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(-) Description

Title :  CRYSTAL STRUCTURE OF GES-11
 
Authors :  H. Delbruck, K. M. V. Hoffmann, C. Bebrone
Date :  14 Dec 11  (Deposition) - 26 Sep 12  (Release) - 19 Jun 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Beta Lactamase Fold, Hydrolase, Beta Lactams (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Delbruck, P. Bogaerts, M. B. Kupper, R. Rezende De Castro, S. Bennink, Y. Glupczynski, M. Galleni, K. M. Hoffmann, C. Bebrone
Kinetic And Crystallographic Studies Of Extended-Spectrum Ges-11, Ges-12, And Ges-14 Beta-Lactamases.
Antimicrob. Agents Chemother. V. 56 5618 2012
PubMed-ID: 22908160  |  Reference-DOI: 10.1128/AAC.01272-12

(-) Compounds

Molecule 1 - EXTENDED SPECTRUM CLASS A BETA-LACTAMASE GES-11
    Chains: A, B
    EC Number: 3.5.2.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28/GES11
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: BETA-LACTAMASE
    Gene: BLAGES-11, GES11
    Organism Scientific: ACINETOBACTER BAUMANNII
    Organism Taxid: 470
    Synonym: EXTENDED-SPECTRUM BETA-LACTAMASE, GES-11

 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  (2, 24)

Asymmetric Unit (2, 24)
No.NameCountTypeFull Name
1IOD23Ligand/IonIODIDE ION
2NA1Ligand/IonSODIUM ION
Biological Unit 1 (1, 11)
No.NameCountTypeFull Name
1IOD11Ligand/IonIODIDE ION
2NA-1Ligand/IonSODIUM ION
Biological Unit 2 (1, 12)
No.NameCountTypeFull Name
1IOD12Ligand/IonIODIDE ION
2NA-1Ligand/IonSODIUM ION

(-) Sites  (20, 20)

Asymmetric Unit (20, 20)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLN A:145 , GLY B:92BINDING SITE FOR RESIDUE IOD A 288
02AC2SOFTWARELYS A:160BINDING SITE FOR RESIDUE IOD A 289
03AC3SOFTWARETHR A:177BINDING SITE FOR RESIDUE IOD A 290
04AC4SOFTWAREARG A:204BINDING SITE FOR RESIDUE IOD A 291
05AC5SOFTWARESER A:64 , SER A:125 , THR A:230BINDING SITE FOR RESIDUE IOD A 292
06AC6SOFTWAREGLY A:92BINDING SITE FOR RESIDUE IOD A 293
07AC7SOFTWAREARG A:84BINDING SITE FOR RESIDUE IOD A 294
08AC8SOFTWAREARG A:105 , GLN B:210BINDING SITE FOR RESIDUE IOD A 295
09AC9SOFTWARELYS A:261BINDING SITE FOR RESIDUE IOD A 296
10BC1SOFTWARETRP A:224BINDING SITE FOR RESIDUE IOD A 297
11BC2SOFTWAREGLN A:210 , ARG B:105BINDING SITE FOR RESIDUE IOD B 288
12BC3SOFTWAREALA A:57 , NA B:300BINDING SITE FOR RESIDUE IOD B 290
13BC4SOFTWAREHIS A:54 , ARG A:55 , ALA B:57 , NA B:300BINDING SITE FOR RESIDUE IOD B 291
14BC5SOFTWARETHR B:177BINDING SITE FOR RESIDUE IOD B 292
15BC6SOFTWARESER B:64 , SER B:125 , THR B:230 , HOH B:389BINDING SITE FOR RESIDUE IOD B 294
16BC7SOFTWARESER B:196BINDING SITE FOR RESIDUE IOD B 296
17BC8SOFTWAREARG B:204BINDING SITE FOR RESIDUE IOD B 297
18BC9SOFTWARETHR B:113BINDING SITE FOR RESIDUE IOD B 298
19CC1SOFTWAREHOH B:356BINDING SITE FOR RESIDUE IOD B 299
20CC2SOFTWAREARG A:55 , MET A:56 , ARG B:55 , MET B:56 , IOD B:290 , IOD B:291BINDING SITE FOR RESIDUE NA B 300

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:63 -A:233
2B:63 -B:233

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Glu A:161 -Pro A:162
2Glu B:161 -Pro B:162

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3V3R)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3V3R)

(-) Exons   (0, 0)

(no "Exon" information available for 3V3R)

(-) 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:266
 aligned with C5HUY1_ACIBA | C5HUY1 from UniProtKB/TrEMBL  Length:287

    Alignment length:266
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278      
         C5HUY1_ACIBA    19 SEKLTFKTDLEKLEREKAAQIGVAIVDPQGEIVAGHRMAQRFAMCSTFKFPLAALVFERIDSGTERGDRKLSYGPDMIVEWSPATERFLASGHMTVLEAAQAAVQLSDNGATNLLLREIGGPAAMTQYFRKIGDSVSRLDRKEPEMGDNTPGDLRDTTTPIAMARTVAKVLYGGALTSTSTHTIERWLIGNQTGDATLRAGFPKDWVVGEKTGTCANGARNDIGFFKAQERDYAVAVYTTAPKLSAVERDELVASVGQVITQLILS 284
               SCOP domains d3v3ra_ A: automated matches                                                                                                                                                                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhh..eeeeeee.....eeeee.....ee.hhhhhhhhhhhhhhhhhh.......eee.hhhhh...hhhhhhhh...eeehhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhh........eehhhhhhhhhhhhhhh...hhhhhhhhhhhhhh......hhhhhh....eeeeeeeee...eeeeeeeeee..eeeeeeeeee....hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3v3r A  19 SEKLTFKTDLEKLEREKAAQIGVAIVDPQGEIVAGHRMAQRFAMCSTFKFPLAALVFERIDSGTERGDRKLSYGPDMIVEWSPATERFLASGHMTVLEAAQAAVQLSDNGATNLLLREIGGPAAMTQYFRKIGDSVSRLDRKEPEMGDNTPGDLRDTTTPIAMARTVAKVLYGGALTSTSTHTIERWLIGNQTGDATLRAGFPKDWVVGEKTGTCANGARNDIGFFKAQERDYAVAVYTTAPKLSAVERDELVASVGQVITQLILS 284
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278      


Chain B from PDB  Type:PROTEIN  Length:265
 aligned with C5HUY1_ACIBA | C5HUY1 from UniProtKB/TrEMBL  Length:287

    Alignment length:265
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278     
         C5HUY1_ACIBA    19 SEKLTFKTDLEKLEREKAAQIGVAIVDPQGEIVAGHRMAQRFAMCSTFKFPLAALVFERIDSGTERGDRKLSYGPDMIVEWSPATERFLASGHMTVLEAAQAAVQLSDNGATNLLLREIGGPAAMTQYFRKIGDSVSRLDRKEPEMGDNTPGDLRDTTTPIAMARTVAKVLYGGALTSTSTHTIERWLIGNQTGDATLRAGFPKDWVVGEKTGTCANGARNDIGFFKAQERDYAVAVYTTAPKLSAVERDELVASVGQVITQLIL 283
               SCOP domains d3v3rb_ B: automated matches                                                                                                                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh.eeeeeee.....eeeee.....ee.hhhhhhhhhhhhhhhhhh.......eee.hhhhh...hhhhhhhh...eeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhh........eehhhhhhhhhhhhhhh...hhhhhhhhhhhhhh......hhhhhh....eeeeeeeee...eeeeeeeee....eeeeeeeee....hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3v3r B  19 SEKLTFKTDLEKLEREKAAQIGVAIVDPQGEIVAGHRMAQRFAMCSTFKFPLAALVFERIDSGTERGDRKLSYGPDMIVEWSPATERFLASGHMTVLEAAQAAVQLSDNGATNLLLREIGGPAAMTQYFRKIGDSVSRLDRKEPEMGDNTPGDLRDTTTPIAMARTVAKVLYGGALTSTSTHTIERWLIGNQTGDATLRAGFPKDWVVGEKTGTCANGARNDIGFFKAQERDYAVAVYTTAPKLSAVERDELVASVGQVITQLIL 283
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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  (1, 2)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3V3R)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3V3R)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (C5HUY1_ACIBA | C5HUY1)
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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2qpn HOLOMOLOGOUS STRUCTURE