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(-) Description

Title :  CRYSTAL STRUCTURE OF BJP-1, A SUBCLASS B3 METALLO-BETA-LACTAMASE OF BRADYRHIZOBIUM JAPONICUM
 
Authors :  V. Calderone, M. Benvenuti, M. Stoczko, J. D. Docquier, G. M. Rossolini S. Mangani
Date :  07 Apr 06  (Deposition) - 24 Apr 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Metallo-Beta-Lactamase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Stoczko, J. M. Frere, G. M. Rossolini, J. D. Docquier
Postgenomic Scan Of Metallo-Beta-Lactamase Homologues In Rhizobacteria: Identification And Characterization Of Bjp-1 A Subclass B3 Ortholog From Bradyrhizobium Japonicum.
Antimicrob. Agents Chemother. V. 50 1973 2006
PubMed-ID: 16723554  |  Reference-DOI: 10.1128/AAC.01551-05

(-) Compounds

Molecule 1 - METALLO-BETA-LACTAMASE
    Chains: A, B
    EC Number: 3.5.2.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: RESIDUES 21-294
    Organism Scientific: BRADYRHIZOBIUM JAPONICUM
    Organism Taxid: 224911
    Strain: USDA 110

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 6)

Asymmetric Unit (1, 6)
No.NameCountTypeFull Name
1ZN6Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:101 , HIS A:103 , HIS A:177 , ZN A:802 , HOH A:806BINDING SITE FOR RESIDUE ZN A 801
2AC2SOFTWAREASP A:105 , HIS A:106 , HIS A:242 , ZN A:801 , HOH A:806 , HOH A:807BINDING SITE FOR RESIDUE ZN A 802
3AC3SOFTWAREASP B:105 , HIS B:106 , HIS B:242 , ZN B:804 , HOH B:807 , HOH B:882BINDING SITE FOR RESIDUE ZN B 803
4AC4SOFTWAREHIS B:101 , HIS B:103 , HIS B:177 , ZN B:803 , HOH B:882BINDING SITE FOR RESIDUE ZN B 804
5AC5SOFTWAREGLU A:158 , HIS A:172 , LYS A:229 , HOH A:858BINDING SITE FOR RESIDUE ZN A 805
6AC6SOFTWAREGLU B:158 , HIS B:172 , LYS B:229 , HOH B:864BINDING SITE FOR RESIDUE ZN B 806

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:181 -A:201
2B:181 -B:201

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2GMN)

(-) Exons   (0, 0)

(no "Exon" information available for 2GMN)

(-) 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:264
 aligned with Q89GW5_BRADU | Q89GW5 from UniProtKB/TrEMBL  Length:294

    Alignment length:264
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288    
         Q89GW5_BRADU    29 VAMKKWTAPFEPFQLIDNIYYVGTDGIAVYVIKTSQGLILMDTAMPQSTGMIKDNIAKLGFKVADIKLILNTHAHLDHTGGFAEIKKETGAQLVAGERDKPLLEGGYYPGDEKNEDLAFPAVKVDRAVKEGDRVTLGDTTLTAHATPGHSPGCTSWEMTVKDGKEDREVLFFCSGTVALNRLVGQPTYAGIVDDYRATFAKAKAMKIDVLLGPHPEVYGMQAKRAEMKDGAPNPFIKPGELVTYATSLSEDFDKQLAKQTAALE 292
               SCOP domains d2gmna1 A:29-292 Zn metallo-beta-lactamase                                                                                                                                                                                                                               SCOP domains
               CATH domains 2gmnA00 A:29-292 Metallo-beta-lactamase, chain A                                                                                                                                                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhh....eeee..eee........eeeee..eeeee...hhhhhhhhhhhhhhh..hhh.eeeee....hhhhhhhhhhhhhhhh.eeeee..hhhhhhhh.......hhhhh.......eee....eeee..eeeeeee........eeeeeeeee..eeeeeee..................hhhhhhhhhhhhhhhh...eee..hhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2gmn A  29 VAMKKWTAPFEPFQLIDNIYYVGTDGIAVYVIKTSQGLILMDTAMPQSTGMIKDNIAKLGFKVADIKLILNTHAHLDHTGGFAEIKKETGAQLVAGERDKPLLEGGYYPGDEKNEDLAFPAVKVDRAVKEGDRVTLGDTTLTAHATPGHSPGCTSWEMTVKDGKEDREVLFFCSGTVALNRLVGQPTYAGIVDDYRATFAKAKAMKIDVLLGPHPEVYGMQAKRAEMKDGAPNPFIKPGELVTYATSLSEDFDKQLAKQTAALE 292
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288    


Chain B from PDB  Type:PROTEIN  Length:264
 aligned with Q89GW5_BRADU | Q89GW5 from UniProtKB/TrEMBL  Length:294

    Alignment length:264
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288    
         Q89GW5_BRADU    29 VAMKKWTAPFEPFQLIDNIYYVGTDGIAVYVIKTSQGLILMDTAMPQSTGMIKDNIAKLGFKVADIKLILNTHAHLDHTGGFAEIKKETGAQLVAGERDKPLLEGGYYPGDEKNEDLAFPAVKVDRAVKEGDRVTLGDTTLTAHATPGHSPGCTSWEMTVKDGKEDREVLFFCSGTVALNRLVGQPTYAGIVDDYRATFAKAKAMKIDVLLGPHPEVYGMQAKRAEMKDGAPNPFIKPGELVTYATSLSEDFDKQLAKQTAALE 292
               SCOP domains d2gmnb_ B: automated matches                                                                                                                                                                                                                                             SCOP domains
               CATH domains 2gmnB00 B:29-292 Metallo-beta-lactamase, chain A                                                                                                                                                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ............eeee..eee........eeeee..eeeee...hhhhhhhhhhhhhhh..hhh.eeeee....hhhhhhhhhhhhhhhh.eeeee..hhhhhhhh.......hhhhh.......eee....eeee..eeeeeee........eeeeeeeee..eeeeeee..................hhhhhhhhhhhhhhhh...eee..hhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2gmn B  29 VAMKKWTAPFEPFQLIDNIYYVGTDGIAVYVIKTSQGLILMDTAMPQSTGMIKDNIAKLGFKVADIKLILNTHAHLDHTGGFAEIKKETGAQLVAGERDKPLLEGGYYPGDEKNEDLAFPAVKVDRAVKEGDRVTLGDTTLTAHATPGHSPGCTSWEMTVKDGKEDREVLFFCSGTVALNRLVGQPTYAGIVDDYRATFAKAKAMKIDVLLGPHPEVYGMQAKRAEMKDGAPNPFIKPGELVTYATSLSEDFDKQLAKQTAALE 292
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288
   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  (2, 2)

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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q89GW5_BRADU | Q89GW5)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

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 Related Entries

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UniProtKB/TrEMBL
        Q89GW5_BRADU | Q89GW5: 3lvz 3m8t

(-) Related Entries Specified in the PDB File

1k07 NATIVE FEZ-1 METALLO-BETA-LACTAMASE FROM LEGIONELLA GORMANII