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(-) Description

Title :  THE MONO-ZINC CARBAPENEMASE CPHA (N220G MUTANT) SHOWS A ZN(II)- NH2 ARG COORDINATION
 
Authors :  G. Garau, O. Dideberg
Date :  18 Aug 04  (Deposition) - 28 Dec 04  (Release) - 17 Feb 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Garau, C. Bebrone, C. Anne, M. Galleni, J. M. Frere, O. Dideberg
A Metallo-Beta-Lactamase Enzyme In Action: Crystal Structures Of The Monozinc Carbapenemase Cpha And Its Complex With Biapenem
J. Mol. Biol. V. 345 785 2005
PubMed-ID: 15588826  |  Reference-DOI: 10.1016/J.JMB.2004.10.070
(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
    Mutation: YES
    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, 7)

Asymmetric/Biological Unit (4, 7)
No.NameCountTypeFull Name
1CO31Ligand/IonCARBONATE ION
2GOL2Ligand/IonGLYCEROL
3SO43Ligand/IonSULFATE ION
4ZN1Ligand/IonZINC ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECO3 A:2 , ASP A:120 , ARG A:121 , CYS A:221 , HIS A:263BINDING SITE FOR RESIDUE ZN A 401
2AC2SOFTWAREASP A:120 , HIS A:196 , CYS A:221 , LYS A:224 , HIS A:263 , ZN A:401 , HOH A:403 , HOH A:404 , HOH A:410BINDING SITE FOR RESIDUE CO3 A 2
3AC3SOFTWAREARG A:143 , LYS A:147 , HOH A:560 , HOH A:561BINDING SITE FOR RESIDUE SO4 A 3
4AC4SOFTWAREARG A:140 , HOH A:496 , HOH A:601BINDING SITE FOR RESIDUE SO4 A 4
5AC5SOFTWARELYS A:97 , ARG A:102 , LYS A:257 , HOH A:446 , HOH A:451 , HOH A:637BINDING SITE FOR RESIDUE SO4 A 5
6AC6SOFTWAREHIS A:176 , ASP A:177 , GLY A:178 , ASP A:179 , HOH A:642BINDING SITE FOR RESIDUE GOL A 6
7AC7SOFTWARELEU A:267 , HIS A:289 , GLY A:290 , GLU A:292 , HOH A:566 , HOH A:645BINDING SITE FOR RESIDUE GOL A 7

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1X8H)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1X8H)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1X8H)

(-) 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 1X8H)

(-) 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_AERHY | P26918 from UniProtKB/Swiss-Prot  Length:254

    Alignment length:228
                                                                                                                                                                                                                                                            254 
                                    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 AGMSLTQVSGPVYVVEDNYYVQENSMVYFGAKGVTVVGATWTPDTARELHKLIKRVSRKPVLEVINTNYHTDRAGGNAYWKSIGAKVVSTRQTRDLMKSDWAEIVAFTRKGLPEYPDLPLVLPNVVHDGDFTLQEGKVRAFYAGPAHTPDGIFVYFPDEQVLYGNCILKEKLGNLSFADVKAYPQTLERLKAMKLPIKTVIGGHDSPLHGPELIDHYEALIKAAPQS-   -
               SCOP domains d1x8ha_ A: Zn metallo-beta-lactamase                                                                                                                                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------Lactamase_B-1x8hA01 A:59-263                                                                                                                                                              ------------------------ Pfam domains
         Sec.struct. author ..eeeeeee..eeeeee.....eeeeeee....eeee....hhhhhhhhhhhhhh.....eeeee....hhhhhhhhhhhhhh..eeeeehhhhhhhhhhhhhhhhhhhhhh............eee...eee....eeee...........eeee....eee.hhhh............hhhhhhhhhhhhh.....eee......ee.hhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------BETA_LACTAMASE_B_1  ------------------------------------------------------------------------BETA_LACTAMAS----------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1x8h A  41 AGMSLTQVSGPVYVVEDNYYVQENSMVYFGAKGVTVVGATWTPDTARELHKLIKRVSRKPVLEVINTNYHTDRAGGNAYWKSIGAKVVSTRQTRDLMKSDWAEIVAFTRKGLPEYPDLPLVLPNVVHDGDFTLQEGKVRAFYAGPAHTPDGIFVYFPDEQVLYGGCILKEKLGNLSFADVKAYPQTLERLKAMKLPIKTVIGGHDSPLHGPELIDHYEALIKAAPQSS 308
                                    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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  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, 1)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1X8H)

(-) 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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  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 1x8i 2gkl 2qds 3f9o 3fai 3iof 3iog 3sw3 3t9m

(-) Related Entries Specified in the PDB File

1x8g THE MONO-ZINC CARBAPENEMASE
1x8i THE SAME PROTEIN WITH THE ANTIBIOTIC BIAPENEM