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(-) Description

Title :  CTX-M-9 S70G IN COMPLEX WITH PIPERACILLIN
 
Authors :  J. Delmas, D. Leyssne, F. Robin, A. Coignoux, R. Bonnet
Date :  15 Dec 10  (Deposition) - 21 Dec 11  (Release) - 21 Dec 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Beta-Lactamase, Esbl, Ctx-M, Ctx-M-9, Beta-Lactam, Piperacillin, Michaelis, Antibiotic Resistance, Hydrolase, Alpha Beta Fold, Hydrolase-Antibiotic Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Leyssne, J. Delmas, A. Coignoux, F. Robin, R. Bonnet
Ctx-M-9 S70G Mutant In Complex With Piperacillin
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: PET-9A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: EXTENDED-SPECTRUM BETA-LACTAMASE, UNP RESIDUES 29-291
    Gene: BLACTX-M-9, BLACTX-M-9A, BLACTX-M-9B
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: BETA-LACTAMASE CTX-M, BETA-LACTAMASE CTX-M-9A, BETALACTAMASE CTX-M-9, CTX-M-9 BETA-LACTAMASE, CTX-M-9 EXTENDED-SPECTRUM BETA- LACTAMASE

 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, 5)

Asymmetric Unit (2, 5)
No.NameCountTypeFull Name
1WPP2Ligand/IonPIPERACILLIN
2YPP3Ligand/IonHYDROLYZED PIPERACILLIN
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1WPP1Ligand/IonPIPERACILLIN
2YPP1Ligand/IonHYDROLYZED PIPERACILLIN
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1WPP1Ligand/IonPIPERACILLIN
2YPP2Ligand/IonHYDROLYZED PIPERACILLIN

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:69 , GLY A:70 , ASN A:104 , SER A:130 , ASN A:132 , PRO A:167 , ASN A:170 , LYS A:234 , THR A:235 , GLY A:236 , SER A:237 , GLY A:238 , ASP A:239 , HOH A:432 , HOH A:527 , HOH A:773BINDING SITE FOR RESIDUE WPP A 300
2AC2SOFTWARECYS A:69 , GLY A:70 , LYS A:73 , ASN A:104 , TYR A:105 , SER A:130 , ASN A:132 , PRO A:167 , THR A:168 , ASN A:170 , GLY A:236 , SER A:237 , GLY A:238 , ASP A:239 , ARG A:254 , HOH A:535 , HOH A:773 , HOH A:786BINDING SITE FOR RESIDUE YPP A 301
3AC3SOFTWAREGLY B:70 , ASN B:104 , SER B:130 , ASN B:132 , PRO B:167 , ASN B:170 , THR B:235 , GLY B:236 , SER B:237 , GLY B:238 , ASP B:239 , ARG B:254 , HOH B:311 , HOH B:359 , HOH B:591BINDING SITE FOR RESIDUE WPP B 400
4AC4SOFTWARECYS B:69 , GLY B:70 , LYS B:73 , ASN B:104 , TYR B:105 , SER B:130 , ASN B:132 , PRO B:167 , THR B:168 , ASN B:170 , GLY B:236 , SER B:237 , GLY B:238 , ASP B:239 , ARG B:254 , HOH B:311 , HOH B:591 , HOH B:777 , HOH B:787BINDING SITE FOR RESIDUE YPP B 401
5AC5SOFTWAREGLN A:32 , LYS A:39 , SER A:40 , LYS A:82 , GLN A:83 , ALA A:150 , ALA A:154 , HOH A:461 , HOH A:494 , HOH A:532 , HOH A:781 , HOH A:783 , HOH B:8 , ALA B:53 , ASP B:54 , ASN B:55 , ARG B:178 , HOH B:661 , HOH B:682BINDING SITE FOR RESIDUE YPP B 402

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3Q07)

(-) 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 3Q07)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3Q07)

(-) Exons   (0, 0)

(no "Exon" information available for 3Q07)

(-) 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:262
 aligned with Q9L5C8_ECOLX | Q9L5C8 from UniProtKB/TrEMBL  Length:291

    Alignment length:262
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289  
         Q9L5C8_ECOLX    30 TSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTAGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGL 291
               SCOP domains d3q07a_ A: automated matches                                                                                                                                                                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh.eeeeeeee.....eeee.....ee.hhhhhhhhhhhhhhhhh...hhhh.eeeehhhhh.....hhhhhh.eeeehhhhhhhhhhh.hhhhhhhhhhhh.hhhhhhhhhhhh...........hhhhh........eehhhhhhhhhhhhhh....hhhhhhhhhhhhhh......hhhhhh....eeeeeeeee...eeeeeeeee......eeeeeeee........hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3q07 A  27 TSAVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCGTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTAGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGL 288
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286  


Chain B from PDB  Type:PROTEIN  Length:260
 aligned with Q9L5C8_ECOLX | Q9L5C8 from UniProtKB/TrEMBL  Length:291

    Alignment length:260
                                    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
         Q9L5C8_ECOLX    32 AVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCSTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTAGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGL 291
               SCOP domains d3q07b_ B: automated matches                                                                                                                                                                                                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh.eeeeeeee.....eeee.....ee.hhhhhhhhhhhhhhhhh...hhhh.eeeehhhhh.....hhhhhh.eeeehhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh...........hhhhh........eehhhhhhhhhhhhhh....hhhhhhhhhhhhhh......hhhhhh....eeeeeeeee...eeeeeeeee......eeeeeeee........hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3q07 B  29 AVQQKLAALEKSSGGRLGVALIDTADNTQVLYRGDERFPMCGTSKVMAAAAVLKQSETQKQLLNQPVEIKPADLVNYNPIAEKHVNGTMTLAELSAAALQYSDNTAMNKLIAQLGGPGGVTAFARAIGDETFRLDRTEPTLNTAIPGDPRDTTTPRAMAQTLRQLTLGHALGETQRAQLVTWLKGNTTGAASIRAGLPTSWTAGDKTGSGDYGTTNDIAVIWPQGRAPLVLVTYFTQPQQNAESRRDVLASAARIIAEGL 288
                                    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
   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  (0, 0)

(no "CATH Domain" information available for 3Q07)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3Q07)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q9L5C8_ECOLX | Q9L5C8)
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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 Related Entries

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

UniProtKB/TrEMBL
        Q9L5C8_ECOLX | Q9L5C8: 1ylj 1ym1 1yms 1ymx 2p74 3g2y 3g2z 3g30 3g31 3g32 3g34 3g35 3hlw 3hre 3huo 3hvf 3q1f 4dds 4ddy 4de0 4de1 4de2 4de3 4len 5ujo

(-) Related Entries Specified in the PDB File

2p74 CTX-M-9 CLASS A BETA-LACTAMASE APO CRYSTAL STRUCTURE AT 0.88 ANGSTROM RESOLUTION
3hlw CTX-M-9 S70G IN COMPLEX WITH CEFOTAXIME
3hre X-RAY CRYSTALLOGRAPHIC STRUCTURE OF CTX-M-9 S70G
3huo X-RAY CRYSTALLOGRAPHIC STRUCTURE OF CTX-M-9 S70G IN COMPLEX WITH ENZYLPENICILLIN
3hvf X-RAY CRYSTALLOGRAPHIC STRUCTURE OF CTX-M-9 S70G IN COMPLEX WITH HYDROLYZED BENZYLPENICILLIN
3q1f CTX-M-9 S70G IN COMPLEX WITH HYDROLYZED PIPERACILLIN