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(-) Description

Title :  4-SUBSTITUTED TRINEMS AS BROAD SPECTRUM-LACTAMASE INHIBITORS: STRUCTURE-BASED DESIGN, SYNTHESIS AND BIOLOGICAL ACTIVITY
 
Authors :  I. Plantan, L. Selic, T. Mesar, P. Stefanic Anderluh, M. Oblak, A. Prezelj, L. Hesse, M. Andrejasic, M. Vilar, D. Turk, A. Kocijan, T. Prevec, G. Vilfan, D. Kocjan, A. Copar, U. Urleb, T. Solmajer
Date :  13 Jun 07  (Deposition) - 21 Aug 07  (Release) - 31 Mar 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A
Keywords :  Beta-Lactamase Inhibitor, Tricyclic Carbapenem, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. Plantan, L. Selic, T. Mesar, P. S. Anderluh, M. Oblak, A. Prezelj, L. Hesse, M. Andrejasic, M. Vilar, D. Turk, A. Kocijan, T. Prevec, G. Vilfan, D. Kocjan, A. Copar, U. Urleb, T. Solmajer
4-Substituted Trinems As Broad Spectrum Beta-Lactamase Inhibitors: Structure-Based Design, Synthesis, And Biological Activity
J. Med. Chem. V. 50 4113 2007
PubMed-ID: 17665896  |  Reference-DOI: 10.1021/JM0703237
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - BETA-LACTAMASE
    Chains: A
    EC Number: 3.5.2.6
    Organism Scientific: ENTEROBACTER CLOACAE
    Organism Taxid: 550
    Synonym: CEPHALOSPORINASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1LK51Ligand/Ion(1S,4R,7AR)-4-BUTOXY-1-[(1R)-1-FORMYLPROPYL]-2,4,5,6,7,7A-HEXAHYDRO-1H-ISOINDOLE-3-CARBOXYLIC ACID

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:64 , LEU A:119 , GLN A:120 , TYR A:150 , ASN A:152 , GLY A:317 , SER A:318 , HOH A:484BINDING SITE FOR RESIDUE LK5 A 0

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Q9N)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Ala A:31 -Val A:32
2Trp A:276 -Pro A:277
3Asn A:302 -Pro A:303

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (7, 7)

Asymmetric/Biological Unit (7, 7)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_AMPC_ENTCL_004 *I36VAMPC_ENTCL  ---  ---AI16V
2UniProtVAR_AMPC_ENTCL_005 *P58SAMPC_ENTCL  ---  ---AP38S
3UniProtVAR_AMPC_ENTCL_006 *A108PAMPC_ENTCL  ---  ---AA88P
4UniProtVAR_AMPC_ENTCL_007 *L152VAMPC_ENTCL  ---  ---AL132V
5UniProtVAR_AMPC_ENTCL_008 *N262KAMPC_ENTCL  ---  ---AN242K
6UniProtVAR_AMPC_ENTCL_009 *A319VAMPC_ENTCL  ---  ---AA299V
7UniProtVAR_AMPC_ENTCL_010 *T362KAMPC_ENTCL  ---  ---AT342K
   * ID not provided by source
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BETA_LACTAMASE_CPS00336 Beta-lactamase class-C active site.AMPC_ENTCL80-87  1A:60-67

(-) Exons   (0, 0)

(no "Exon" information available for 2Q9N)

(-) 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:359
 aligned with AMPC_ENTCL | P05364 from UniProtKB/Swiss-Prot  Length:381

    Alignment length:359
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371         
           AMPC_ENTCL    22 PVSEKQLAEVVANTITPLMKAQSVPGMAVAVIYQGKPHYYTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDAVTRYWPQLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMPYEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGVKTNVQDMANWVMANMAPENVADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVEANTVVEGSDSKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANTSYPNPARVEAAYHILEAL 380
               SCOP domains d2q9na_ A: automated matches                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains 2q9nA00 A:2-360 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                                                                                                                                                 CATH domains
               Pfam domains ----------Beta-lactamase-2q9nA01 A:12-360                                                                                                                                                                                                                                                                                                                               Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhh..eeeeeeee..ee..eeeeeee....ee......ee...hhhhhhhhhhhhhhhh.......hhhhhh....hhhhh..hhhhhhh...............hhhhhhhhhhhh........ee..hhhhhhhhhhhhh.....hhhhhhhhhhhhhhh...ee...hhhhhhhh..eee..eee......hhhhhh..eehhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh.eeeee..eee....eeee...hhhhhhhhhhhhhhh..ee.eeeeeee.....eeeeeeee....eeeeeeehhh.eeeeeee....hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------V---------------------S-------------------------------------------------P-------------------------------------------V-------------------------------------------------------------------------------------------------------------K--------------------------------------------------------V------------------------------------------K------------------ SAPs(SNPs)
                    PROSITE ----------------------------------------------------------BETA_LAC----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2q9n A   2 PVSEKQLAEVVANTITPLMKAQSVPGMAVAVIYQGKPHYYTFGKADIAANKPVTPQTLFELGSISKTFTGVLGGDAIARGEISLDDAVTRYWPQLTGKQWQGIRMLDLATYTAGGLPLQVPDEVTDNASLLRFYQNWQPQWKPGTTRLYANASIGLFGALAVKPSGMPYEQAMTTRVLKPLKLDHTWINVPKAEEAHYAWGYRDGKAVRVSPGMLDAQAYGVKTNVQDMANWVMANMAPENVADASLKQGIALAQSRYWRIGSMYQGLGWEMLNWPVEANTVVEGSDSKVALAPLPVAEVNPPAPPVKASWVHKTGSTGGFGSYVAFIPEKQIGIVMLANTSYPNPARVEAAYHILEAL 360
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351
   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, 1)

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

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

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

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (AMPC_ENTCL | P05364)
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: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.
cellular component
    GO:0030288    outer membrane-bounded periplasmic space    The region between the inner (cytoplasmic or plasma) membrane and outer membrane of organisms with two membranes such as Gram negative bacteria. These periplasmic spaces are relatively thick and contain a thin peptidoglycan layer (PGL), also referred to as a thin cell wall.
    GO:0042597    periplasmic space    The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

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 Related Entries

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

UniProtKB/Swiss-Prot
        AMPC_ENTCL | P05364: 1bls 1gce 1rgz 1xx2 1y54 2q9m 3s4x 4xux 5hai

(-) Related Entries Specified in the PDB File

1xx2