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(-) Description

Title :  CRYSTAL STRUCTURE OF THE CLASS A BETA-LACTAMSE L2 FROM STENOTROPHOMONAS MALTOPHILIA AT 1.51 ANGSTROM
 
Authors :  L. Pernot, S. Petrella, W. Sougakoff
Date :  02 Nov 02  (Deposition) - 26 Feb 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.51
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Hydrolase, Beta-Lactamase, Class A, L2 (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Petrella, L. Pernot, D. Lascoux, E. Forest, V. Jarlier, W. Sougakoff
Role Of The Disulfide Bridge Cys69-Cys238 In Class A B-Lactamases : A Structural And Biochemical Investigation On The B-Lactamase L2 From Stenotrophomonas Maltophilia
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - L2 BETA LACTAMASE
    Chains: A, B
    EC Number: 3.5.2.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET29-(A+)
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Organism Scientific: STENOTROPHOMONAS MALTOPHILIA
    Organism Taxid: 40324
    Strain: 405

 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, 16)

Asymmetric Unit (2, 16)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
2SO413Ligand/IonSULFATE ION
Biological Unit 1 (2, 8)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2SO47Ligand/IonSULFATE ION
Biological Unit 2 (2, 8)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2SO46Ligand/IonSULFATE ION

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:70 , SER A:130 , LYS A:234 , THR A:235 , GLY A:236 , SER A:237 , HOH A:2079 , HOH A:2327 , HOH A:2328 , HOH A:2329BINDING SITE FOR RESIDUE SO4 A1293
02AC2SOFTWAREARG A:178 , HOH A:2203 , HOH A:2331 , HOH A:2332BINDING SITE FOR RESIDUE SO4 A1294
03AC3SOFTWARELYS A:38 , ARG A:61 , HOH A:2023 , HOH A:2072 , HOH A:2333 , HOH A:2334 , HOH A:2335BINDING SITE FOR RESIDUE SO4 A1295
04AC4SOFTWARELYS A:38 , LYS A:174 , HOH A:2336 , HOH A:2337 , HOH A:2338BINDING SITE FOR RESIDUE SO4 A1296
05AC5SOFTWAREARG A:65 , LYS A:174 , GLY A:175 , HOH A:2078 , HOH A:2337 , HOH A:2339 , HOH A:2340 , HOH A:2341 , HOH A:2342BINDING SITE FOR RESIDUE SO4 A1297
06AC6SOFTWAREARG A:153 , HOH A:2343 , MET B:87 , ARG B:93BINDING SITE FOR RESIDUE SO4 A1298
07AC7SOFTWAREARG A:204 , GLN A:205 , HOH A:2344 , HOH A:2345BINDING SITE FOR RESIDUE SO4 A1299
08AC8SOFTWARESER B:70 , SER B:130 , LYS B:234 , THR B:235 , GLY B:236 , SER B:237 , HOH B:2321 , HOH B:2372 , HOH B:2373 , HOH B:2374 , HOH B:2375 , HOH B:2376BINDING SITE FOR RESIDUE SO4 B1294
09AC9SOFTWARETHR B:23 , ASP B:24 , HOH B:2378 , HOH B:2379BINDING SITE FOR RESIDUE SO4 B1295
10BC1SOFTWAREARG B:61 , HOH B:2381 , HOH B:2382BINDING SITE FOR RESIDUE SO4 B1296
11BC2SOFTWAREGLY B:59 , HIS B:60 , ARG B:61 , GLN B:62 , HOH B:2090 , HOH B:2383 , HOH B:2384BINDING SITE FOR RESIDUE SO4 B1297
12BC3SOFTWAREARG B:178 , HOH B:2236BINDING SITE FOR RESIDUE SO4 B1298
13BC4SOFTWAREARG B:65 , LYS B:174 , GLY B:175 , HOH B:2104 , HOH B:2385 , HOH B:2386 , HOH B:2387 , HOH B:2388BINDING SITE FOR RESIDUE SO4 B1299
14BC5SOFTWAREARG A:93 , GLY A:140 , VAL A:141 , HOH A:2326 , SER B:82 , ARG B:86 , ALA B:154 , GOL B:1292BINDING SITE FOR RESIDUE GOL A1292
15BC6SOFTWAREARG A:93 , GOL A:1292 , ALA B:154 , SER B:155 , VAL B:198 , HOH B:2370BINDING SITE FOR RESIDUE GOL B1292
16BC7SOFTWAREASN B:170 , SER B:171 , ASN B:238 , GLY B:240 , GLU B:241 , HOH B:2327 , HOH B:2371BINDING SITE FOR RESIDUE GOL B1293

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1O7E)

(-) 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 1O7E)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1O7E)

(-) Exons   (0, 0)

(no "Exon" information available for 1O7E)

(-) 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:267
 aligned with Q9RBQ1_STEMA | Q9RBQ1 from UniProtKB/TrEMBL  Length:303

    Alignment length:267
                                    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       296       
         Q9RBQ1_STEMA    37 TDAAITAASDFAALEKACAGRLGVTLLDTASGRRIGHRQDERFPMCSTFKSMLAATVLSQAERMPALLDRRVPVGEADLLSHAPVTRRHAGKDMTVRDLCRATIITSDNTAANLLFGVVGGPPAVTAFLRASGDTVSRSDRLEPELNSFAKGDPRDTTTPAAMAATLQRVVLGEVLQPASRQQLADWLIDNETGDACLRAGLGKRWRVGDKTGSNGEDARNDIAVLWPVAGGAPWVLTAYLQAGAISYEQRASVLAQVGRIADRLIG 303
               SCOP domains d1o7ea_ A: beta-Lactamase, class A                                                                                                                                                                                                                                          SCOP domains
               CATH domains 1o7eA00 A:23-291 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                                                    CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhh.hhhhhhhhhh.eeeeeeee.....eeee.....ee.hhhhhhhhhhhhhhhhh........eeeehhhhh.....hhhhhh.eeeehhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhh........eehhhhhhhhhhhhhh....hhhhhhhhhhhhhh......hhhhhh...eeeeeeeee....eeeeeeeeee......eeeeeeee....hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1o7e A  23 TDAAITAASDFAALEKACAGRLGVTLLDTASGRRIGHRQDERFPMCSTFKSMLAATVLSQAERMPALLDRRVPVGEADLLSHAPVTRRHAGKDMTVRDLCRATIITSDNTAANLLFGVVGGPPAVTAFLRASGDTVSRSDRLEPELNSFAKGDPRDTTTPAAMAATLQRVVLGEVLQPASRQQLADWLIDNETGDACLRAGLGKRWRVGDKTGSNGEDARNDIAVLWPVAGGAPWVLTAYLQAGAISYEQRASVLAQVGRIADRLIG 291
                                    32        42        52    ||  63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233    || 244       254       264       274       284       
                                                             57|                                                                                                                                                                                238|                                                   
                                                              59                                                                                                                                                                                 240                                                   


Chain B from PDB  Type:PROTEIN  Length:272
 aligned with Q9RBQ1_STEMA | Q9RBQ1 from UniProtKB/TrEMBL  Length:303

    Alignment length:272
                                    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  
         Q9RBQ1_STEMA    32 TANAPTDAAITAASDFAALEKACAGRLGVTLLDTASGRRIGHRQDERFPMCSTFKSMLAATVLSQAERMPALLDRRVPVGEADLLSHAPVTRRHAGKDMTVRDLCRATIITSDNTAANLLFGVVGGPPAVTAFLRASGDTVSRSDRLEPELNSFAKGDPRDTTTPAAMAATLQRVVLGEVLQPASRQQLADWLIDNETGDACLRAGLGKRWRVGDKTGSNGEDARNDIAVLWPVAGGAPWVLTAYLQAGAISYEQRASVLAQVGRIADRLIG 303
               SCOP domains d1o7eb_ B: beta-Lactamase, class A                                                                                                                                                                                                                                               SCOP domains
               CATH domains 1o7eB00 B:18-291 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                                                         CATH domains
           Pfam domains (1) ---------------------------------Beta-lactamase2-1o7eB01 B:51-263                                                                                                                                                                                   ---------------------------- Pfam domains (1)
           Pfam domains (2) ---------------------------------Beta-lactamase2-1o7eB02 B:51-263                                                                                                                                                                                   ---------------------------- Pfam domains (2)
         Sec.struct. author .....hhhhhhhh.hhhhhhhhh..eeeeeeee.....eeee.....ee.hhhhhhhhhhhhhhhhh.hhhhhh.eee.hhhhh.....hhhhhh..eeehhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhh........eehhhhhhhhhhhhhh....hhhhhhhhhhhhhh......hhhhhh...eeeeeeeee....eeeeeeeeee......eeeeeeee....hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1o7e B  18 TANAPTDAAITAASDFAALEKACAGRLGVTLLDTASGRRIGHRQDERFPMCSTFKSMLAATVLSQAERMPALLDRRVPVGEADLLSHAPVTRRHAGKDMTVRDLCRATIITSDNTAANLLFGVVGGPPAVTAFLRASGDTVSRSDRLEPELNSFAKGDPRDTTTPAAMAATLQRVVLGEVLQPASRQQLADWLIDNETGDACLRAGLGKRWRVGDKTGSNGEDARNDIAVLWPVAGGAPWVLTAYLQAGAISYEQRASVLAQVGRIADRLIG 291
                                    27        37        47        57|       68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238|      249       259       269       279       289  
                                                                  57|                                                                                                                                                                                238|                                                   
                                                                   59                                                                                                                                                                                 240
   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   (Q9RBQ1_STEMA | Q9RBQ1)
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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  1o7e
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 Related Entries

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        Q9RBQ1_STEMA | Q9RBQ1: 1n4o

(-) Related Entries Specified in the PDB File

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