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(-) Description

Title :  STRUCTURAL BASIS FOR THE INTERACTION OF LACTIVICINS WITH SERINE BETA-LACTAMASES
 
Authors :  E. Sauvage, R. Herman, F. Kerff, M. Rocaboy, P. Charlier
Date :  22 Feb 10  (Deposition) - 14 Jul 10  (Release) - 02 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Hydrolase-Antibiotic Complex, Antibiotic (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Brown, P. Charlier, R. Herman, C. J. Schofield, E. Sauvage
Structural Basis For The Interaction Of Lactivicins With Serine Beta-Lactamases.
J. Med. Chem. V. 53 5890 2010
PubMed-ID: 20593835  |  Reference-DOI: 10.1021/JM100437U

(-) Compounds

Molecule 1 - BETA-LACTAMASE
    Chains: A, B
    EC Number: 3.5.2.6
    Organism Scientific: BACILLUS LICHENIFORMIS
    Organism Taxid: 1402
    Strain: BS3

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric Unit (3, 6)
No.NameCountTypeFull Name
1EOH4Ligand/IonETHANOL
2L4C1Ligand/Ion(2E)-2-{[(2S)-2-(ACETYLAMINO)-2-CARBOXYETHOXY]IMINO}PENTANEDIOIC ACID
3SO41Ligand/IonSULFATE ION
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1EOH2Ligand/IonETHANOL
2L4C1Ligand/Ion(2E)-2-{[(2S)-2-(ACETYLAMINO)-2-CARBOXYETHOXY]IMINO}PENTANEDIOIC ACID
3SO4-1Ligand/IonSULFATE ION
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1EOH2Ligand/IonETHANOL
2L4C-1Ligand/Ion(2E)-2-{[(2S)-2-(ACETYLAMINO)-2-CARBOXYETHOXY]IMINO}PENTANEDIOIC ACID
3SO41Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:70 , ASN A:104 , TYR A:105 , SER A:130 , ASN A:132 , ASN A:170 , THR A:216 , LYS A:234 , THR A:235 , GLY A:236 , ALA A:237 , ARG A:244 , HOH A:2091 , HOH A:2135BINDING SITE FOR RESIDUE L4C A1291
2AC2SOFTWARESER B:70 , SER B:130 , LYS B:234 , THR B:235 , GLY B:236 , ALA B:237 , ARG B:244 , HOH B:2034BINDING SITE FOR RESIDUE SO4 B1291
3AC3SOFTWARELYS A:140 , GLY A:143 , GLY A:144 , PHE A:165 , GLY B:143 , GLY B:144 , PHE B:165BINDING SITE FOR RESIDUE EOH A1292
4AC4SOFTWARELYS A:288 , ALA A:289 , HOH A:2167BINDING SITE FOR RESIDUE EOH A1293
5AC5SOFTWARELYS B:288 , LEU B:290BINDING SITE FOR RESIDUE EOH B1292
6AC6SOFTWARELYS B:273 , TYR B:274 , HOH B:2137BINDING SITE FOR RESIDUE EOH B1293

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2X71)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Glu A:166 -Pro A:167
2Glu B:166 -Pro B:167

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2X71)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2X71)

(-) Exons   (0, 0)

(no "Exon" information available for 2X71)

(-) Sequences/Alignments

Asymmetric 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:255
 aligned with P94458_BACLI | P94458 from UniProtKB/TrEMBL  Length:265

    Alignment length:255
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255     
         P94458_BACLI     6 DDFAKLEEQFDAKLGIFALDTGTNRTVTYRPDERFAFASTIKALTVGVLLQQKSIEDLNQRITYTRDDLVNYNPITEKHVDTGMTLKELADASLRYSDNTAQNLILKQIGGPESLKKELRKIGDEVTNPERFEPELNEVNPGETQDTSTARALATSLQAFALEDKLPSEKRELLIDWMKRNTTGDALIRAGVPEGWEVADKTGAGSYGTRNDIAIIWPPKGDPVVLAVLSSRDKKDAKYDDKLIAEATKVVVKAL 260
               SCOP domains d2x71a_ A: automated matches                                                                                                                                                                                                                                    SCOP domains
               CATH domains 2x71A00 A:31-290 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                                        CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhh.eeeeeeee.....eeee....eee...hhhhhhhhhhhhhh.hhhhh.ee............hhhhh....eehhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh...........hhhhh........eeehhhhhhhhhhhhhh...hhhhhhhhhhhhhh......hhhhhh....eeeeeeee.....eeeeeeee......eeeeeeee.........hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2x71 A  31 DDFAKLEEQFDAKLGIFALDTGTNRTVTYRPDERFAFASTIKALTVGVLLQQKSIEDLNQRITYTRDDLVNYNPITEKHVDTGMTLKELADASLRYSDNTAQNLILKQIGGPESLKKELRKIGDEVTNPERFEPELNEVNPGETQDTSTARALATSLQAFALEDKLPSEKRELLIDWMKRNTTGDALIRAGVPEGWEVADKTGAGSYGTRNDIAIIWPPKGDPVVLAVLSSRDKKDAKYDDKLIAEATKVVVKAL 290
                                    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:255
 aligned with P94458_BACLI | P94458 from UniProtKB/TrEMBL  Length:265

    Alignment length:255
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255     
         P94458_BACLI     6 DDFAKLEEQFDAKLGIFALDTGTNRTVTYRPDERFAFASTIKALTVGVLLQQKSIEDLNQRITYTRDDLVNYNPITEKHVDTGMTLKELADASLRYSDNTAQNLILKQIGGPESLKKELRKIGDEVTNPERFEPELNEVNPGETQDTSTARALATSLQAFALEDKLPSEKRELLIDWMKRNTTGDALIRAGVPEGWEVADKTGAGSYGTRNDIAIIWPPKGDPVVLAVLSSRDKKDAKYDDKLIAEATKVVVKAL 260
               SCOP domains d2x71b_ B: automated matches                                                                                                                                                                                                                                    SCOP domains
               CATH domains 2x71B00 B:31-290 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                                        CATH domains
           Pfam domains (1) --------------------Beta-lactamase2-2x71B01 B:51-263                                                                                                                                                                                --------------------------- Pfam domains (1)
           Pfam domains (2) --------------------Beta-lactamase2-2x71B02 B:51-263                                                                                                                                                                                --------------------------- Pfam domains (2)
         Sec.struct. author hhhhhhhhhhh.eeeeeeee.....eeee....eee...hhhhhhhhhhhhhh..hhhh.ee............hhhhh....eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhh........eeehhhhhhhhhhhhh....hhhhhhhhhhhhhh......hhhhhh....eeeeeeeee...eeeeeeeee......eeeeeeee........hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2x71 B  31 DDFAKLEEQFDAKLGIFALDTGTNRTVTYRPDERFAFASTIKALTVGVLLQQKSIEDLNQRITYTRDDLVNYNPITEKHVDTGMTLKELADASLRYSDNTAQNLILKQIGGPESLKKELRKIGDEVTNPERFEPELNEVNPGETQDTSTARALATSLQAFALEDKLPSEKRELLIDWMKRNTTGDALIRAGVPEGWEVADKTGAGSYGTRNDIAIIWPPKGDPVVLAVLSSRDKKDAKYDDKLIAEATKVVVKAL 290
                                    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)
  - → 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 Unit
(-)
Class: Multi-domain proteins (alpha and beta) (2421)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

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

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (P94458_BACLI | P94458)
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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  2x71
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 Related Entries

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

UniProtKB/Swiss-Prot
        P94458_BACLI | P94458: 1w7f 2wk0 2y91 3b3x
UniProtKB/TrEMBL
        P94458_BACLI | P94458: 4a5r

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2X71)