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(-) Description

Title :  CRYSTAL STRUCTURE OF METALLO-BETA-LACTAMASE IND-7
 
Authors :  Y. Yamaguchi, H. Kurosaki, Y. Yamagata
Date :  23 Dec 09  (Deposition) - 14 Apr 10  (Release) - 12 Feb 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydolase, Metallo-Beta-Lactamase, Antibiotics Resistance, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Yamaguchi, N. Takashio, J. -I. Wachino, Y. Yamagata, Y. Arakawa, K. Matsuda, H. Kurosaki
Structure Of Metallo-Beta-Lactamase Ind-7 From A Chryseobacterium Indologenes Clinical Isolate At 1. 65-A Resolution
J. Biochem. V. 147 905 2010
PubMed-ID: 20305272  |  Reference-DOI: 10.1093/JB/MVQ029

(-) Compounds

Molecule 1 - METALLO-BETA-LACTAMASE
    Chains: A
    EC Number: 3.5.2.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET29A(+)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: BLAIND-7
    Organism Scientific: CHRYSEOBACTERIUM INDOLOGENES
    Organism Taxid: 253
    Strain: YMC 94/1/3047

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION
2ZN2Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:96 , HIS A:98 , HIS A:159 , ZN A:302 , HOH A:625 , HOH A:800BINDING SITE FOR RESIDUE ZN A 301
2AC2SOFTWAREASP A:100 , ARG A:101 , CYS A:178 , HIS A:220 , ZN A:301 , HOH A:625BINDING SITE FOR RESIDUE ZN A 302
3AC3SOFTWARELYS A:23 , THR A:80 , LYS A:83 , HOH A:582 , HOH A:640BINDING SITE FOR RESIDUE SO4 A 401
4AC4SOFTWAREILE A:216 , GLY A:226 , GLY A:227 , HIS A:228 , VAL A:229 , HOH A:545 , HOH A:619 , HOH A:826BINDING SITE FOR RESIDUE SO4 A 402

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3L6N)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3L6N)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3L6N)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3L6N)

(-) Exons   (0, 0)

(no "Exon" information available for 3L6N)

(-) 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:218
 aligned with A4GRB2_9FLAO | A4GRB2 from UniProtKB/TrEMBL  Length:239

    Alignment length:218
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230        
         A4GRB2_9FLAO    21 QVKDFVIEPPIKNNLHIYKTFGVFGGKEYSANSMYLVTKKGVVLFDVPWEKVQYQSLMDTIKKRHNLPVVAVFATHSHDDRAGDLSFFNNKGIKTYATAKTNEFLKKDGKATSTEIIKTGKPYRIGGEEFVVDFLGEGHTADNVVVWFPKYNVLDGGCLVKSNSATDLGYIKEANVEQWPKTINKLKAKYSKATLIIPGHDEWKGGGHVEHTLELLNK 238
               SCOP domains d3l6na_ A: automated matches                                                                                                                                                                                               SCOP domains
               CATH domains 3l6nA00 A:21-238 Metallo-beta-lactamase, chain A                                                                                                                                                                           CATH domains
               Pfam domains --------------------------Lactamase_B-3l6nA01 A:47-220                                                                                                                                                  ------------------ Pfam domains
         Sec.struct. author .....ee.......eeeeeeeeee..eeeeeeeeeeee..eeeee....hhhhhhhhhhhhhhhhh..eeeee...........hhhhhhh..eeeehhhhhhhhhhh......ee.....eeee..eeeeee...........eee.....eeeeehhh.................hhhhhhhhhhhhh....eeee........hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3l6n A  21 QVKDFVIEPPIKNNLHIYKTFGVFGGKEYSANSMYLVTKKGVVLFDVPWEKVQYQSLMDTIKKRHNLPVVAVFATHSHDDRAGDLSFFNNKGIKTYATAKTNEFLKKDGKATSTEIIKTGKPYRIGGEEFVVDFLGEGHTADNVVVWFPKYNVLDGGCLVKSNSATDLGYIKEANVEQWPKTINKLKAKYSKATLIIPGHDEWKGGGHVEHTLELLNK 238
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230
   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  (1, 1)

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

(-) Pfam Domains  (1, 1)

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

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (A4GRB2_9FLAO | A4GRB2)
molecular function
    GO:0008800    beta-lactamase activity    Catalysis of the reaction: a beta-lactam + H2O = a substituted beta-amino acid.
    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.

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