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(-) Description

Title :  CRYSTAL STRUCTURE OF THE OXA-10 K70C MUTANT AT PH 7.0
 
Authors :  L. Vercheval, C. Bauvois, F. Kerff, E. Sauvage, R. Guiet, P. Charlier,
Date :  11 Jun 09  (Deposition) - 25 Aug 10  (Release) - 08 Dec 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Class D, Plasmid Encoded, Hydrolase, Antibiotic Resistance, Beta-Lactamase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Vercheval, C. Bauvois, A. Di Paolo, F. Borel, J. L. Ferrer, E. Sauvage, A. Matagne, J. M. Frere, P. Charlier, M. Galleni, F. Kerff
Three Factors That Modulate The Activity Of Class D Beta-Lactamases And Interfere With The Post- Translational Carboxylation Of Lys70.
Biochem. J. V. 432 495 2010
PubMed-ID: 21108605  |  Reference-DOI: 10.1042/BJ20101122

(-) Compounds

Molecule 1 - BETA-LACTAMASE OXA-10
    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: 469008
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Scientific: PSEUDOMONAS AERUGINOSA
    Organism Taxid: 287
    Synonym: BETA-LACTAMASE PSE-2

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 18)

Asymmetric/Biological Unit (3, 18)
No.NameCountTypeFull Name
1EDO9Ligand/Ion1,2-ETHANEDIOL
2GOL5Ligand/IonGLYCEROL
3SO44Ligand/IonSULFATE ION

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:115 , THR A:206 , GLY A:207 , PHE A:208 , ARG A:250 , HOH A:2145 , HOH A:2146BINDING SITE FOR RESIDUE SO4 A1265
02AC2SOFTWAREARG A:160 , HOH A:2147BINDING SITE FOR RESIDUE SO4 A1266
03AC3SOFTWARELYS A:134 , LYS A:138 , LYS A:152 , HOH A:2085BINDING SITE FOR RESIDUE SO4 A1267
04AC4SOFTWAREGLU A:199 , GLU A:227 , GLU A:229 , GOL A:1269 , HOH A:2148 , THR B:107 , ARG B:109 , GLY B:110BINDING SITE FOR RESIDUE GOL A1268
05AC5SOFTWAREPRO A:198 , GLU A:199 , GLU A:229 , GOL A:1268 , ARG B:104 , LEU B:106 , GLY B:110 , VAL B:114BINDING SITE FOR RESIDUE GOL A1269
06AC6SOFTWARESER A:21 , SER A:48 , VAL A:164 , GLU A:168 , HOH A:2149BINDING SITE FOR RESIDUE EDO A1270
07AC7SOFTWAREALA A:98 , GLU A:129 , ILE A:146 , GLY A:149 , ILE A:150BINDING SITE FOR RESIDUE EDO A1271
08AC8SOFTWAREARG A:125 , GLY A:128 , GLU A:129 , HOH A:2064 , HOH A:2069 , HOH A:2150BINDING SITE FOR RESIDUE EDO A1272
09AC9SOFTWAREPHE A:139 , GLU A:168 , PHE A:169 , SER A:172 , HOH A:2151 , HOH A:2152BINDING SITE FOR RESIDUE EDO A1273
10BC1SOFTWARETHR A:194 , GLU A:195 , TRP A:222 , LYS A:251 , HOH A:2111BINDING SITE FOR RESIDUE EDO A1274
11BC2SOFTWAREARG A:131 , LYS A:134 , TYR A:135 , LYS A:152 , GLU A:156 , HOH A:2031BINDING SITE FOR RESIDUE EDO A1275
12BC3SOFTWARESER B:115 , THR B:206 , GLY B:207 , PHE B:208 , ARG B:250 , HOH B:2128 , HOH B:2129BINDING SITE FOR RESIDUE SO4 B1266
13BC4SOFTWAREARG B:131 , LYS B:134 , TYR B:135 , HOH B:2130BINDING SITE FOR RESIDUE GOL B1267
14BC5SOFTWARETHR A:107 , ARG A:109 , GLY A:110 , GLU B:199 , TYR B:200 , LEU B:201 , GLU B:227 , GLU B:229 , HOH B:2099 , HOH B:2108 , HOH B:2131BINDING SITE FOR RESIDUE GOL B1268
15BC6SOFTWAREARG B:250 , LYS B:251 , HOH B:2132BINDING SITE FOR RESIDUE GOL B1269
16BC7SOFTWAREPHE B:139 , GLU B:168 , SER B:172 , HOH B:2133BINDING SITE FOR RESIDUE EDO B1270
17BC8SOFTWARETHR B:194 , TRP B:222 , LYS B:251 , HOH B:2134BINDING SITE FOR RESIDUE EDO B1271
18BC9SOFTWARELYS B:45 , TYR B:233 , GLU B:261 , ILE B:263 , HOH B:2126BINDING SITE FOR RESIDUE EDO B1272

(-) SS Bonds  (2, 2)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2WKI)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) 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 2WKI)

(-) 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:244
 aligned with BLO10_PSEAI | P14489 from UniProtKB/Swiss-Prot  Length:266

    Alignment length:244
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260    
          BLO10_PSEAI    21 SITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNDLARASKEYLPASTFKIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLTLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFWLEGQLRISAVNQVEFLESLYLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKETEVYFFAFNMDIDNESKLPLRKSIPTKIMESEGII 264
               SCOP domains d2wkia_ A: Class D beta-lactamase                                                                                                                                                                                                                    SCOP domains
               CATH domains 2wkiA00 A:21-264 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                             CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee...hhhhhhh....eeeeeee.....eee.hhhhhh.ee.hhhhhhhhhhhhhhhh........ee........hhhhh..eehhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh.....................eehhhhhhhhhhhhh.....hhhhhhhhhhhheeeee..eeeeeeeee.........eeeeeeeeeee..eeeeeeeeeee.hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------BETA_LACTAM--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wki A  21 SITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNDLARASKEYLPASTFCIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLTLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFWLEGQLRISAVNQVEFLESLYLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKETEVYFFAFNMDIDNESKLPLRKSIPTKIMESEGII 264
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260    


Chain B from PDB  Type:PROTEIN  Length:247
 aligned with BLO10_PSEAI | P14489 from UniProtKB/Swiss-Prot  Length:266

    Alignment length:247
                                    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 AGSITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNDLARASKEYLPASTFKIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLTLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFWLEGQLRISAVNQVEFLESLYLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKETEVYFFAFNMDIDNESKLPLRKSIPTKIMESEGIIG 265
               SCOP domains d2wkib_ B: Class D beta-lactamase                                                                                                                                                                                                                       SCOP domains
               CATH domains 2wkiB00 B:19-265 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...hhhhhhh....eeeeeee....eeee.hhhhhhhee.hhhhhhhhhhhhhhhh........ee........hhhhh..eehhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh.....................eehhhhhhhhhhhhh.....hhhhhhhhhhhheeee...eeeeeeeee.........eeeeeeeeeee..eeeeeeeeeee.hhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------BETA_LACTAM---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wki B  19 MGSITENTSWNKEFSAEAVNGVFVLCKSSSKSCATNDLARASKEYLPASTFCIPNAIIGLETGVIKNEHQVFKWDGKPRAMKQWERDLTLRGAIQVSAVPVFQQIAREVGEVRMQKYLKKFSYGNQNISGGIDKFWLEGQLRISAVNQVEFLESLYLNKLSASKENQLIVKEALVTEAAPEYLVHSKTGFSGVGTESNPGVAWWVGWVEKETEVYFFAFNMDIDNESKLPLRKSIPTKIMESEGIIG 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
   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 2WKI)

(-) 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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 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 2rl3 2wgi 2wgv 2wgw 2wkh 2x01 2x02 3lce 4s2o 4wz5 5fq9 5mmy 5mnu 5mox 5moz

(-) Related Entries Specified in the PDB File

1e3u MAD STRUCTURE OF OXA10 CLASS D BETA- LACTAMASE
1e4d STRUCTURE OF OXA10 BETA-LACTAMASE AT PH 8 .3
1ewz CRYSTAL STRUCTURE OF THE OXA-10 BETA- LACTAMASE FROM PSEUDOMONAS AERUGINOSA
1fof CRYSTAL STRUCTURE OF THE CLASS D BETA- LACTAMASE OXA-10
1k4e CRYSTAL STRUCTURE OF THE CLASS D BETA- LACTAMASES OXA-10DETERMINED BY MAD PHASING WITH SELENOMETHIONINE
1k4f CRYSTAL STRUCTURE OF THE CLASS D BETA- LACTAMASE OXA-10 AT1.6 A RESOLUTION
1k54 OXA-10 CLASS D BETA-LACTAMASE PARTIALLY ACYLATED WITHREACTED 6BETA-(1-HYDROXY-1- METHYLETHYL) PENICILLANIC ACID
1k55 OXA 10 CLASS D BETA-LACTAMASE AT PH 7. 5
1k56 OXA 10 CLASS D BETA-LACTAMASE AT PH 6. 5
1k57 OXA 10 CLASS D BETA-LACTAMASE AT PH 6.0
1k6r STRUCTURE OF THE CLASS D BETA-LACTAMASE OXA-10 IN COMPLEXWITH MOXALACTAM
1k6s STRUCTURE OF THE CLASS D BETA-LACTAMASE OXA-10 IN COMPLEXWITH A PHENYLBORONIC ACID
2wgi CRYSTAL STRUCTURE OF THE ACYL-ENZYME OXA- 10 W154A-BENZYLPENICILLIN AT PH 6
2wgv CRYSTAL STRUCTURE OF THE OXA-10 V117T MUTANT AT PH 6.5 INHIBITED BY A CHLORIDE ION
2wgw CRYSTAL STRUCTURE OF THE OXA-10 V117T MUTANT AT PH 8.0
2wkh CRYSTAL STRUCTURE OF THE ACYL-ENZYME OXA- 10 K70C-AMPICILLIN AT PH 7