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(-) Description

Title :  CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN CLASS B3 BETA-LACTAMASE BJP-1 AND 4-NITROBENZENE-SULFONAMIDE
 
Authors :  J. D. Docquier, M. Benvenuti, V. Calderone, N. Menciassi, S. Mangani
Date :  19 Mar 10  (Deposition) - 12 Jan 11  (Release) - 12 Jan 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.33
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Subclass B3 Beta-Lactamase, Zinc Enzyme, Sulfonamide Complex, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. D. Docquier, M. Benvenuti, V. Calderone, M. Stoczko, N. Menciassi, G. M. Rossolini, S. Mangani
High-Resolution Crystal Structure Of The Subclass B3 Metallo-Beta-Lactamase Bjp-1: Rational Basis For Substrate Specificity And Interaction With Sulfonamides.
Antimicrob. Agents Chemother. V. 54 4343 2010
PubMed-ID: 20696874  |  Reference-DOI: 10.1128/AAC.00409-10

(-) Compounds

Molecule 1 - 'BLR6230 PROTEIN
    Chains: A, B
    EC Number: 3.5.2.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-9A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: BLR6230
    Organism Scientific: BRADYRHIZOBIUM JAPONICUM
    Organism Taxid: 224911
    Strain: USDA 110
    Synonym: BJP-1 BETA-LACTAMASE, SUBCLASS B3 METALLO-BETA-LACTAMASE

 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  (4, 12)

Asymmetric Unit (4, 12)
No.NameCountTypeFull Name
14NZ2Ligand/Ion4-NITROBENZENESULFONAMIDE
2DMS1Ligand/IonDIMETHYL SULFOXIDE
3FMT1Ligand/IonFORMIC ACID
4ZN8Ligand/IonZINC ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
14NZ1Ligand/Ion4-NITROBENZENESULFONAMIDE
2DMS1Ligand/IonDIMETHYL SULFOXIDE
3FMT-1Ligand/IonFORMIC ACID
4ZN-1Ligand/IonZINC ION
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
14NZ1Ligand/Ion4-NITROBENZENESULFONAMIDE
2DMS-1Ligand/IonDIMETHYL SULFOXIDE
3FMT1Ligand/IonFORMIC ACID
4ZN-1Ligand/IonZINC ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:101 , HIS A:103 , HIS A:177 , 4NZ A:295 , ZN A:301BINDING SITE FOR RESIDUE ZN A 300
02AC2SOFTWAREASP A:105 , HIS A:106 , HIS A:242 , 4NZ A:295 , HOH A:299 , ZN A:300BINDING SITE FOR RESIDUE ZN A 301
03AC3SOFTWAREGLU A:158 , HIS A:172 , LYS A:229 , LYS A:294BINDING SITE FOR RESIDUE ZN A 302
04AC4SOFTWARETRP A:34 , HIS A:101 , HIS A:103 , LEU A:104 , ASP A:105 , HIS A:106 , LEU A:145 , HIS A:177 , ALA A:206 , HIS A:242 , HOH A:299 , ZN A:300 , ZN A:301 , HOH A:348 , HOH A:521 , HOH A:590BINDING SITE FOR RESIDUE 4NZ A 295
05AC5SOFTWARELYS A:81 , GLU A:112 , GLU A:116 , HOH A:612BINDING SITE FOR RESIDUE ZN A 296
06AC6SOFTWAREGLU A:39 , LYS A:86 , LYS B:61 , HOH B:592BINDING SITE FOR RESIDUE ZN A 297
07AC7SOFTWAREHIS A:172 , GLU A:185 , MET A:233 , LYS A:234 , LYS A:294BINDING SITE FOR RESIDUE DMS A 298
08AC8SOFTWAREHIS B:101 , HIS B:103 , HIS B:177 , 4NZ B:295 , ZN B:301BINDING SITE FOR RESIDUE ZN B 300
09AC9SOFTWAREASP B:105 , HIS B:106 , HIS B:242 , 4NZ B:295 , ZN B:300BINDING SITE FOR RESIDUE ZN B 301
10BC1SOFTWAREGLU B:158 , HIS B:172 , LYS B:229 , MET B:233 , LYS B:294BINDING SITE FOR RESIDUE ZN B 302
11BC2SOFTWARETRP B:34 , HIS B:101 , HIS B:103 , ASP B:105 , HIS B:106 , LEU B:145 , HIS B:177 , ALA B:206 , HIS B:242 , HOH B:297 , ZN B:300 , ZN B:301 , HOH B:345 , HOH B:471 , HOH B:568BINDING SITE FOR RESIDUE 4NZ B 295
12BC3SOFTWAREGLN B:42 , LEU B:43 , ILE B:44 , ASP B:45BINDING SITE FOR RESIDUE FMT B 296

(-) 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 3M8T)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3M8T)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3M8T)

(-) Exons   (0, 0)

(no "Exon" information available for 3M8T)

(-) 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:263
 aligned with Q89GW5_BRADU | Q89GW5 from UniProtKB/TrEMBL  Length:294

    Alignment length:263
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291   
         Q89GW5_BRADU    32 KKWTAPFEPFQLIDNIYYVGTDGIAVYVIKTSQGLILMDTAMPQSTGMIKDNIAKLGFKVADIKLILNTHAHLDHTGGFAEIKKETGAQLVAGERDKPLLEGGYYPGDEKNEDLAFPAVKVDRAVKEGDRVTLGDTTLTAHATPGHSPGCTSWEMTVKDGKEDREVLFFCSGTVALNRLVGQPTYAGIVDDYRATFAKAKAMKIDVLLGPHPEVYGMQAKRAEMKDGAPNPFIKPGELVTYATSLSEDFDKQLAKQTAALEKK 294
               SCOP domains d3m8ta_ A: automated matches                                                                                                                                                                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 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
                 3m8t A  32 KKWTAPFEPFQLIDNIYYVGTDGIAVYVIKTSQGLILMDTAMPQSTGMIKDNIAKLGFKVADIKLILNTHAHLDHTGGFAEIKKETGAQLVAGERDKPLLEGGYYPGDEKNEDLAFPAVKVDRAVKEGDRVTLGDTTLTAHATPGHSPGCTSWEMTVKDGKEDREVLFFCSGTVALNRLVGQPTYAGIVDDYRATFAKAKAMKIDVLLGPHPEVYGMQAKRAEMKDGAPNPFIKPGELVTYATSLSEDFDKQLAKQTAALEKK 294
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291   


Chain B from PDB  Type:PROTEIN  Length:263
 aligned with Q89GW5_BRADU | Q89GW5 from UniProtKB/TrEMBL  Length:294

    Alignment length:263
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291   
         Q89GW5_BRADU    32 KKWTAPFEPFQLIDNIYYVGTDGIAVYVIKTSQGLILMDTAMPQSTGMIKDNIAKLGFKVADIKLILNTHAHLDHTGGFAEIKKETGAQLVAGERDKPLLEGGYYPGDEKNEDLAFPAVKVDRAVKEGDRVTLGDTTLTAHATPGHSPGCTSWEMTVKDGKEDREVLFFCSGTVALNRLVGQPTYAGIVDDYRATFAKAKAMKIDVLLGPHPEVYGMQAKRAEMKDGAPNPFIKPGELVTYATSLSEDFDKQLAKQTAALEKK 294
               SCOP domains d3m8tb_ B: automated matches                                                                                                                                                                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 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..hhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3m8t B  32 KKWTAPFEPFQLIDNIYYVGTDGIAVYVIKTSQGLILMDTAMPQSTGMIKDNIAKLGFKVADIKLILNTHAHLDHTGGFAEIKKETGAQLVAGERDKPLLEGGYYPGDEKNEDLAFPAVKVDRAVKEGDRVTLGDTTLTAHATPGHSPGCTSWEMTVKDGKEDREVLFFCSGTVALNRLVGQPTYAGIVDDYRATFAKAKAMKIDVLLGPHPEVYGMQAKRAEMKDGAPNPFIKPGELVTYATSLSEDFDKQLAKQTAALEKK 294
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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, 2)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3M8T)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3M8T)

(-) 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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        Q89GW5_BRADU | Q89GW5: 2gmn 3lvz

(-) Related Entries Specified in the PDB File

3lvz NEW REFINEMENT OF THE CRYSTAL STRUCTURE OF BJP1, A SUBCLASS B3 METALLO BETA LACTAMASE OF BRADYRHIZOBIUM JAPONICUM