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(-) Description

Title :  CRYSTAL STRUCTURE OF THE ZINC CARBAPENEMASE CPHA IN COMPLEX WITH THE INHIBITOR D-CAPTOPRIL
 
Authors :  G. Garau, O. Dideberg
Date :  21 Jun 07  (Deposition) - 17 Jul 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.66
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase, Lactamase, Inhibitor, Zn (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. M. Lienard, G. Garau, L. Horsfall, A. I. Karsisiotis, C. Damblon, P. Lassaux, C. Papamicael, G. C. Roberts, M. Galleni, O. Dideberg, J. M. Frere, C. J. Schofield
Structural Basis For The Broad-Spectrum Inhibition Of Metallo-Beta-Lactamases By Thiols.
Org. Biomol. Chem. V. 6 2282 2008
PubMed-ID: 18563261  |  Reference-DOI: 10.1039/B802311E
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - BETA-LACTAMASE
    Chains: A
    EC Number: 3.5.2.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PUC20-CPHA
    Expression System Strain: BL21(DE3)PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: CPHA
    Organism Scientific: AEROMONAS HYDROPHILA
    Organism Taxid: 644

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 8)

Asymmetric/Biological Unit (4, 8)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2MCO1Ligand/Ion1-(3-MERCAPTO-2-METHYL-PROPIONYL)-PYRROLIDINE-2-CARBOXYLIC ACID
3SO44Ligand/IonSULFATE ION
4ZN1Ligand/IonZINC ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:120 , CYS A:221 , HIS A:263 , MCO A:501BINDING SITE FOR RESIDUE ZN A 401
2AC2SOFTWARESER A:104 , ARG A:105 , LYS A:106 , HOH A:622 , HOH A:768 , HOH A:779BINDING SITE FOR RESIDUE SO4 A 601
3AC3SOFTWARELYS A:129 , ARG A:140 , ASN A:173 , LYS A:302 , HOH A:712 , HOH A:774BINDING SITE FOR RESIDUE SO4 A 602
4AC4SOFTWARELYS A:147 , LEU A:171 , HOH A:754BINDING SITE FOR RESIDUE SO4 A 603
5AC5SOFTWARELYS A:97 , LEU A:98 , ARG A:102 , LYS A:257 , HOH A:647 , HOH A:652 , HOH A:780BINDING SITE FOR RESIDUE SO4 A 604
6AC6SOFTWAREHIS A:118 , THR A:119 , ASP A:120 , LEU A:161 , HIS A:196 , CYS A:221 , ASN A:233 , HIS A:263 , ZN A:401 , HOH A:608 , HOH A:609BINDING SITE FOR RESIDUE MCO A 501
7AC7SOFTWAREHIS A:176 , ASP A:177 , GLY A:178 , ASP A:179BINDING SITE FOR RESIDUE GOL A 605
8AC8SOFTWAREASP A:179 , ARG A:188 , PHE A:190 , TYR A:204 , HOH A:686BINDING SITE FOR RESIDUE GOL A 606

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological 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

(-) Exons   (0, 0)

(no "Exon" information available for 2QDS)

(-) 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:225
 aligned with BLAB_AERHY | P26918 from UniProtKB/Swiss-Prot  Length:254

    Alignment length:225
                                    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 AGMSLTQVSGPVYVVEDNYYVQENSMVYFGAKGVTVVGATWTPDTARELHKLIKRVSRKPVLEVINTNYHTDRAGGNAYWKSIGAKVVSTRQTRDLMKSDWAEIVAFTRKGLPEYPDLPLVLPNVVHDGDFTLQEGKVRAFYAGPAHTPDGIFVYFPDEQVLYGNCILKEKLGNLSFADVKAYPQTLERLKAMKLPIKTVIGGHDSPLHGPELIDHYEALIKAAP 252
               SCOP domains d2qdsa_ A: Zn metallo-beta-lactamase                                                                                                                                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------Lactamase_B-2qdsA01 A:59-263                                                                                                                                                              --------------------- 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
                 2qds A  41 AGMSLTQVSGPVYVVEDNYYVQENSMVYFGAKGVTVVGATWTPDTARELHKLIKRVSRKPVLEVINTNYHTDRAGGNAYWKSIGAKVVSTRQTRDLMKSDWAEIVAFTRKGLPEYPDLPLVLPNVVHDGDFTLQEGKVRAFYAGPAHTPDGIFVYFPDEQVLYGNCILKEKLGNLSFADVKAYPQTLERLKAMKLPIKTVIGGHDSPLHGPELIDHYEALIKAAP 305
                                    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
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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/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: Metallo-HOrase (67)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological 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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 Related Entries

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

UniProtKB/Swiss-Prot
        BLAB_AERHY | P26918: 1x8g 1x8h 1x8i 2gkl 3f9o 3fai 3iof 3iog 3sw3 3t9m

(-) Related Entries Specified in the PDB File

1x8g 1x8i 2gkl