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(-) Description

Title :  X-RAY STRUCTURE OF CTX-M-16 BETA-LACTAMASE
 
Authors :  Y. Chen, J. Delmas, J. Sirot, B. Shoichet, R. Bonnet
Date :  19 Jan 05  (Deposition) - 19 Apr 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.74
Chains :  Asym./Biol. Unit :  A
Keywords :  Ctx-M, Beta-Lactamase, Anisotropy, Extended-Spectrum, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Chen, J. Delmas, J. Sirot, B. Shoichet, R. Bonnet
Atomic Resolution Structures Of Ctx-M Beta-Lactamases: Extended Spectrum Activities From Increased Mobility And Decreased Stability.
J. Mol. Biol. V. 348 349 2005
PubMed-ID: 15811373  |  Reference-DOI: 10.1016/J.JMB.2005.02.010
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CTX-M-16 BETA-LACTAMASE
    Chains: A
    EC Number: 3.5.2.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET-9A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: CTX-M
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 7)

Asymmetric/Biological Unit (1, 7)
No.NameCountTypeFull Name
1SO47Ligand/IonSULFATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:70 , SER A:130 , LYS A:234 , THR A:235 , GLY A:236 , SER A:237 , HOH A:2080 , HOH A:2093 , HOH A:2362BINDING SITE FOR RESIDUE SO4 A 1001
2AC2SOFTWAREILE A:108 , HIS A:112 , HOH A:2014 , HOH A:2073 , HOH A:2284 , HOH A:2293 , HOH A:2356BINDING SITE FOR RESIDUE SO4 A 1002
3AC3SOFTWAREARG A:153 , ARG A:191 , HIS A:197 , HOH A:2139 , HOH A:2150 , HOH A:2156 , HOH A:2265BINDING SITE FOR RESIDUE SO4 A 1003
4AC4SOFTWAREGLN A:25 , THR A:26 , ASN A:271 , HOH A:2039 , HOH A:2187 , HOH A:2263 , HOH A:2282BINDING SITE FOR RESIDUE SO4 A 1004
5AC5SOFTWARESER A:274 , ARG A:276 , ASP A:277 , HOH A:2103 , HOH A:2115 , HOH A:2147BINDING SITE FOR RESIDUE SO4 A 1005
6AC6SOFTWARELYS A:88 , ARG A:178 , THR A:202 , HOH A:2091 , HOH A:2133 , HOH A:2138 , HOH A:2303BINDING SITE FOR RESIDUE SO4 A 1006
7AC7SOFTWAREARG A:161 , GLN A:192 , HOH A:2242BINDING SITE FOR RESIDUE SO4 A 1007

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1YLW)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Glu A:166 -Pro A:167

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1YLW)

(-) 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:263
 aligned with Q939N4_ECOLX | Q939N4 from UniProtKB/TrEMBL  Length:291

    Alignment length:263
                                    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       288   
         Q939N4_ECOLX    29 QTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTAGDKTGSGGYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGL 291
               SCOP domains d1ylwa_ A: automated matches                                                                                                                                                                                                                                            SCOP domains
               CATH domains 1ylwA00 A:25-290 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                                                CATH domains
               Pfam domains --------------------------Beta-lactamase2-1ylwA01 A:51-263                                                                                                                                                                                  --------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhh.eeeeeeee.....eeee.....ee.hhhhhhhhhhhhhhhhh...hhhh.eeeehhhhh.....hhhhhh.eeeehhhhhhhhhhh.hhhhhhhhhhhh.hhhhhhhhhhhh...........hhhhh........eehhhhhhhhhhhhhh....hhhhhhhhhhhhhh......hhhhhh....eeeeeeee.....eeeeeeee......eeeeeeee........hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ylw A  25 QTSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTAGDKTGSGGYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGL 290
                                    34        44        54  ||    65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235  ||   246     ||257       267       277       287   
                                                           57|                                                                                                                                                                                238|         252|                                    
                                                            59                                                                                                                                                                                 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, 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  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q939N4_ECOLX | Q939N4)
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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