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(-) Description

Title :  CRYSTAL STRUCTURE OF THE OXA-10 W154H MUTANT AT PH 7
 
Authors :  L. Vercheval, F. Kerff, R. Herman, E. Sauvage, R. Guiet, P. Charlier, J. M. Galleni
Date :  18 Oct 07  (Deposition) - 28 Oct 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Oxa-10, Carboxylated Lysine, Class D Beta-Lactamase, Antibiotic Resistance, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Baurin, L. Vercheval, F. Bouillenne, C. Falzone, A. Brans, L. Jacquamet, J. L. Ferrer, E. Sauvage, D. Dehareng, J. M. Frere, P. Charlier, M. Galleni, F. Kerff
Critical Role Of Tryptophan 154 For The Activity And Stability Of Class D Beta-Lactamases.
Biochemistry V. 48 11252 2009
PubMed-ID: 19860471  |  Reference-DOI: 10.1021/BI901548C

(-) Compounds

Molecule 1 - BETA-LACTAMASE PSE-2
    Chains: A, B
    EC Number: 3.5.2.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET 22B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PSE2, OXA10
    Mutation: YES
    Organism Scientific: PSEUDOMONAS AERUGINOSA
    Organism Taxid: 287
    Synonym: BETA LACTAMASE OXA-10

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 14)

Asymmetric/Biological Unit (4, 14)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
2GOL7Ligand/IonGLYCEROL
3KCX1Mod. ResidueLYSINE NZ-CARBOXYLIC ACID
4SO45Ligand/IonSULFATE ION

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC2SOFTWAREGOL A:8 , SER A:67 , SER A:115 , LYS A:205 , THR A:206 , GLY A:207 , PHE A:208 , ARG A:250 , HOH A:300 , HOH A:364BINDING SITE FOR RESIDUE SO4 A 1
02AC3SOFTWARELYS A:134 , LYS A:138 , LYS A:152BINDING SITE FOR RESIDUE SO4 A 4
03AC4SOFTWAREARG A:250 , HOH A:346 , HOH A:454BINDING SITE FOR RESIDUE SO4 A 11
04AC5SOFTWARESER B:115 , THR B:206 , GLY B:207 , PHE B:208 , ARG B:250 , HOH B:372 , HOH B:396BINDING SITE FOR RESIDUE SO4 B 2
05AC6SOFTWARETHR B:80 , ARG B:131 , LYS B:134 , TYR B:135BINDING SITE FOR RESIDUE SO4 B 3
06AC7SOFTWAREARG A:160 , HOH A:446BINDING SITE FOR RESIDUE EDO A 12
07AC8SOFTWAREGOL A:9 , MET A:99 , LYS A:100 , SER A:147 , GLY A:148 , GLY A:149 , HOH A:277BINDING SITE FOR RESIDUE GOL A 7
08AC9SOFTWARESO4 A:1 , SER A:67 , TRP A:102 , SER A:115 , VAL A:117 , GLU A:129 , PHE A:208 , HOH A:300BINDING SITE FOR RESIDUE GOL A 8
09BC1SOFTWAREGOL A:7 , ALA A:98 , MET A:99 , GLU A:129 , ILE A:146 , GLY A:149 , ILE A:150BINDING SITE FOR RESIDUE GOL A 9
10BC2SOFTWARELYS A:138 , PHE A:139 , SER A:140 , GLU A:168 , SER A:172 , HOH A:283 , HOH A:434BINDING SITE FOR RESIDUE GOL A 13
11BC3SOFTWAREPRO A:198 , GLU A:199 , GLU A:227 , GLU A:229 , HOH A:343 , THR B:107 , ARG B:109 , GLY B:110 , HOH B:330BINDING SITE FOR RESIDUE GOL B 5
12BC4SOFTWARELEU B:43 , SER B:50 , TYR B:233BINDING SITE FOR RESIDUE GOL B 6
13BC5SOFTWARELEU B:247 , PRO B:248 , ARG B:250 , LYS B:251 , HOH B:355BINDING SITE FOR RESIDUE GOL B 10

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:44 -A:51
2B:44 -B:51

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gly B:265 -Gly B:266

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2RL3)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BETA_LACTAMASE_DPS00337 Beta-lactamase class-D active site.BLO10_PSEAI65-75
 		  2A:65-75
B:65-75

(-) Exons   (0, 0)

(no "Exon" information available for 2RL3)

(-) 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:246
 aligned with BLO10_PSEAI | P14489 from UniProtKB/Swiss-Prot  Length:266

    Alignment length:246
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258      
          BLO10_PSEAI    19 AGSITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNDLARASKEYLPASTFKIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLTLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFWLEGQLRISAVNQVEFLESLYLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKETEVYFFAFNMDIDNESKLPLRKSIPTKIMESEGII 264
               SCOP domains d2rl3a_ A: Class D beta-lactamase                                                                                                                                                                                                                      SCOP domains
               CATH domains 2rl3A00 A:19-264 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeee...hhhhhhh....eeeeeee....eeee.hhhhhh.ee.hhhhhhhhhhhhhhhh........ee........hhhhh..eehhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh.....................eehhhhhhhhhhhhh.....hhhhhhhhhhhheeee...eeeeeeeee.........eeeeeeeeeee..eeeeeeeeeee.hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------------------------------BETA_LACTAM--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2rl3 A  19 MGSITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNDLARASKEYLPASTFKIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLTLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFHLEGQLRISAVNQVEFLESLYLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKETEVYFFAFNMDIDNESKLPLRKSIPTKIMESEGII 264
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258      


Chain B from PDB  Type:PROTEIN  Length:248
 aligned with BLO10_PSEAI | P14489 from UniProtKB/Swiss-Prot  Length:266

    Alignment length:248
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258        
          BLO10_PSEAI    19 AGSITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNDLARASKEYLPASTFKIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLTLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFWLEGQLRISAVNQVEFLESLYLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKETEVYFFAFNMDIDNESKLPLRKSIPTKIMESEGIIGG 266
               SCOP domains d2rl3b_ B: Class D beta-lactamase                                                                                                                                                                                                                        SCOP domains
               CATH domains 2rl3B00 B:19-266 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                                 CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...hhhhhhh....eeeeeee....eeee.hhhhhhh...hhhhhhhhhhhhhhhh..................hhhhh...hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh............hhhhhh....hhhhhhhhhhhhhh.....hhhhhhhhhhhheeee...eeeeeeeee.........eeeeeeeeeee..eeeeeeeeeee.hhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------BETA_LACTAM----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2rl3 B  19 MGSITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNDLARASKEYLPASTFKIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLTLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFHLEGQLRISAVNQVEFLESLYLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKETEVYFFAFNMDIDNESKLPLRKSIPTKIMESEGIIGG 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
   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/Biological Unit
(-)
Class: Multi-domain proteins (alpha and beta) (2421)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2RL3)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (BLO10_PSEAI | P14489)
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.
    GO:0008658    penicillin binding    Interacting selectively and non-covalently with penicillin, any antibiotic that contains the condensed beta-lactamthiazolidine ring system.
biological process
    GO:0017001    antibiotic catabolic process    The chemical reactions and pathways resulting in the breakdown of antibiotic, a substance produced by or derived from certain fungi, bacteria, and other organisms, that can destroy or inhibit the growth of other microorganisms.
    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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  2rl3
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  BLO10_PSEAI | P14489
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 Related Entries

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

UniProtKB/Swiss-Prot
        BLO10_PSEAI | P14489: 1e3u 1e4d 1ewz 1fof 1k4e 1k4f 1k54 1k55 1k56 1k57 1k6r 1k6s 2hp5 2hp6 2hp9 2hpb 2wgi 2wgv 2wgw 2wkh 2wki 2x01 2x02 3lce 4s2o 4wz5 5fq9 5mmy 5mnu 5mox 5moz

(-) Related Entries Specified in the PDB File

1k4f CRYSTAL STRUCTURE OF THE CLASS D BETA-LACTAMASE OXA-10 AT 1.6 A RESOLUTION
2hp5 CRYSTAL STRUCTURE OF THE OXA-10 W154G MUTANT AT PH 7.0
2hp6 CRYSTAL STRUCTURE OF THE OXA-10 W154A MUTANT AT PH 7.5
2hp9 CRYSTAL STRUCTURE OF THE OXA-10 W154A MUTANT AT PH 6.0
2hpb CRYSTAL STRUCTURE OF THE OXA-10 W154A MUTANT AT PH 9.0