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(-) Description

Title :  CRYSTAL STRUCTURE OF THE CLASS D BETA-LACTAMASE OXA-13 IN COMPLEX WITH MEROPENEM
 
Authors :  L. Pernot, F. Frenois, T. Rybkine, G. L'Hermite, S. Petrella, J. Delett V. Jarlier, E. Collatz, W. Sougakoff
Date :  17 Feb 01  (Deposition) - 12 Jul 01  (Release) - 06 Feb 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Hydrolase, Beta-Lactamase, Class D, Oxa-13, Meropenem, Acyl- Enzyme (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Pernot, F. Frenois, T. Rybkine, G. L'Hermite, S. Petrella, J. Delettre, V. Jarlier, E. Collatz, W. Sougakoff
Crystal Structures Of The Class D B-Lactamase Oxa-13 In The Native Form And In Complex With Meropenem
J. Mol. Biol. V. 310 859 2001
PubMed-ID: 11453693  |  Reference-DOI: 10.1006/JMBI.2001.4805
(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: BLA OXA-13
    Expression System Plasmid: PAZ304
    Expression System Strain: HB101
    Expression System Taxid: 562
    Gene: BLA OXA-13
    Organism Scientific: PSEUDOMONAS AERUGINOSA
    Organism Taxid: 287
    Other Details: THERE IS AN ESTER LINK BETWEEN SER A 67 OG AND MER A 300 C7 AND BETWEEN SER B 67 OG AND MER B 300 C7
    Strain: PAE391
    Synonym: BETA-LACTAMASE OXA-13

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric/Biological Unit (2, 6)
No.NameCountTypeFull Name
1MER2Ligand/Ion(4R,5S)-3-{[(3S,5S)-5-(DIMETHYLCARBAMOYL)PYRROLIDIN-3-YL]SULFANYL}-5-[(2S,3R)-3-HYDROXY-1-OXOBUTAN-2-YL]-4-METHYL-4,5-DIHYDRO-1H-PYRROLE-2-CARBOXYLIC ACID
2SO44Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:131 , LYS A:134 , TYR A:135BINDING SITE FOR RESIDUE SO4 A1268
2AC2SOFTWAREPHE A:174 , THR A:230 , GLU A:231 , HOH A:2156 , HOH A:2157 , HIS B:87BINDING SITE FOR RESIDUE SO4 A1269
3AC3SOFTWARETHR B:80 , ARG B:131 , LYS B:134 , TYR B:135BINDING SITE FOR RESIDUE SO4 B1268
4AC4SOFTWAREASN A:85 , ASN B:176 , LYS B:182 , HOH B:2167BINDING SITE FOR RESIDUE SO4 B1269
5AC5SOFTWAREALA A:66 , SER A:67 , LEU A:155 , THR A:206 , GLY A:207 , PHE A:208 , LEU A:247 , ARG A:250BINDING SITE FOR RESIDUE MER A 300
6AC6SOFTWAREALA B:66 , SER B:67 , TRP B:102 , VAL B:117 , LEU B:155 , THR B:206 , GLY B:207 , PHE B:208 , GLU B:244 , LEU B:247 , ARG B:250 , HOH B:2143 , HOH B:2166BINDING SITE FOR RESIDUE MER B 300

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:44 -A:51
2B:44 -B:51

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1H8Y)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1H8Y)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1H8Y)

(-) Exons   (0, 0)

(no "Exon" information available for 1H8Y)

(-) 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:247
 aligned with Q51400_PSEAI | Q51400 from UniProtKB/TrEMBL  Length:266

    Alignment length:247
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       
         Q51400_PSEAI    20 SSITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNNLARASKEYLPASTFKIPSAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLSLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFWLEGQLRISAVNQVEFLESLFLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKGTEVYFFAFNMDIDNENKLPLRKSIPTKIMASEGIIGG 266
               SCOP domains d1h8ya_ A: Class D beta-lactamase                                                                                                                                                                                                                       SCOP domains
               CATH domains 1h8yA00 A:20-266 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee....hhhhhh....eeeeeee.....eee..hhhhh.ee..hhhhhhhhhhhhhh....................hhh.....hhhhhh...hhhhhhhhhhh.hhhhhhhhhh..............hhhh....eehhhhhhhhhhhh.......hhhhhhhhhh.eeeee..eeeeeeeee.......eeeeeeeeeeeee..eeeeeeeeeee..hhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1h8y A  20 SSITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNNLARASKEYLPASTFKIPSAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLSLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFWLEGQLRISAVNQVEFLESLFLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKGTEVYFFAFNMDIDNENKLPLRKSIPTKIMASEGIIGG 266
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       


Chain B from PDB  Type:PROTEIN  Length:247
 aligned with Q51400_PSEAI | Q51400 from UniProtKB/TrEMBL  Length:266

    Alignment length:247
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       
         Q51400_PSEAI    20 SSITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNNLARASKEYLPASTFKIPSAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLSLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFWLEGQLRISAVNQVEFLESLFLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKGTEVYFFAFNMDIDNENKLPLRKSIPTKIMASEGIIGG 266
               SCOP domains d1h8yb_ B: Class D beta-lactamase                                                                                                                                                                                                                       SCOP domains
               CATH domains 1h8yB00 B:20-266 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee....hhhhhh....eeeeeee.....eee..hhhhh.ee..hhhhhhhhhhhhhh....................hhh.....hhhhhh...hhhhhhhhhhh.hhhhhhhhhh..............hhhh....eehhhhhhhhhhhh.......hhhhhhhhhh.eeeee..eeeeeeeee.......eeeeeeeeeeeee..eeeeeeeeeee..hhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1h8y B  20 SSITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNNLARASKEYLPASTFKIPSAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLSLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFWLEGQLRISAVNQVEFLESLFLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKGTEVYFFAFNMDIDNENKLPLRKSIPTKIMASEGIIGG 266
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259
   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  (0, 0)

(no "Pfam Domain" information available for 1H8Y)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q51400_PSEAI | Q51400)
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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 Related Entries

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

UniProtKB/TrEMBL
        Q51400_PSEAI | Q51400: 1h5x 1h8z

(-) Related Entries Specified in the PDB File

1h8z CRYSTAL STRUCTURE OF THE CLASS D BETA- LACTAMASE OXA-13