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(-) Description

Title :  METALLO-BETA-LACTAMASE
 
Authors :  A. Carfi, E. Duee, O. Dideberg
Date :  17 Sep 98  (Deposition) - 23 Sep 98  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Beta-Lactamase, Metallo Beta-Lactamase, Zinc, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Carfi, E. Duee, R. Paul-Soto, M. Galleni, J. M. Frere, O. Dideberg
X-Ray Structure Of The Znii Beta-Lactamase From Bacteroides Fragilis In An Orthorhombic Crystal Form.
Acta Crystallogr. , Sect. D V. 54 45 1998
PubMed-ID: 9761816  |  Reference-DOI: 10.1107/S090744499700927X
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN (CLASS B BETA-LACTAMASE)
    Chains: A, B
    EC Number: 3.5.2.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Gene: CCRA
    Expression System Plasmid: PJST241
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Gene: CCRA
    Organism Scientific: BACTEROIDES FRAGILIS
    Organism Taxid: 817
    Other Details: METALLO-BETA-LACTAMASE, CLASS B BETA- LACTAMASE
    Strain: BL21
    Synonym: BETA-LACTAMASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric/Biological Unit (2, 6)
No.NameCountTypeFull Name
1NA2Ligand/IonSODIUM ION
2ZN4Ligand/IonZINC ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:82 , HIS A:84 , HIS A:145 , ZN A:272 , HOH A:276BINDING SITE FOR RESIDUE ZN A 271
02AC2SOFTWAREHIS B:82 , HIS B:84 , HIS B:145 , ZN B:272 , HOH B:278BINDING SITE FOR RESIDUE ZN B 271
03AC3SOFTWAREASP A:86 , CYS A:164 , HIS A:206 , ZN A:271 , HOH A:276 , HOH A:492BINDING SITE FOR RESIDUE ZN A 272
04AC4SOFTWAREASN A:38 , ASP A:52 , ASP A:86 , HOH A:493 , HOH A:494BINDING SITE FOR RESIDUE NA A 275
05AC5SOFTWAREASP B:86 , CYS B:164 , HIS B:206 , ZN B:271 , HOH B:278 , HOH B:474BINDING SITE FOR RESIDUE ZN B 272
06AC6SOFTWAREASN B:38 , ASP B:52 , ASP B:86 , HOH B:279 , HOH B:475BINDING SITE FOR RESIDUE NA B 275
07AS1AUTHORHIS A:82 , HIS A:84 , HIS A:145PROTEIN ZINC LIGANDS
08AS2AUTHORHIS A:206 , CYS A:164 , ASP A:86PROTEIN ZINC LIGANDS
09BS1AUTHORHIS B:82 , HIS B:84 , HIS B:145PROTEIN ZINC LIGANDS
10BS2AUTHORHIS B:206 , CYS B:164 , ASP B:86PROTEIN ZINC LIGANDS

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Lys B:231 -Pro B:232

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BETA_LACTAMASE_B_1PS00743 Beta-lactamases class B signature 1.BLAB_BACFG96-115
 		  2A:79-98
B:79-98
2BETA_LACTAMASE_B_2PS00744 Beta-lactamases class B signature 2.BLAB_BACFG172-184
 		  2A:155-167
B:155-167

(-) Exons   (0, 0)

(no "Exon" information available for 2BMI)

(-) Sequences/Alignments

Asymmetric/Biological 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:228
 aligned with BLAB_BACFG | P25910 from UniProtKB/Swiss-Prot  Length:249

    Alignment length:228
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240        
           BLAB_BACFG    21 SVKISDDISITQLSDKVYTYVSLAEIEGWGMVPSNGMIVINNHQAALLDTPINDAQTEMLVNWVTDSLHAKVTTFIPNHWHGDCIGGLGYLQRKGVQSYANQMTIDLAKEKGLPVPEHGFTDSLTVSLDGMPLQCYYLGGGHATDNIVVWLPTENILFGGCMLKDNQATSIGNISDADVTAWPKTLDKVKAKFPSARYVVPGHGDYGGTELIEHTKQIVNQYIESTSK 248
               SCOP domains d2bmia_ A: Zn metallo-beta-lactamase                                                                                                                                                                                                 SCOP domains
               CATH domains 2bmiA00 A:4-231 Metallo-beta-lactamase, chain A                                                                                                                                                                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
     Sec.struct. author (1) .eeee..eeeeeee..eeeeeeeeee...eeeeeeeeeeee..eeeee.....hhhhhhhhhhhhhh...eeeeee.....hhhh..hhhhhh...eeeeehhhhhhhhhh......eee..eeeeee..eeeeeee.........eeeee....----hhh................hhhhhhhhhhhhhh.....eeee.......hhhhhhhhhhhhhhhhh... Sec.struct. author (1)
     Sec.struct. author (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------eeeee-------------------------------------------------------------------- Sec.struct. author (2)
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------BETA_LACTAMASE_B_1  --------------------------------------------------------BETA_LACTAMAS---------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2bmi A   4 SVKISDDISITQLSDKVYTYVSLAEIEGWGMVPSNGMIVINNHQAALLDTPINDAQTEMLVNWVTDSLHAKVTTFIPNHWHGDCIGGLGYLQRKGVQSYANQMTIDLAKEKGLPVPEHGFTDSLTVSLDGMPLQCYYLGGGHATDNIVVWLPTENILFGGCMLKDNQATSIGNISDADVTAWPKTLDKVKAKFPSARYVVPGHGDYGGTELIEHTKQIVNQYIESTSK 231
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223        


Chain B from PDB  Type:PROTEIN  Length:230
 aligned with BLAB_BACFG | P25910 from UniProtKB/Swiss-Prot  Length:249

    Alignment length:230
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249
           BLAB_BACFG    20 KSVKISDDISITQLSDKVYTYVSLAEIEGWGMVPSNGMIVINNHQAALLDTPINDAQTEMLVNWVTDSLHAKVTTFIPNHWHGDCIGGLGYLQRKGVQSYANQMTIDLAKEKGLPVPEHGFTDSLTVSLDGMPLQCYYLGGGHATDNIVVWLPTENILFGGCMLKDNQATSIGNISDADVTAWPKTLDKVKAKFPSARYVVPGHGDYGGTELIEHTKQIVNQYIESTSKP 249
               SCOP domains d2bmib_ B: Zn metallo-beta-lactamase                                                                                                                                                                                                   SCOP domains
               CATH domains 2bmiB00 B:3-232 Metallo-beta-lactamase, chain A                                                                                                                                                                                        CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
     Sec.struct. author (1) ........eeeeeee..eeeeeeeeee...eeeeeeeeeeee..eeeee.....hhhhhhhhhhhhhhh..eeeeee.....hhhh..hhhhhh...eeeeehhhhhhhhh.......eee..eeeeee..eeeeee...........eeee....----hhh................hhhhhhhhhhhhhh.....eeee.......hhhhhhhhhhhhhhhhh.... Sec.struct. author (1)
     Sec.struct. author (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------eeeee--------------------------------------------------------------------- Sec.struct. author (2)
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------BETA_LACTAMASE_B_1  --------------------------------------------------------BETA_LACTAMAS----------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bmi B   3 KSVKISDDISITQLSDKVYTYVSLAEIEGWGMVPSNGMIVINNHQAALLDTPINDAQTEMLVNWVTDSLHAKVTTFIPNHWHGDCIGGLGYLQRKGVQSYANQMTIDLAKEKGLPVPEHGFTDSLTVSLDGMPLQCYYLGGGHATDNIVVWLPTENILFGGCMLKDNQATSIGNISDADVTAWPKTLDKVKAKFPSARYVVPGHGDYGGTELIEHTKQIVNQYIESTSKP 232
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232
   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/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (BLAB_BACFG | P25910)
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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 Related Entries

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UniProtKB/Swiss-Prot
        BLAB_BACFG | P25910: 1a7t 1a8t 1hlk 1kr3 1znb 2znb 3znb 4znb

(-) Related Entries Specified in the PDB File

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