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(-) Description

Title :  SOLUTION STRUCTURE OF THE BACILLUS CEREUS METALLO-BETA-LACTAMASE BCII IN COMPLEX WITH R-THIOMANDELIC ACID
 
Authors :  A. I. Karsisiotis, C. F. Damblon, G. C. K. Roberts
Date :  20 Feb 13  (Deposition) - 09 Oct 13  (Release) - 09 Oct 13  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
NMR Structure *:  A  (1x)
Keywords :  Bcii, Metallo-Beta-Lactamase, R-Thiomandelic Acid, Mercaptocarboxylate Inhibitor, Broad Spectrum Inhibitor, Hydrolase- Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. I. Karsisiotis, C. F. Damblon, G. C. K. Roberts
Solution Structures Of The Bacillus Cereus Metallo-Beta-Lactamase Bcii And Its Complex With The Broad Spectrum Inhibitor R-Thiomandelic Acid
Biochem. J. 2013
PubMed-ID: 24059435  |  Reference-DOI: 10.1042/BJ20131003
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - BETA-LACTAMASE 2
    Chains: A
    EC Number: 3.5.2.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector: PET9A/BCII
    Expression System Vector Type: VECTOR
    Gene: BLM
    Organism Scientific: BACILLUS CEREUS
    Organism Taxid: 1396
    Strain: 569/H
    Synonym: BCII, BETA-LACTAMASE II, CEPHALOSPORINASE, PENICILLINASE

 Structural Features

(-) Chains, Units

  1
NMR Structure (20x): A
NMR Structure * (1x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

NMR Structure (2, 3)
No.NameCountTypeFull Name
1RTD1Ligand/Ion(2R)-PHENYL(SULFANYL)ETHANOIC ACID
2ZN2Ligand/IonZINC ION
NMR Structure * (1, 1)
No.NameCountTypeFull Name
1RTD1Ligand/Ion(2R)-PHENYL(SULFANYL)ETHANOIC ACID
2ZN-1Ligand/IonZINC ION

(-) Sites  (3, 3)

NMR Structure (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:86 , HIS A:88 , ASP A:90 , HIS A:149 , CYS A:168 , ZN A:302 , RTD A:303BINDING SITE FOR RESIDUE ZN A 301
2AC2SOFTWAREASP A:90 , ARG A:91 , CYS A:168 , HIS A:210 , ZN A:301 , RTD A:303BINDING SITE FOR RESIDUE ZN A 302
3AC3SOFTWAREPHE A:34 , VAL A:39 , TRP A:59 , ASP A:90 , HIS A:149 , CYS A:168 , HIS A:210 , ZN A:301 , ZN A:302BINDING SITE FOR RESIDUE RTD A 303

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2M5D)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2M5D)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2M5D)

(-) PROSITE Motifs  (2, 2)

NMR Structure (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BETA_LACTAMASE_B_1PS00743 Beta-lactamases class B signature 1.BLA2_BACCE113-132  1A:83-102
2BETA_LACTAMASE_B_2PS00744 Beta-lactamases class B signature 2.BLA2_BACCE189-201  1A:159-171
NMR Structure * (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BETA_LACTAMASE_B_1PS00743 Beta-lactamases class B signature 1.BLA2_BACCE113-132  1A:83-102
2BETA_LACTAMASE_B_2PS00744 Beta-lactamases class B signature 2.BLA2_BACCE189-201  1A:159-171

(-) Exons   (0, 0)

(no "Exon" information available for 2M5D)

(-) Sequences/Alignments

NMR Structure
   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:227
 aligned with BLA2_BACCE | P04190 from UniProtKB/Swiss-Prot  Length:257

    Alignment length:227
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       
           BLA2_BACCE    31 SQKVEKTVIKNETGTISISQLNKNVWVHTELGSFNGEAVPSNGLVLNTSKGLVLVDSSWDDKLTKELIEMVEKKFQKRVTDVIITHAHADRIGGIKTLKERGIKAHSTALTAELAKKNGYEEPLGDLQTVTNLKFGNMKVETFYPGKGHTEDNIVVWLPQYNILVGGCLVKSTSAKDLGNVADAYVNEWSTSIENVLKRYRNINAVVPGHGEVGDKGLLLHTLDLLK 257
               SCOP domains d2m5da_ A: Zn metallo-beta-lactamase                                                                                                                                                                                                SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........................ee...eeeee..eeeee...ee.....eee.....hhhhhhhhhhhhhhhh...eeee.....hhhhhhhhhhhh........hhhhhhhhhhhh............ee......eeee...........eee.....eeeee.................hhhhhhhhhhhhhhhh....eeee.......hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------BETA_LACTAMASE_B_1  --------------------------------------------------------BETA_LACTAMAS-------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2m5d A   1 SQKVEKTVIKNETGTISISQLNKNVWVHTELGSFNGEAVPSNGLVLNTSKGLVLVDSSWDDKLTKELIEMVEKKFQKRVTDVIITHAHADRIGGIKTLKERGIKAHSTALTAELAKKNGYEEPLGDLQTVTNLKFGNMKVETFYPGKGHTEDNIVVWLPQYNILVGGCLVKSTSAKDLGNVADAYVNEWSTSIENVLKRYRNINAVVPGHGEVGDKGLLLHTLDLLK 227
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

NMR Structure
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2M5D)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2M5D)

(-) Gene Ontology  (7, 7)

NMR Structure(hide GO term definitions)
Chain A   (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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 Related Entries

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

UniProtKB/Swiss-Prot
        BLA2_BACCE | P04190: 1bc2 1bmc 1bvt 1dxk 1mqo 2bc2 2bfk 2bfl 2bfz 2bg2 2bg6 2bg7 2bg8 2bga 2m5c 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

2m5c