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(-) Description

Title :  CRYSTAL STRUCTURE OF BETA-LACTAMSE PENP_E166S IN COMPLEX WITH MEROPENEM
 
Authors :  X. Pan, W. Wong, Y. Zhao
Date :  21 Oct 13  (Deposition) - 10 Sep 14  (Release) - 10 Sep 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Hydrolase, Hydrolase-Antibiotic Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. Pan, W. Wong, Y. He, Y. Jiang, Y. Zhao
Perturbing The General Base Residue Glu166 In The Active Site Of Class A Beta-Lactamase Leads To Enhanced Carbapenem Binding And Acylation
Biochemistry V. 53 5414 2014
PubMed-ID: 25020031  |  Reference-DOI: 10.1021/BI401609H

(-) Compounds

Molecule 1 - BETA-LACTAMASE
    Chains: B, A
    EC Number: 3.5.2.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET30
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: SMALL EXOPENICILLINASE
    Gene: BLAP, PENP, PENP BLAP
    Mutation: YES
    Organism Scientific: BACILLUS LICHENIFORMIS
    Organism Taxid: 1402
    Synonym: PENICILLINASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1DWZ2Ligand/Ion(2S,3R,4S)-4-{[(3S,5S)-5-(DIMETHYLCARBAMOYL)PYRROLIDIN-3-YL]SULFANYL}-2-[(1S,2R)-1-FORMYL-2-HYDROXYPROPYL]-3-METHYL-3,4-DIHYDRO-2H-PYRROLE-5-CARBOXYLIC ACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA B:69 , SER B:70 , SER B:130 , ASN B:132 , LYS B:234 , THR B:235 , GLY B:236 , ALA B:237 , TYR B:274 , HOH B:533 , HOH B:569 , HOH B:611 , HOH B:649BINDING SITE FOR RESIDUE DWZ B 400
2AC2SOFTWAREALA A:69 , SER A:70 , SER A:130 , ASN A:132 , THR A:235 , GLY A:236 , ALA A:237 , TYR A:274 , HOH A:536 , HOH A:615BINDING SITE FOR RESIDUE DWZ A 400

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4N9L)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ser B:166 -Pro B:167
2Ser A:166 -Pro A:167

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4N9L)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4N9L)

(-) Exons   (0, 0)

(no "Exon" information available for 4N9L)

(-) 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:256
                                                                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh.eeeeeeee.....eeee....eee...hhhhhhhhhhhhhh.hhhhh.ee............hhhhh....eehhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh..........hhhhh........eeehhhhhhhhhhhhhh...hhhhhhhhhhhhhh......hhhhhh....eeeeeeeee...eeeeeeeee......eeeeeeee........hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4n9l A  31 DDFAKLEEQFDAKLGIFALDTGTNRTVAYRPDERFAFASTIKALTVGVLLQQKSIEDLNQRITYTRDDLVNYNPITEKHVDTGMTLKELADASLRYSDNAAQNLILKQIGGPESLKKELRKIGDEVTNPERFSPELNEVNPGETQDTSTARALVTSLRAFALEDKLPSEKRELLIDWMKRNTTGDALIRAGVPDGWEVADKTGAASYGTRNDIAIIWPPKGDPVVLAVLSSRDKKDAKYDDKLIAEATKVVMKALN 291
                                    40        50      ||61        71        81 ||     93       103       113       123       133       143       153       163       173       183       193       203       213       223       233    || 244       255       265       275       285      
                                                     57|                      83|                                                                                                                                                     238|         252|                                     
                                                      59                       86                                                                                                                                                      240          254                                     


Chain B from PDB  Type:PROTEIN  Length:256
                                                                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhh.eeeeeeee.....eeee....eee...hhhhhhhhhhhhh..hhhhh.ee..hhhhh.....hhhhh....eehhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh...........hhhhh........eeehhhhhhhhhhhhh....hhhhhhhhhhhhhh......hhhhhh....eeeeeeeee...eeeeeeeee......eeeeeeee........hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4n9l B  31 DDFAKLEEQFDAKLGIFALDTGTNRTVAYRPDERFAFASTIKALTVGVLLQQKSIEDLNQRITYTRDDLVNYNPITEKHVDTGMTLKELADASLRYSDNAAQNLILKQIGGPESLKKELRKIGDEVTNPERFSPELNEVNPGETQDTSTARALVTSLRAFALEDKLPSEKRELLIDWMKRNTTGDALIRAGVPDGWEVADKTGAASYGTRNDIAIIWPPKGDPVVLAVLSSRDKKDAKYDDKLIAEATKVVMKALN 291
                                    40        50      ||61        71        81 ||     93       103       113       123       133       143       153       163       173       183       193       203       213       223       233    || 244       255       265       275       285      
                                                     57|                      83|                                                                                                                                                     238|         252|                                     
                                                      59                       86                                                                                                                                                      240          254
   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  (0, 0)

(no "SCOP Domain" information available for 4N9L)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4N9L)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4N9L)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)

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    Ser A:166 - Pro A:167   [ RasMol ]  
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        BLAC_BACLI | P00808: 1i2s 1i2w 1mbl 1w7f 2blm 2wk0 2y91 3b3x 3ly3 3ly4 3m2j 3m2k 3sh7 3sh8 3sh9 3soi 4blm 4m3k 4n1h 4n92 4n9k 5ghx 5ghy 5ghz

(-) Related Entries Specified in the PDB File

4n92 4n9k