNPGETQDTSTARALVTSLRAFALEDKLPSEKRELLIDWMKRNTTGDALIRAGVPDGWEVADKTGAASYGTRNDIAIIWPPKGDPVVLAVLSSRDKKDAKYDDKLIAEATKVVMKALN 291
                                    39        49       |60        70        80  ||    92       102       112       122       132       142       152       162  |    172       182       192       202       212       222       232     ||243       254       264       274       284       
                                                      57|                      83|                                                                            165    172                                                               238|         252|                                     
                                                       59                       86                                                                                                                                                      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  (0, 0)

(no "SCOP Domain" information available for 3M2K)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3M2K)

(-) Pfam Domains  (1, 2)

Asymmetric Unit

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (BLAC_BACLI | P00808)
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.
cellular component
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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 Related Entries

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        BLAC_BACLI | P008081i2s 1i2w 1mbl 1w7f 2blm 2wk0 2y91 3b3x 3ly3 3ly4 3m2j 3sh7 3sh8 3sh9 3soi 4blm 4m3k 4n1h 4n92 4n9k 4n9l 5ghx 5ghy 5ghz

(-) Related Entries Specified in the PDB File

3ly3 3ly4 3m2j