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(-) Description

Title :  CRYSTAL STRUCTURE OF THE CLASS D BETA-LACTAMASE OXA-13 COMPLEXED WITH IMIPENEM
 
Authors :  C. Mayer, L. Pernot, W. Sougakoff
Date :  29 May 01  (Deposition) - 23 May 02  (Release) - 07 Dec 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Hydrolase, Acyl-Enzyme (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Pernot, C. Mayer, W. Sougakoff
Crystal Structure Of The Acyl-Enzyme Intermediate Oxa-13:Imipenem
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - BETA-LACTAMASE
    Chains: A, B
    EC Number: 3.5.2.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PAZ304
    Expression System Strain: HB101
    Expression System Taxid: 562
    Organism Scientific: PSEUDOMONAS AERUGINOSA
    Organism Taxid: 287
    Other Details: ACYL-ENZYME COMPLEX
    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, 7)

Asymmetric/Biological Unit (2, 7)
No.NameCountTypeFull Name
1IM22Ligand/Ion(5R)-5-[(1S,2R)-1-FORMYL-2-HYDROXYPROPYL]-3-[(2-{[(E)-IMINOMETHYL]AMINO}ETHYL)SULFANYL]-4,5-DIHYDRO-1H-PYRROLE-2-CARBOXYLIC ACID
2SO45Ligand/IonSULFATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:62 , GLY A:142 , ASN A:143BINDING SITE FOR RESIDUE SO4 A1268
2AC2SOFTWARELEU A:175 , ASN A:176 , LYS A:182 , HOH A:2201 , HOH A:2202 , ASN B:85BINDING SITE FOR RESIDUE SO4 A1269
3AC3SOFTWARETHR A:80 , ARG A:131 , LYS A:134 , TYR A:135 , GLU B:126BINDING SITE FOR RESIDUE SO4 A1270
4AC4SOFTWAREGLU B:62 , GLY B:142 , ASN B:143BINDING SITE FOR RESIDUE SO4 B1268
5AC5SOFTWAREASN B:176 , LYS B:182 , HOH B:2182 , HOH B:2183BINDING SITE FOR RESIDUE SO4 B1269
6AC6SOFTWAREALA A:66 , SER A:67 , SER A:115 , LEU A:155 , THR A:206 , GLY A:207 , PHE A:208 , GLU A:244 , LEU A:247 , ARG A:250 , HOH A:2198 , HOH A:2199 , HOH A:2200BINDING SITE FOR RESIDUE IM2 A1267
7AC7SOFTWAREALA B:66 , SER B:67 , LEU B:155 , GLY B:207 , PHE B:208 , ARG B:250 , HOH B:2086BINDING SITE FOR RESIDUE IM2 B1267

(-) 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 1H5X)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1H5X)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1H5X)

(-) Exons   (0, 0)

(no "Exon" information available for 1H5X)

(-) 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:237
 aligned with Q51400_PSEAI | Q51400 from UniProtKB/TrEMBL  Length:266

    Alignment length:246
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260      
         Q51400_PSEAI    21 SITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNNLARASKEYLPASTFKIPSAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLSLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFWLEGQLRISAVNQVEFLESLFLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKGTEVYFFAFNMDIDNENKLPLRKSIPTKIMASEGIIGG 266
               SCOP domains d1h5xa_ A: Class D beta-lactamase                                                                                                                                                                                                                      SCOP domains
               CATH domains 1h5xA00 A:21-266 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eee....hhhhhh....eeeeeee.....eee..hhhhh.ee..hhhhhhhhhhhhhh............---------hh.....hhhhhh...hhhhhhhhhhh.hhhhhhhhhh..............hhhh....eehhhhhhhhhhhh.......hhhhhhhhhh.eeee...eeeeeeeee.......eeeeeeeeeeeee..eeeeeeeeeee..hhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1h5x A  21 SITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNNLARASKEYLPASTFKIPSAIIGLETGVIKNEHQVFK---------QWERDLSLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFWLEGQLRISAVNQVEFLESLFLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKGTEVYFFAFNMDIDNENKLPLRKSIPTKIMASEGIIGG 266
                                    30        40        50        60        70        80        90|        -|      110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260      
                                                                                                 91       101                                                                                                                                                                     


Chain B from PDB  Type:PROTEIN  Length:234
 aligned with Q51400_PSEAI | Q51400 from UniProtKB/TrEMBL  Length:266

    Alignment length:246
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260      
         Q51400_PSEAI    21 SITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNNLARASKEYLPASTFKIPSAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLSLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFWLEGQLRISAVNQVEFLESLFLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKGTEVYFFAFNMDIDNENKLPLRKSIPTKIMASEGIIGG 266
               SCOP domains d1h5xb_ B: Class D beta-lactamase                                                                                                                                                                                                                      SCOP domains
               CATH domains 1h5xB00 B:21-266 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eee....hhhhhh....eeeeeee.....eee..hhhhh.ee..hhhhhhhhhhhhhh.............------------...hhhhhh...hhhhhhhhhhh.hhhhhhhhhh..............hhhh....eehhhhhhhhhhhh.......hhhhhhhhhh.eeeee..eeeeeeeee.......eeeeeeeeeeeee..eeeeeeeeeee..hhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1h5x B  21 SITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNNLARASKEYLPASTFKIPSAIIGLETGVIKNEHQVFKW------------DLSLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFWLEGQLRISAVNQVEFLESLFLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKGTEVYFFAFNMDIDNENKLPLRKSIPTKIMASEGIIGG 266
                                    30        40        50        60        70        80        90 |       -    |  110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260      
                                                                                                  92          105
   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 1H5X)

(-) 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: 1h8y 1h8z

(-) Related Entries Specified in the PDB File

1h8y CRYSTAL STRUCTURE OF THE CLASS D BETA- LACTAMASE OXA-13 IN COMPLEX WITH MEROPENEM
1h8z CRYSTAL STRUCTURE OF THE CLASS D BETA- LACTAMASE OXA-13