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(-) Description

Title :  CRYSTAL STRUCTURE OF THE CLASS A BETA-LACTAMASE BS3 INHIBITED BY 6-BETA-IODOPENICILLANATE.
 
Authors :  E. Sauvage, A. Zervosen, G. Dive, R. Herman, F. Kerff, A. Amoroso, E. Fon R. F. Pratt, A. Luxen, P. Charlier
Date :  03 Jun 09  (Deposition) - 01 Dec 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Hydrolase, Beta- Lactamase, Iodopenicillanate, Antibiotic Resistance, Bacillus Licheniformis (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  E. Sauvage, A. Zervosen, G. Dive, R. Herman, A. Amoroso, B. Joris, E. Fonze, R. F. Pratt, A. Luxen, P. Charlier, F. Kerff
Structural Basis Of The Inhibition Of Class A Beta- Lactamases And Penicillin-Binding Proteins By 6- Beta-Iodopenicillanate.
J. Am. Chem. Soc. V. 131 15262 2009
PubMed-ID: 19919161  |  Reference-DOI: 10.1021/JA9051526

(-) Compounds

Molecule 1 - BETA-LACTAMASE
    ChainsA, B
    EC Number3.5.2.6
    Organism ScientificBACILLUS LICHENIFORMIS
    Organism Taxid1402
    StrainBS3

 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  (5, 10)

Asymmetric Unit (5, 10)
No.NameCountTypeFull Name
1BIY2Ligand/Ion(3S)-2,2-DIMETHYL-3,4-DIHYDRO-2H-1,4-THIAZINE-3,6-DICARBOXYLIC ACID
2CIT1Ligand/IonCITRIC ACID
3CL2Ligand/IonCHLORIDE ION
4EOH4Ligand/IonETHANOL
5SO41Ligand/IonSULFATE ION
Biological Unit 1 (3, 5)
No.NameCountTypeFull Name
1BIY1Ligand/Ion(3S)-2,2-DIMETHYL-3,4-DIHYDRO-2H-1,4-THIAZINE-3,6-DICARBOXYLIC ACID
2CIT-1Ligand/IonCITRIC ACID
3CL-1Ligand/IonCHLORIDE ION
4EOH3Ligand/IonETHANOL
5SO41Ligand/IonSULFATE ION
Biological Unit 2 (3, 3)
No.NameCountTypeFull Name
1BIY1Ligand/Ion(3S)-2,2-DIMETHYL-3,4-DIHYDRO-2H-1,4-THIAZINE-3,6-DICARBOXYLIC ACID
2CIT1Ligand/IonCITRIC ACID
3CL-1Ligand/IonCHLORIDE ION
4EOH1Ligand/IonETHANOL
5SO4-1Ligand/IonSULFATE ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREALA A:69 , SER A:70 , ASN A:104 , TYR A:105 , SER A:130 , ASN A:132 , ASN A:170 , GLY A:236 , ALA A:237 , CL A:301 , HOH A:2116 , HOH A:2201BINDING SITE FOR RESIDUE BIY A 300
02AC2SOFTWARESER A:70 , SER A:130 , LYS A:234 , THR A:235 , BIY A:300BINDING SITE FOR RESIDUE CL A 301
03AC3SOFTWAREALA B:69 , SER B:70 , ASN B:104 , TYR B:105 , SER B:130 , ASN B:132 , ASN B:170 , GLY B:236 , ALA B:237 , CL B:301 , HOH B:2076 , HOH B:2156 , HOH B:2157BINDING SITE FOR RESIDUE BIY B 300
04AC4SOFTWARESER B:70 , SER B:130 , LYS B:234 , THR B:235 , BIY B:300BINDING SITE FOR RESIDUE CL B 301
05AC5SOFTWAREASN A:161 , GLU A:163 , GLU A:176 , THR A:177 , GLN A:178 , HOH A:2120 , GLU B:171 , ASN B:173 , HOH B:2158BINDING SITE FOR RESIDUE CIT B1292
06AC6SOFTWARELYS A:140 , GLY A:143 , GLY A:144 , PHE A:165 , HOH A:2202 , HOH A:2203 , LYS B:140 , PHE B:165BINDING SITE FOR RESIDUE SO4 A1292
07AC7SOFTWAREALA A:42 , ARG A:61BINDING SITE FOR RESIDUE EOH A1293
08AC8SOFTWAREASP A:32 , LYS A:35 , HOH A:2204BINDING SITE FOR RESIDUE EOH A1294
09AC9SOFTWAREASN A:173 , GLU A:176BINDING SITE FOR RESIDUE EOH A1295
10BC1SOFTWAREARG B:65 , VAL B:172 , HOH B:2035 , HOH B:2084 , HOH B:2120 , HOH B:2160BINDING SITE FOR RESIDUE EOH B1293

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2WK0)

(-) Cis Peptide Bonds  (2, 2)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2WK0)

(-) 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 2WK0)

(-) 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:256
 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 d2wk0a_ A: automated matches                                                                                                                                                                                                                                     SCOP domains
               CATH domains 2wk0A00 A:31-291 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                                         CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhh.eeeeeeee.....eeee....eee...hhhhhhhhhhhhhh.hhhhh.ee............hhhhh....eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhh........eeehhhhhhhhhhhhh....hhhhhhhhhhhhhh......hhhhhh....eeeeeeeee...eeeeeeeee......eeeeeeee.........hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------BETA_LACTAMASE_A-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wk0 A  31 DDFAKLEEQFDAKLGIFALDTGTNRTVTYRPDERFAFASTIKALTVGVLLQQKSIEDLNQRITYTRDDLVNYNPITEKHVDTGMTLKELADASLRYSDNTAQNLILKQIGGPESLKKELRKIGDEVTNPERFEPELNEVNPGETQDTSTARALATSLQAFALEDKLPSEKRELLIDWMKRNTTGDALIRAGVPEGWEVADKTGAGSYGTRNDIAIIWPPKGDPVVLAVLSSRDKKDAKYDDKLIAEATKVVVKALN 291
                                    40        50      ||61        71        81 ||     93       103       113       123       133       143       153       163       173       183       193       203       213       223       233    || 244       255       265       275       285      
                                                     57|                      83|                                                                                                                                                     238|         252|                                     
                                                      59                       86                                                                                                                                                      240          254                                     

Chain A from PDB  Type:PROTEIN  Length:256
 aligned with P94458_BACLI | P94458 from UniProtKB/TrEMBL  Length:265

    Alignment length:256
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255      
         P94458_BACLI     6 DDFAKLEEQFDAKLGIFALDTGTNRTVTYRPDERFAFASTIKALTVGVLLQQKSIEDLNQRITYTRDDLVNYNPITEKHVDTGMTLKELADASLRYSDNTAQNLILKQIGGPESLKKELRKIGDEVTNPERFEPELNEVNPGETQDTSTARALATSLQAFALEDKLPSEKRELLIDWMKRNTTGDALIRAGVPEGWEVADKTGAGSYGTRNDIAIIWPPKGDPVVLAVLSSRDKKDAKYDDKLIAEATKVVVKALN 261
               SCOP domains d2wk0a_ A: automated matches                                                                                                                                                                                                                                     SCOP domains
               CATH domains 2wk0A00 A:31-291 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                                         CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhh.eeeeeeee.....eeee....eee...hhhhhhhhhhhhhh.hhhhh.ee............hhhhh....eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhh........eeehhhhhhhhhhhhh....hhhhhhhhhhhhhh......hhhhhh....eeeeeeeee...eeeeeeeee......eeeeeeee.........hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wk0 A  31 DDFAKLEEQFDAKLGIFALDTGTNRTVTYRPDERFAFASTIKALTVGVLLQQKSIEDLNQRITYTRDDLVNYNPITEKHVDTGMTLKELADASLRYSDNTAQNLILKQIGGPESLKKELRKIGDEVTNPERFEPELNEVNPGETQDTSTARALATSLQAFALEDKLPSEKRELLIDWMKRNTTGDALIRAGVPEGWEVADKTGAGSYGTRNDIAIIWPPKGDPVVLAVLSSRDKKDAKYDDKLIAEATKVVVKALN 291
                                    40        50      ||61        71        81 ||     93       103       113       123       133       143       153       163       173       183       193       203       213       223       233    || 244       255       265       275       285      
                                                     57|                      83|                                                                                                                                                     238|         252|                                     
                                                      59                       86                                                                                                                                                      240          254                                     

Chain B from PDB  Type:PROTEIN  Length:256
 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 d2wk0b_ B: automated matches                                                                                                                                                                                                                                     SCOP domains
               CATH domains 2wk0B00 B:31-291 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                                         CATH domains
           Pfam domains (1) --Beta-lactamase-2wk0B01 B:33-284                                                                                                                                                                                                                        ------- Pfam domains (1)
           Pfam domains (2) --Beta-lactamase-2wk0B02 B:33-284                                                                                                                                                                                                                        ------- Pfam domains (2)
         Sec.struct. author hhhhhhhhhhh.eeeeeeee.....eeee.....ee...hhhhhhhhhhhhhh..hhhh.ee..hhhhh.....hhhhh....eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhh........eehhhhhhhhhhhhhh....hhhhhhhhhhhhhh......hhhhhh....eeeeeeeee...eeeeeeeee......eeeeeeee........hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------BETA_LACTAMASE_A-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wk0 B  31 DDFAKLEEQFDAKLGIFALDTGTNRTVTYRPDERFAFASTIKALTVGVLLQQKSIEDLNQRITYTRDDLVNYNPITEKHVDTGMTLKELADASLRYSDNTAQNLILKQIGGPESLKKELRKIGDEVTNPERFEPELNEVNPGETQDTSTARALATSLQAFALEDKLPSEKRELLIDWMKRNTTGDALIRAGVPEGWEVADKTGAGSYGTRNDIAIIWPPKGDPVVLAVLSSRDKKDAKYDDKLIAEATKVVVKALN 291
                                    40        50      ||61        71        81 ||     93       103       113       123       133       143       153       163       173       183       193       203       213       223       233    || 244       255       265       275       285      
                                                     57|                      83|                                                                                                                                                     238|         252|                                     
                                                      59                       86                                                                                                                                                      240          254                                     

Chain B from PDB  Type:PROTEIN  Length:256
 aligned with P94458_BACLI | P94458 from UniProtKB/TrEMBL  Length:265

    Alignment length:256
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255      
         P94458_BACLI     6 DDFAKLEEQFDAKLGIFALDTGTNRTVTYRPDERFAFASTIKALTVGVLLQQKSIEDLNQRITYTRDDLVNYNPITEKHVDTGMTLKELADASLRYSDNTAQNLILKQIGGPESLKKELRKIGDEVTNPERFEPELNEVNPGETQDTSTARALATSLQAFALEDKLPSEKRELLIDWMKRNTTGDALIRAGVPEGWEVADKTGAGSYGTRNDIAIIWPPKGDPVVLAVLSSRDKKDAKYDDKLIAEATKVVVKALN 261
               SCOP domains d2wk0b_ B: automated matches                                                                                                                                                                                                                                     SCOP domains
               CATH domains 2wk0B00 B:31-291 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                                         CATH domains
           Pfam domains (1) --Beta-lactamase-2wk0B01 B:33-284                                                                                                                                                                                                                        ------- Pfam domains (1)
           Pfam domains (2) --Beta-lactamase-2wk0B02 B:33-284                                                                                                                                                                                                                        ------- Pfam domains (2)
         Sec.struct. author hhhhhhhhhhh.eeeeeeee.....eeee.....ee...hhhhhhhhhhhhhh..hhhh.ee..hhhhh.....hhhhh....eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhh........eehhhhhhhhhhhhhh....hhhhhhhhhhhhhh......hhhhhh....eeeeeeeee...eeeeeeeee......eeeeeeee........hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wk0 B  31 DDFAKLEEQFDAKLGIFALDTGTNRTVTYRPDERFAFASTIKALTVGVLLQQKSIEDLNQRITYTRDDLVNYNPITEKHVDTGMTLKELADASLRYSDNTAQNLILKQIGGPESLKKELRKIGDEVTNPERFEPELNEVNPGETQDTSTARALATSLQAFALEDKLPSEKRELLIDWMKRNTTGDALIRAGVPEGWEVADKTGAGSYGTRNDIAIIWPPKGDPVVLAVLSSRDKKDAKYDDKLIAEATKVVVKALN 291
                                    40        50      ||61        71        81 ||     93       103       113       123       133       143       153       163       173       183       193       203       213       223       233    || 244       255       265       275       285      
                                                     57|                      83|                                                                                                                                                     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  (1, 2)

Asymmetric Unit

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit

(-) Gene Ontology  (6, 10)

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.

Chain A,B   (P94458_BACLI | P94458)
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/Swiss-Prot
        BLAC_BACLI | P008081i2s 1i2w 1mbl 1w7f 2blm 2y91 3b3x 3ly3 3ly4 3m2j 3m2k 3sh7 3sh8 3sh9 3soi 4blm 4m3k 4n1h 4n92 4n9k 4n9l 5ghx 5ghy 5ghz
        P94458_BACLI | P944581w7f 2y91 3b3x
UniProtKB/TrEMBL
        P94458_BACLI | P944582x71 4a5r

(-) Related Entries Specified in the PDB File

1w7f CRYSTAL STRUCTURE OF THE CLASS A BETA- LACTAMASE BS3 INHIBITED WITH ISOCITRATE