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(-) Description

Title :  CRYSTAL STRUCTURE OF OXA-46 BETA-LACTAMASE FROM P. AERUGINOSA
 
Authors :  J. D. Docquier, M. Benvenuti, V. Calderone, F. Giuliani, D. Kapetis, F. G. M. Rossolini, S. Mangani
Date :  24 Jul 09  (Deposition) - 16 Mar 10  (Release) - 19 Feb 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (2x)
Biol. Unit 2:  B,C  (1x)
Keywords :  Serine Beta-Lactamase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. D. Docquier, M. Benvenuti, V. Calderone, F. Giuliani, D. Kapetis, F. De Luca, G. M. Rossolini, S. Mangani
Crystal Structure Of The Narrow-Spectrum Oxa-46 Class D Beta-Lactamase: Relationship Between Active-Site Lysine Carbamylation And Inhibition By Polycarboxylates
Antimicrob. Agents Chemother. V. 54 2167 2010
PubMed-ID: 20145076  |  Reference-DOI: 10.1128/AAC.01517-09
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - OXA-46 OXACILLINASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PET-9A
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Organism Scientific: PSEUDOMONAS AERUGINOSA
    Organism Taxid: 287
    Strain: PPV-97
    Synonym: OXA-LIKE PROTEIN
 
Molecule 2 - OXA-46 OXACILLINASE
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PET-9A
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Organism Scientific: PSEUDOMONAS AERUGINOSA
    Organism Taxid: 287
    Strain: PPV-97
    Synonym: OXA-LIKE PROTEIN
 
Molecule 3 - OXA-46 OXACILLINASE
    Chains: C
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PET-9A
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Organism Scientific: PSEUDOMONAS AERUGINOSA
    Organism Taxid: 287
    Strain: PPV-97
    Synonym: OXA-LIKE PROTEIN

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (2x): A  
Biological Unit 2 (1x):  BC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 11)

Asymmetric Unit (4, 11)
No.NameCountTypeFull Name
1EDO6Ligand/Ion1,2-ETHANEDIOL
2KCX2Mod. Amino AcidLYSINE NZ-CARBOXYLIC ACID
3P6G1Ligand/IonHEXAETHYLENE GLYCOL
4TLA2Ligand/IonL(+)-TARTARIC ACID
Biological Unit 1 (3, 8)
No.NameCountTypeFull Name
1EDO4Ligand/Ion1,2-ETHANEDIOL
2KCX2Mod. Amino AcidLYSINE NZ-CARBOXYLIC ACID
3P6G-1Ligand/IonHEXAETHYLENE GLYCOL
4TLA2Ligand/IonL(+)-TARTARIC ACID
Biological Unit 2 (4, 7)
No.NameCountTypeFull Name
1EDO4Ligand/Ion1,2-ETHANEDIOL
2KCX1Mod. Amino AcidLYSINE NZ-CARBOXYLIC ACID
3P6G1Ligand/IonHEXAETHYLENE GLYCOL
4TLA1Ligand/IonL(+)-TARTARIC ACID

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:72 , LYS A:75 , ASN A:119 , SER A:120 , LYS A:210 , THR A:211 , GLY A:212 , TRP A:213 , ARG A:249 , ARG B:242BINDING SITE FOR RESIDUE TLA A 267
2AC2SOFTWAREMET A:117 , ARG A:118 , LEU A:196 , ILE A:198 , THR A:199 , ALA A:209 , LYS A:210 , HOH A:286 , HOH A:379BINDING SITE FOR RESIDUE EDO A 268
3AC3SOFTWAREGLU A:62 , ALA A:65 , HOH A:415BINDING SITE FOR RESIDUE EDO A 269
4AC4SOFTWARESER B:72 , LYS B:75 , SER B:120 , LYS B:210 , THR B:211 , ARG B:249 , HOH B:276 , HOH B:279 , HOH B:346BINDING SITE FOR RESIDUE TLA B 267
5AC5SOFTWARELEU A:38 , GLN A:39 , PHE A:247 , TRP B:97 , PHE B:104 , ALA B:105 , SER B:120 , THR B:121 , VAL B:122 , TRP B:123 , GLU B:126 , LEU B:127 , HOH B:356 , HOH B:393BINDING SITE FOR RESIDUE P6G B 268
6AC6SOFTWAREALA B:65 , SER B:167 , HIS B:169 , EDO B:272BINDING SITE FOR RESIDUE EDO B 269
7AC7SOFTWAREMET B:117 , ARG B:118 , LEU B:196 , THR B:199 , ALA B:209 , HOH B:331 , HOH B:361BINDING SITE FOR RESIDUE EDO B 270
8AC8SOFTWAREVAL B:94 , ASP B:112 , HOH B:273 , PRO C:227BINDING SITE FOR RESIDUE EDO B 271
9AC9SOFTWAREALA B:65 , ARG B:67 , EDO B:269BINDING SITE FOR RESIDUE EDO B 272

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3IF6)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3IF6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3IF6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3IF6)

(-) Exons   (0, 0)

(no "Exon" information available for 3IF6)

(-) 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:228
 aligned with Q8GRH0_PSEAI | Q8GRH0 from UniProtKB/TrEMBL  Length:266

    Alignment length:242
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264  
         Q8GRH0_PSEAI    25 VVIRSDWKKFFSDLQAEGAIVIADERQAKHTLSVFDQERAAKRYSPASTFKIPHTLFALDADAVRDEFQVFRWDGVNRSFAGHNQDQDLRSAMRNSTVWVYELFAKDIGEDKARRYLKQIDYGNVDPSTIKGDYWIDGNLKISAHEQILFLRKLYRNQLPFKVEHQRLVKDLMITEAGRSWILRAKTGWEGRFGWWVGWIEWPTGPVFFALNIDTPNRTDDLFKREAIARAILRSIDALPPN 266
               SCOP domains d3if6a_ A: automated matches                                                                                                                                                                                                                       SCOP domains
               CATH domains 3if6A00 A:25-266 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                           CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee...hhhhhhh....eeeeeee......eeeeehhhhhh....hhhhhhhhhhhhhhhh............-----------...hhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh........---...........hhhhhhhhhhhhhhh....hhhhhhhhhhhheeee....eeeeeeee...eeeeeeeeee..eeeeeeeeee..hhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3if6 A  25 VVIRSDWKKFFSDLQAEGAIVIADERQAKHTLSVFDQERAAKRYSPASTFKIPHTLFALDADAVRDEFQVFRW-----------QDQDLRSAMRNSTVWVYELFAKDIGEDKARRYLKQIDYGNVDPS---GDYWIDGNLKISAHEQILFLRKLYRNQLPFKVEHQRLVKDLMITEAGRSWILRAKTGWEGRFGWWVGWIEWPTGPVFFALNIDTPNRTDDLFkREAIARAILRSIDALPPN 266
                                    34        44        54        64        74        84        94  |      -    |  114       124       134       144       | - |     164       174       184       194       204       214       224       234       244   |   254       264  
                                                                                                   97         109                                        152 156                                                                                         248-KCX              


Chain B from PDB  Type:PROTEIN  Length:242
 aligned with Q8GRH0_PSEAI | Q8GRH0 from UniProtKB/TrEMBL  Length:266

    Alignment length:242
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264  
         Q8GRH0_PSEAI    25 VVIRSDWKKFFSDLQAEGAIVIADERQAKHTLSVFDQERAAKRYSPASTFKIPHTLFALDADAVRDEFQVFRWDGVNRSFAGHNQDQDLRSAMRNSTVWVYELFAKDIGEDKARRYLKQIDYGNVDPSTIKGDYWIDGNLKISAHEQILFLRKLYRNQLPFKVEHQRLVKDLMITEAGRSWILRAKTGWEGRFGWWVGWIEWPTGPVFFALNIDTPNRTDDLFKREAIARAILRSIDALPPN 266
               SCOP domains d3if6b_ B: automated matches                                                                                                                                                                                                                       SCOP domains
               CATH domains 3if6B00 B:25-266 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                           CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee...hhhhhhh....eeeeeee......eeee.hhhhhh.ee.hhhhhhhhhhhhhhhh..........................hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh....................eehhhhhhhhhhhhh.....hhhhhhhhhhhheeee....eeeeeeee...eeeeeeeeee..eeeeeeeeee..hhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3if6 B  25 VVIRSDWKKFFSDLQAEGAIVIADERQAKHTLSVFDQERAAKRYSPASTFKIPHTLFALDADAVRDEFQVFRWDGVNRSFAGHNQDQDLRSAMRNSTVWVYELFAKDIGEDKARRYLKQIDYGNVDPSTIKGDYWIDGNLKISAHEQILFLRKLYRNQLPFKVEHQRLVKDLMITEAGRSWILRAKTGWEGRFGWWVGWIEWPTGPVFFALNIDTPNRTDDLFKREAIARAILRSIDALPPN 266
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264  


Chain C from PDB  Type:PROTEIN  Length:232
 aligned with Q8GRH0_PSEAI | Q8GRH0 from UniProtKB/TrEMBL  Length:266

    Alignment length:242
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264  
         Q8GRH0_PSEAI    25 VVIRSDWKKFFSDLQAEGAIVIADERQAKHTLSVFDQERAAKRYSPASTFKIPHTLFALDADAVRDEFQVFRWDGVNRSFAGHNQDQDLRSAMRNSTVWVYELFAKDIGEDKARRYLKQIDYGNVDPSTIKGDYWIDGNLKISAHEQILFLRKLYRNQLPFKVEHQRLVKDLMITEAGRSWILRAKTGWEGRFGWWVGWIEWPTGPVFFALNIDTPNRTDDLFKREAIARAILRSIDALPPN 266
               SCOP domains d3if6c_ C: automated matches                                                                                                                                                                                                                       SCOP domains
               CATH domains 3if6C00 C:25-266 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                           CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee...hhhhhhh....eeeeeee......eeeeehhhhhhh...hhhhhhhhhhhhhhhh............--............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....--------..........hhhhhhhhhhhhhh.....hhhhhhhhhhhheeee....eeeeeeee...eeeeeeeeee..eeeeeeeeee..hhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3if6 C  25 VVIRSDWKKFFSDLQAEGAIVIADERQAKHTLSVFDQERAAKRYSPASTFkIPHTLFALDADAVRDEFQVFRW--VNRSFAGHNQDQDLRSAMRNSTVWVYELFAKDIGEDKARRYLKQIDYGN--------DYWIDGNLKISAHEQILFLRKLYRNQLPFKVEHQRLVKDLMITEAGRSWILRAKTGWEGRFGWWVGWIEWPTGPVFFALNIDTPNRTDDLFKREAIARAILRSIDALPPN 266
                                    34        44        54        64        74|       84        94  |  | 104       114       124       134       144   |     -  |    164       174       184       194       204       214       224       234       244       254       264  
                                                                             75-KCX                97  |                                             148      157                                                                                                             
                                                                                                     100
   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, 3)

Asymmetric Unit
(-)
Class: Multi-domain proteins (alpha and beta) (2421)

(-) CATH Domains  (1, 3)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3IF6)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (Q8GRH0_PSEAI | Q8GRH0)
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:0008658    penicillin binding    Interacting selectively and non-covalently with penicillin, any antibiotic that contains the condensed beta-lactamthiazolidine ring system.
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.

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