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(-) Description

Title :  BACILLUS CEREUS METALLO-BETA-LACTAMASE (BCII) ARG (121) CYS MUTANT. SOLVED AT PH5 USING 20MM ZNSO4 IN BUFFER. 1MM DTT WAS USED AS A REDUCING AGENT.
 
Authors :  A. M. Davies, R. M. Rasia, A. J. Vila, B. J. Sutton, S. M. Fabiane
Date :  08 Dec 04  (Deposition) - 31 Mar 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Hydrolase, Zinc, Metallo-Beta-Lactamase, Antibiotic Resistance (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. M. Davies, R. M. Rasia, A. J. Vila, B. J. Sutton, S. M. Fabiane
Effect Of Ph On The Active Site Of An Arg121Cys Mutant Of The Metallo-Beta-Lactamase From Bacillus Cereus: Implications For The Enzyme Mechanism
Biochemistry V. 44 4841 2005
PubMed-ID: 15779910  |  Reference-DOI: 10.1021/BI047709T
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - BETA-LACTAMASE II
    Chains: A, B
    EC Number: 3.5.2.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Mutation: YES
    Organism Scientific: BACILLUS CEREUS
    Organism Taxid: 1396
    Strain: 569/H/9
    Synonym: METALLO-BETA-LACTAMASE, PENICILLINASE, CEPHALOSPORINASE

 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  (4, 20)

Asymmetric Unit (4, 20)
No.NameCountTypeFull Name
1AZI1Ligand/IonAZIDE ION
2GOL10Ligand/IonGLYCEROL
3SO45Ligand/IonSULFATE ION
4ZN4Ligand/IonZINC ION
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
1AZI-1Ligand/IonAZIDE ION
2GOL4Ligand/IonGLYCEROL
3SO42Ligand/IonSULFATE ION
4ZN-1Ligand/IonZINC ION
Biological Unit 2 (3, 10)
No.NameCountTypeFull Name
1AZI1Ligand/IonAZIDE ION
2GOL6Ligand/IonGLYCEROL
3SO43Ligand/IonSULFATE ION
4ZN-1Ligand/IonZINC ION

(-) Sites  (20, 20)

Asymmetric Unit (20, 20)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:116 , HIS A:118 , HIS A:196 , HOH A:2235 , HOH A:2236BINDING SITE FOR RESIDUE ZN A1296
02AC2SOFTWARECYS A:221 , HIS A:263 , HOH A:2236 , HOH A:2237 , HOH A:2238BINDING SITE FOR RESIDUE ZN A1297
03AC3SOFTWARESER A:225 , THR A:226 , SER A:227 , GLY A:264 , GLU A:265 , HOH A:2239 , HOH A:2240 , HOH A:2241BINDING SITE FOR RESIDUE SO4 A1298
04AC4SOFTWARELYS A:93 , GLU A:97 , ARG A:131 , ILE A:256 , LYS A:280 , HOH A:2060 , HOH A:2068BINDING SITE FOR RESIDUE SO4 A1299
05AC5SOFTWAREHIS B:196 , LYS B:224 , GLY B:232 , ASN B:233 , ZN B:1299 , HOH B:2240 , HOH B:2241BINDING SITE FOR RESIDUE AZI B1295
06AC6SOFTWAREHIS B:116 , HIS B:118 , HIS B:196 , HOH B:2241 , HOH B:2244BINDING SITE FOR RESIDUE ZN B1298
07AC7SOFTWAREASP B:120 , CYS B:221 , HIS B:263 , AZI B:1295 , HOH B:2244 , HOH B:2245BINDING SITE FOR RESIDUE ZN B1299
08AC8SOFTWARESER B:225 , THR B:226 , SER B:227 , GLY B:264 , GLU B:265 , HOH B:2217 , HOH B:2246 , HOH B:2247BINDING SITE FOR RESIDUE SO4 B1300
09AC9SOFTWARELYS B:181 , LYS B:186 , ARG B:252 , HOH B:2248BINDING SITE FOR RESIDUE SO4 B1301
10BC1SOFTWAREASN B:49 , LYS B:50 , HOH B:2174BINDING SITE FOR RESIDUE SO4 B1302
11BC2SOFTWARELYS A:148 , GLU B:97 , ARG B:107 , ARG B:131BINDING SITE FOR RESIDUE GOL A1292
12BC3SOFTWAREASN A:215BINDING SITE FOR RESIDUE GOL A1293
13BC4SOFTWARELYS A:186 , GLN A:210BINDING SITE FOR RESIDUE GOL A1294
14BC5SOFTWAREALA A:228 , LYS A:229 , ASP A:230 , HOH A:2177 , HOH A:2234BINDING SITE FOR RESIDUE GOL A1295
15BC6SOFTWARESER B:227 , ALA B:228 , LYS B:229 , ASP B:230 , HOH B:2236BINDING SITE FOR RESIDUE GOL B1292
16BC7SOFTWAREASP B:88 , ASP B:89 , LYS B:90 , HOH B:2104BINDING SITE FOR RESIDUE GOL B1293
17BC8SOFTWAREASN B:255 , GOL B:1296 , HOH B:2238 , HOH B:2239BINDING SITE FOR RESIDUE GOL B1294
18BC9SOFTWARETRP B:204 , ARG B:252 , TYR B:253 , ARG B:254 , ASN B:255 , GOL B:1294 , HOH B:2242BINDING SITE FOR RESIDUE GOL B1296
19CC1SOFTWARELYS B:129 , GLU B:168 , GLU B:169BINDING SITE FOR RESIDUE GOL B1297
20CC2SOFTWARELYS B:50 , LYS B:103 , HOH B:2031 , HOH B:2249 , HOH B:2250BINDING SITE FOR RESIDUE GOL B1303

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2BFL)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 4)

Asymmetric Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BETA_LACTAMASE_B_1PS00743 Beta-lactamases class B signature 1.BLA2_BACCE113-132
 		  2A:113-133
B:113-133
2BETA_LACTAMASE_B_2PS00744 Beta-lactamases class B signature 2.BLA2_BACCE189-201
 		  2A:209-224
B:209-224
Biological Unit 1 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BETA_LACTAMASE_B_1PS00743 Beta-lactamases class B signature 1.BLA2_BACCE113-132
 		  1A:113-133
-
2BETA_LACTAMASE_B_2PS00744 Beta-lactamases class B signature 2.BLA2_BACCE189-201
 		  1A:209-224
-
Biological Unit 2 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BETA_LACTAMASE_B_1PS00743 Beta-lactamases class B signature 1.BLA2_BACCE113-132
 		  1-
B:113-133
2BETA_LACTAMASE_B_2PS00744 Beta-lactamases class B signature 2.BLA2_BACCE189-201
 		  1-
B:209-224

(-) Exons   (0, 0)

(no "Exon" information available for 2BFL)

(-) 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:216
 aligned with BLA2_BACCE | P04190 from UniProtKB/Swiss-Prot  Length:257

    Alignment length:221
                                    46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256 
           BLA2_BACCE    37 TVIKNETGTISISQLNKNVWVHTELGSFNGEAVPSNGLVLNTSKGLVLVDSSWDDKLTKELIEMVEKKFQKRVTDVIITHAHADRIGGIKTLKERGIKAHSTALTAELAKKNGYEEPLGDLQTVTNLKFGNMKVETFYPGKGHTEDNIVVWLPQYNILVGGCLVKSTSAKDLGNVADAYVNEWSTSIENVLKRYRNINAVVPGHGEVGDKGLLLHTLDLLK 257
               SCOP domains d2bfla_ A: automated match     es                                                                                                                                                                                             SCOP domains
               CATH domains 2bflA00 A:33-291 Metallo-b     eta-lactamase, chain A                                                                                                                                                                         CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.....eeeeeee..eeeeeee.-----..eeeeeeeee..eeeee....hhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhh..eee.hhhhhhhhhhh...........eeeeee..eeeeee...........eee.....eeeeehhh..............hhhhhhhhhhhhhhhh....eeee.......hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------BETA_LACTAMASE_B_1  --------------------------------------------------------BETA_LACTAMAS-------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bfl A  33 TVIKNETGTISISQLNKNVWVHTELG-----AVPSNGLVLNTSKGLVLVDSSWDDKLTKELIEMVEKKFQKRVTDVIITHAHADCIGGIKTLKERGIKAHSTALTAELAKKNGYEEPLGDLQTVTNLKFGNMKVETFYPGKGHTEDNIVVWLPQYNILVGGCLVKSTSAKDLGNVADAYVNEWSTSIENVLKRYRNINAVVPGHGEVGDKGLLLHTLDLLK 291
                                    42  ||    53     |   - |      74        84        94     ||105 ||    116       126    || 137       147  ||   173       183       193       203 || || 219       229       239       249       259     ||280       290 
                                       45|          59    66                               100|  107|                   131|              150|                                   205| ||                                               265|              
                                        47                                                  102   109                    133               167                                    209 ||                                                277              
                                                                                                                                                                                    211|                                                                 
                                                                                                                                                                                     215                                                                 


Chain B from PDB  Type:PROTEIN  Length:220
 aligned with BLA2_BACCE | P04190 from UniProtKB/Swiss-Prot  Length:257

    Alignment length:222
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255  
           BLA2_BACCE    36 KTVIKNETGTISISQLNKNVWVHTELGSFNGEAVPSNGLVLNTSKGLVLVDSSWDDKLTKELIEMVEKKFQKRVTDVIITHAHADRIGGIKTLKERGIKAHSTALTAELAKKNGYEEPLGDLQTVTNLKFGNMKVETFYPGKGHTEDNIVVWLPQYNILVGGCLVKSTSAKDLGNVADAYVNEWSTSIENVLKRYRNINAVVPGHGEVGDKGLLLHTLDLLK 257
               SCOP domains d2bflb_ B: automated matches                                                                                                                                                                                                   SCOP domains
               CATH domains 2bflB00 B:32-291 Metallo-beta-  lactamase, chain A                                                                                                                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eee.....eeeeeee..eeeeeeee...--.eeeeeeeeee..eeeee....hhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhh..eee.hhhhhhhhhhh...........eeeeee..eeeeee...........eee.....eeeeehhh..............hhhhhhhhhhhhhhhh....eeee.......hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------BETA_LACTAMASE_B_1  --------------------------------------------------------BETA_LACTAMAS-------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2bfl B  32 KTVIKNETGTISISQLNKNVWVHTELGSFG--AVPSNGLVLNTSKGLVLVDSSWDDKLTKELIEMVEKKFQKRVTDVIITHAHADCIGGIKTLKERGIKAHSTALTAELAKKNGYEEPLGDLQTVTNLKFGNMKVETFYPGKGHTEDNIVVWLPQYNILVGGCLVKSTSAKDLGNVADAYVNEWSTSIENVLKRYRNINAVVPGHGEVGDKGLLLHTLDLLK 291
                                    41   ||   52        62  |     73        83        93      |104  ||   115       125     ||136       146   ||  172       182       192       202  || ||218       228       238       248       258      |279       289  
                                        45|             62 66                               100|  107|                   131|              150|                                   205| ||                                               265|              
                                         47                                                  102   109                    133               167                                    209 ||                                                277              
                                                                                                                                                                                     211|                                                                 
                                                                                                                                                                                      215
   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
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2BFL)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (BLA2_BACCE | P04190)
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.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0017001    antibiotic catabolic process    The chemical reactions and pathways resulting in the breakdown of antibiotic, a substance produced by or derived from certain fungi, bacteria, and other organisms, that can destroy or inhibit the growth of other microorganisms.
    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:0042597    periplasmic space    The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

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  2bfl
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  BLA2_BACCE | P04190
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  3.5.2.6
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 Related Entries

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

UniProtKB/Swiss-Prot
        BLA2_BACCE | P04190: 1bc2 1bmc 1bvt 1dxk 1mqo 2bc2 2bfk 2bfz 2bg2 2bg6 2bg7 2bg8 2bga 2m5c 2m5d 2nxa 2nyp 2nze 2nzf 2uyx 3bc2 3fcz 3i0v 3i11 3i13 3i14 3i15 3knr 3kns 4c09 4c1c 4c1h 4nq4 4nq5 4nq6 4nq7 4tyt 5fqa 5fqb 5jmx 5w8w

(-) Related Entries Specified in the PDB File

1bc2 ZN-DEPENDENT METALLO-BETA-LACTAMASE FROM BACILLUS CEREUS
1bmc STRUCTURE OF A ZINC METALLO-BETA-LACTAMASE FROM BACILLUS CEREUS
1bvt METALLO-BETA-LACTAMASE FROM BACILLUS CEREUS 569/H/9
1dxk METALLO-BETA-LACTAMASE FROM BACILLUS CEREUS 569/H/9 C168S MUTANT
1mqo METALLO-BETA-LACTAMASE BCII CD SUBSTITUTED FROM BACILLUSCEREUS AT 1.35 ANGSTROMS RESOLUTION
2bc2 METALLO BETA-LACTAMASE II FROM BACILLUS CEREUS 569/H/9 AT PH 6.0, TRIGONAL CRYSTAL FORM
2bfk BACILLUS CEREUS METALLO-BETA-LACTAMASE (BCII ) ARG (121) CYS MUTANT. SOLVED AT PH7 USING 20MM ZNSO4 IN BUFFER. 1MM DTT WAS USED AS A REDUCING AGENT
2bfz BACILLUS CEREUS METALLO-BETA-LACTAMASE (BCII ) ARG (121) CYS MUTANT. SOLVED AT PH4.5 USING 20MM ZNSO4 IN BUFFER. 1MM DTT WAS USED AS A REDUCING AGENT. CYS221 IS OXIDIZED.
2bg2 BACILLUS CEREUS METALLO-BETA-LACTAMASE (BCII ) ARG (121) CYS MUTANT. SOLVED AT PH4.5 USING 20MM ZNSO4 IN THE BUFFER. 1MM DTT AND 1MM TCEP-HCL WERE USED AS REDUCING AGENTS. CYS221 IS REDUCED.
2bg6 BACILLUS CEREUS METALLO-BETA-LACTAMASE (BCII ) ARG (121) CYS MUTANT. SOLVED AT PH5 USING 20 MICROMOLAR ZNSO4 IN THE BUFFER. 1MM DTT WAS USED AS A REDUCING AGENT. CYS221 IS OXIDIZED.
2bg7 BACILLUS CEREUS METALLO-BETA-LACTAMASE (BCII ) ARG (121) CYS MUTANT. SOLVED AT PH4.5 USING 20 MICROMOLAR ZNSO4 IN THE BUFFER. 1MM DTT WAS USED AS A REDUCING AGENT. CYS221 IS OXIDIZED.
2bg8 BACILLUS CEREUS METALLO-BETA-LACTAMASE (BCII ) ARG (121) CYS MUTANT. SOLVED AT PH4.5 USING 20 MICROMOLAR ZNSO4 IN THE BUFFER. 1MM DTT AND 1MM TCEP-HCL WERE USED AS REDUCING AGENTS.
2bga BACILLUS CEREUS METALLO-BETA-LACTAMASE (BCII ) ARG (121) CYS MUTANT. SOLVED AT PH7 USING 20 MICROMOLAR ZNSO4 IN THE BUFFER. 1MM DTT WAS USED AS A REDUCING AGENT. CYS221 IS OXIDIZED.
3bc2 METALLO BETA-LACTAMASE II FROM BACILLUS CEREUS 569/H/9 AT PH 6.0, MONOCLINIC CRYSTAL FORM