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(-) Description

Title :  CRYSTAL STRUCTURE OF THE OMEGA LOOP DELETION MUTANT (RESIDUES 163-178 DELETED) OF BETA-LACTAMASE FROM STAPHYLOCOCCUS AUREUS PC1
 
Authors :  S. Banerjee, U. Pieper, O. Herzberg
Date :  09 Feb 98  (Deposition) - 27 May 98  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Hydrolase, Beta-Lactamase, Beta-Lactam Antibiotic Resistance (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Banerjee, U. Pieper, G. Kapadia, L. K. Pannell, O. Herzberg
Role Of The Omega-Loop In The Activity, Substrate Specificity, And Structure Of Class A Beta-Lactamase.
Biochemistry V. 37 3286 1998
PubMed-ID: 9521648  |  Reference-DOI: 10.1021/BI972127F
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - BETA-LACTAMASE
    Chains: A, B
    EC Number: 3.5.2.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Gene: BLAZ
    Expression System Plasmid: PTS32
    Expression System Strain: TG1
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: BLAZ
    Mutation: YES
    Organism Scientific: STAPHYLOCOCCUS AUREUS
    Organism Taxid: 1280
    Other Details: INDUCIBLE TRC PROMOTOR PKK233-2 DERIVATIVE WITH TN9 CAT GENE INSERTED INTO TEM BLAZ
    Strain: PC1
    Synonym: PENICILLINASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY B:236 , ALA B:238 , ARG B:244 , ASN B:245BINDING SITE FOR RESIDUE CL B 1
2CATUNKNOWNSER A:70 , LYS A:73 , LYS A:234 , GLN A:237ACTIVE SITE. THE NUCLEOPHILIC RESIDUE IS SER 70.

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BETA_LACTAMASE_APS00146 Beta-lactamase class-A active site.BLAC_STAAU59-74
 		  2A:66-81
B:66-81

(-) Exons   (0, 0)

(no "Exon" information available for 1OME)

(-) 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:241
 aligned with BLAC_STAAU | P00807 from UniProtKB/Swiss-Prot  Length:281

    Alignment length:257
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       
           BLAC_STAAU    25 KELNDLEKKYNAHIGVYALDTKSGKEVKFNSDKRFAYASTSKAINSAILLEQVPYNKLNKKVHINKDDIVAYSPILEKYVGKDITLKALIEASMTYSDNTANNKIIKEIGGIKKVKQRLKELGDKVTNPVRYEIELNYYSPKSKKDTSTPAAFGKTLNKLIANGKLSKENKKFLLDLMLNNKSGDTLIKDGVPKDYKVADKSGQAITYASRNDVAFVYPKGQSEPIVLVIFTNKDNKSDKPNDKLISETAKSVMKEF 281
               SCOP domains d1omea_ A: beta-Lactamase, class A                                                                                                                                                                                                                                SCOP domains
               CATH domains 1omeA00 A:31-290 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                                          CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhh.eeeeeeeee.....eeee....eee..hhhhhhhhhhhh....hhhhh.eeee...........hhhh..eeeehhhhhhhhhhh..hhhhhhhhhhh..hhhhhhhhhh........----------------.eeehhhhhhhhhhh.......hhhhhhhhhhhh........hhhh.....eeeeeee......eeeeeeeee.......eeeeeeeee........hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------BETA_LACTAMASE_A--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ome A  31 KELNDLEKKYNAHIGVYALDTKSGKEVKFNSDKRFAYASTSKAINSAILLEQVPYNKLNKKVHINKDDIVAYSPILEKYVGKDITLKALIEASMTYSDNTANNKIIKEIGGIKKVKQRLKELGDKVTNP----------------DTSTPAAFGKTLNKLIANGKLSKENKKFLLDLMLNNKSGDTLIKDGVPKDYKVADKSGQAITYASRNDVAFVYPKGQSEPIVLVIFTNKDNKSDKPNDKLISETAKSVMKEF 290
                                    40        50      ||61        71        81  ||    93       103       113       123       133       143       153        |-         -     | 183       193       203       213       223       233       243       253       263       273       283       
                                                     57|                       84|                                                                        162              179                                                                                                               
                                                      59                        87                                                                                                                                                                                                           


Chain B from PDB  Type:PROTEIN  Length:240
 aligned with BLAC_STAAU | P00807 from UniProtKB/Swiss-Prot  Length:281

    Alignment length:256
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275      
           BLAC_STAAU    26 ELNDLEKKYNAHIGVYALDTKSGKEVKFNSDKRFAYASTSKAINSAILLEQVPYNKLNKKVHINKDDIVAYSPILEKYVGKDITLKALIEASMTYSDNTANNKIIKEIGGIKKVKQRLKELGDKVTNPVRYEIELNYYSPKSKKDTSTPAAFGKTLNKLIANGKLSKENKKFLLDLMLNNKSGDTLIKDGVPKDYKVADKSGQAITYASRNDVAFVYPKGQSEPIVLVIFTNKDNKSDKPNDKLISETAKSVMKEF 281
               SCOP domains d1omeb_ B: beta-Lactamase, class A                                                                                                                                                                                                                               SCOP domains
               CATH domains 1omeB00 B:32-290 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                                         CATH domains
           Pfam domains (1) -Beta-lactamase-1omeB01 B:33-284                                                                                                                                                                                                                          ------ Pfam domains (1)
           Pfam domains (2) -Beta-lactamase-1omeB02 B:33-284                                                                                                                                                                                                                          ------ Pfam domains (2)
         Sec.struct. author .hhhhhhhh..eeeeeeee.....eeee....eee.hhhhhhhhhhhhh.....hhhh.eeee.hhh.......hhh...eeeehhhhhhhhhhh..hhhhhhhhhhh..hhhhhhhhhhh.......----------------.eeehhhhhhhhhhh.......hhhhhhhhhhhh..hhh...hhhh.....eeeeee.........eeeeeee.......eeeeeeee.........hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------BETA_LACTAMASE_A--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ome B  32 ELNDLEKKYNAHIGVYALDTKSGKEVKFNSDKRFAYASTSKAINSAILLEQVPYNKLNKKVHINKDDIVAYSPILEKYVGKDITLKALIEASMTYSDNTANNKIIKEIGGIKKVKQRLKELGDKVTNP----------------DTSTPAAFGKTLNKLIANGKLSKENKKFLLDLMLNNKSGDTLIKDGVPKDYKVADKSGQAITYASRNDVAFVYPKGQSEPIVLVIFTNKDNKSDKPNDKLISETAKSVMKEF 290
                                    41        51     || 62        72        82 ||     94       104       114       124       134       144       154       | -         -    |  184       194       204       214       224       234       244       254       264       274       284      
                                                    57|                       84|                                                                        162              179                                                                                                               
                                                     59                        87
   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/Biological Unit
(-)
Class: Multi-domain proteins (alpha and beta) (2421)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: Beta-lactamase (210)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (BLAC_STAAU | P00807)
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.
biological process
    GO:0030655    beta-lactam antibiotic catabolic process    The chemical reactions and pathways resulting in the breakdown of a beta-lactam antibiotic, any member of a class of natural or semisynthetic antibiotics whose characteristic feature is a strained, four-membered beta-lactam ring. They include the penicillins and many of the cephalosporins.
    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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 Related Entries

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UniProtKB/Swiss-Prot
        BLAC_STAAU | P00807: 1alq 1blc 1blh 1blp 1dja 1djb 1djc 1ghi 1ghm 1ghp 1kge 1kgf 1kgg 1pio 3blm

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