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(-) Description

Title :  CRYSTAL STRUCTURE OF THE DI-ZINC CARBAPENEMASE CPHA FROM AEROMONAS HYDROPHILA
 
Authors :  H. Delbruck, K. M. V. Hoffmann
Date :  14 Nov 08  (Deposition) - 01 Sep 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.03
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Hydrolase, Antibiotic Resistance, Metal-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Bebrone, H. Delbruck, M. B. Kupper, P. Schlomer, C. Willmann, J. -M. Frere, R. Fischer, M. Galleni, K. M. V. Hoffmann
The Structure Of The Dizinc Subclass B2 Metallo-Beta-Lactamase Cpha Reveals That The Second Inhibitory Zinc Ion Binds In The Histidine Site
Antimicrob. Agents Chemother. V. 53 4464 2009
PubMed-ID: 19651913  |  Reference-DOI: 10.1128/AAC.00288-09

(-) Compounds

Molecule 1 - BETA-LACTAMASE
    Chains: A
    EC Number: 3.5.2.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET9A-CPHA
    Expression System Strain: BL21(DE3) PLYS S
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: CPHA
    Organism Scientific: AEROMONAS HYDROPHILA
    Organism Taxid: 644

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (1x): A
Biological Unit 2 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 15)

Asymmetric Unit (4, 15)
No.NameCountTypeFull Name
1CL6Ligand/IonCHLORIDE ION
2CO32Ligand/IonCARBONATE ION
3SO44Ligand/IonSULFATE ION
4ZN3Ligand/IonZINC ION
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2CO32Ligand/IonCARBONATE ION
3SO44Ligand/IonSULFATE ION
4ZN-1Ligand/IonZINC ION
Biological Unit 2 (2, 12)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2CO34Ligand/IonCARBONATE ION
3SO48Ligand/IonSULFATE ION
4ZN-1Ligand/IonZINC ION

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHOH A:107 , HIS A:118 , ASP A:120 , HIS A:196 , HIS A:263 , ZN A:308 , ZN A:309 , HOH A:334 , HOH A:474BINDING SITE FOR RESIDUE SO4 A 1
02AC2SOFTWAREHIS A:176 , ASP A:177 , HOH A:465BINDING SITE FOR RESIDUE SO4 A 2
03AC3SOFTWAREALA A:237 , ASP A:238 , VAL A:239 , LYS A:240BINDING SITE FOR RESIDUE SO4 A 3
04AC4SOFTWARESER A:104 , LYS A:106 , HOH A:348 , HOH A:466BINDING SITE FOR RESIDUE SO4 A 4
05AC5SOFTWARELEU A:249 , LYS A:250 , LYS A:253 , LEU A:254 , ILE A:256 , HOH A:365 , HOH A:421BINDING SITE FOR RESIDUE CO3 A 5
06AC6SOFTWAREARG A:158 , ASP A:166 , HOH A:449BINDING SITE FOR RESIDUE CO3 A 6
07AC7SOFTWAREHOH A:19 , ASN A:116 , ASN A:220 , CYS A:221 , ILE A:222BINDING SITE FOR RESIDUE CL A 7
08AC8SOFTWAREGLN A:47 , HOH A:393BINDING SITE FOR RESIDUE CL A 9
09AC9SOFTWARECL A:11 , ZN A:310BINDING SITE FOR RESIDUE CL A 10
10BC1SOFTWARECL A:10 , HIS A:289 , LEU A:293 , ZN A:310BINDING SITE FOR RESIDUE CL A 11
11BC2SOFTWAREHIS A:289 , GLY A:290 , ZN A:310BINDING SITE FOR RESIDUE CL A 12
12BC3SOFTWARESO4 A:1 , ASP A:120 , CYS A:221 , HIS A:263BINDING SITE FOR RESIDUE ZN A 308
13BC4SOFTWARESO4 A:1 , HIS A:118 , HIS A:196 , HOH A:474BINDING SITE FOR RESIDUE ZN A 309
14BC5SOFTWARECL A:10 , CL A:11 , CL A:12 , HIS A:289BINDING SITE FOR RESIDUE ZN A 310

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3F9O)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Pro A:305 -Gln A:306

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3F9O)

(-) PROSITE Motifs  (2, 2)

Asymmetric Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BETA_LACTAMASE_B_1PS00743 Beta-lactamases class B signature 1.BLAB_AERHY92-111  1A:113-133
2BETA_LACTAMASE_B_2PS00744 Beta-lactamases class B signature 2.BLAB_AERHY184-196  1A:209-224
Biological Unit 1 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BETA_LACTAMASE_B_1PS00743 Beta-lactamases class B signature 1.BLAB_AERHY92-111  1A:113-133
2BETA_LACTAMASE_B_2PS00744 Beta-lactamases class B signature 2.BLAB_AERHY184-196  1A:209-224
Biological Unit 2 (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BETA_LACTAMASE_B_1PS00743 Beta-lactamases class B signature 1.BLAB_AERHY92-111  2A:113-133
2BETA_LACTAMASE_B_2PS00744 Beta-lactamases class B signature 2.BLAB_AERHY184-196  2A:209-224

(-) Exons   (0, 0)

(no "Exon" information available for 3F9O)

(-) 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:226
 aligned with BLAB_AERHY | P26918 from UniProtKB/Swiss-Prot  Length:254

    Alignment length:226
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247      
           BLAB_AERHY    28 AGMSLTQVSGPVYVVEDNYYVQENSMVYFGAKGVTVVGATWTPDTARELHKLIKRVSRKPVLEVINTNYHTDRAGGNAYWKSIGAKVVSTRQTRDLMKSDWAEIVAFTRKGLPEYPDLPLVLPNVVHDGDFTLQEGKVRAFYAGPAHTPDGIFVYFPDEQVLYGNCILKEKLGNLSFADVKAYPQTLERLKAMKLPIKTVIGGHDSPLHGPELIDHYEALIKAAPQ 253
               SCOP domains d3f9oa_ A: Zn metallo-beta-lactamase                                                                                                                                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee..eeeeee.....eeeeeee....eeee....hhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhh..eeeeehhhhhhhhhhhhhhhhhhhhhh............eee...eee....eeee...........eeee....eee.................hhhhhhhhhhhhh.....eee......ee.hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------BETA_LACTAMASE_B_1  ------------------------------------------------------------------------BETA_LACTAMAS--------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3f9o A  41 AGMSLTQVSGPVYVVEDNYYVQENSMVYFGAKGVTVVGATWTPDTARELHKLIKRVSRKPVLEVINTNYHTDRAGGNAYWKSIGAKVVSTRQTRDLMKSDWAEIVAFTRKGLPEYPDLPLVLPNVVHDGDFTLQEGKVRAFYAGPAHTPDGIFVYFPDEQVLYGNCILKEKLGNLSFADVKAYPQTLERLKAMKLPIKTVIGGHDSPLHGPELIDHYEALIKAAPQ 306
                                    50        60|       76        86        96   ||  108       118       128  ||   139       149       159       169       179       189       199     ||215       225||     239       249       259       290       300      
                                              60|                              100| 106|                    131|                                                                     205| ||        226|                                 267|                 
                                               67                               102  108                     133                                                                      209 ||         231                                  289                 
                                                                                                                                                                                        211|                                                                  
                                                                                                                                                                                         215
   Legend:   → Mismatch (orange background)
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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)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3F9O)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3F9O)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A   (BLAB_AERHY | P26918)
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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  BLAB_AERHY | P26918
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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
        BLAB_AERHY | P26918: 1x8g 1x8h 1x8i 2gkl 2qds 3fai 3iof 3iog 3sw3 3t9m

(-) Related Entries Specified in the PDB File

1x8g MONO-ZINC STRUCTURE
1x8h MONO-ZINC N220G MUTANT STRUCTURE
1x8i COMPLEX WITH THE ANTIBIOTIC BIAPENEM
2gkl COMPLEX WITH THE INHIBITOR PYRIDINE-2,4-DICARBOXYLATE
2qds COMPLEX WITH THE INHIBITOR D-CAPTOPRIL
3fai DI-ZINC N220G MUTANT STRUCTURE