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(-) Description

Title :  STRUCTURE OF THE CLASS D BETA-LACTAMASE OXA-1 IN COMPLEX WITH DORIPENEM
 
Authors :  R. A. Powers
Date :  25 Aug 09  (Deposition) - 01 Dec 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Hydrolase, Lysine Carboxylation, Antibiotic Resistance (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. D. Schneider, M. E. Karpen, R. A. Bonomo, D. A. Leonard, R. A. Powers
The 1. 4 A Crystal Structure Of The Class D Beta-Lactamase Oxa-1 Complexed With Doripenem.
Biochemistry V. 48 11840 2009
PubMed-ID: 19919101  |  Reference-DOI: 10.1021/BI901690R

(-) Compounds

Molecule 1 - BETA-LACTAMASE OXA-1
    ChainsA, B
    EC Number3.5.2.6
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET12A
    Expression System StrainBL21
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 26-276
    GeneBLA, OXA1
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562
    SynonymPENICILLINASE

 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  (3, 5)

Asymmetric Unit (3, 5)
No.NameCountTypeFull Name
1DRW2Ligand/Ion(2S,3R,4S)-2-[(2S,3R)-3-HYDROXY-1-OXOBUTAN-2-YL]-3-METHYL-4-({(3S,5S)-5-[(SULFAMOYLAMINO)METHYL]PYRROLIDIN-3-YL}SULFANYL)-3,4-DIHYDRO-2H-PYRROLE-5-CARBOXYLIC ACID
2KCX2Mod. Amino AcidLYSINE NZ-CARBOXYLIC ACID
3MPD1Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1DRW1Ligand/Ion(2S,3R,4S)-2-[(2S,3R)-3-HYDROXY-1-OXOBUTAN-2-YL]-3-METHYL-4-({(3S,5S)-5-[(SULFAMOYLAMINO)METHYL]PYRROLIDIN-3-YL}SULFANYL)-3,4-DIHYDRO-2H-PYRROLE-5-CARBOXYLIC ACID
2KCX1Mod. Amino AcidLYSINE NZ-CARBOXYLIC ACID
3MPD-1Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
Biological Unit 2 (3, 3)
No.NameCountTypeFull Name
1DRW1Ligand/Ion(2S,3R,4S)-2-[(2S,3R)-3-HYDROXY-1-OXOBUTAN-2-YL]-3-METHYL-4-({(3S,5S)-5-[(SULFAMOYLAMINO)METHYL]PYRROLIDIN-3-YL}SULFANYL)-3,4-DIHYDRO-2H-PYRROLE-5-CARBOXYLIC ACID
2KCX1Mod. Amino AcidLYSINE NZ-CARBOXYLIC ACID
3MPD1Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:66 , SER A:67 , KCX A:70 , MET A:99 , SER A:115 , VAL A:117 , LEU A:161 , LYS A:212 , THR A:213 , GLY A:214 , ALA A:215 , LEU A:255 , HOH A:306 , HOH A:357 , HOH A:370BINDING SITE FOR RESIDUE DRW A 300
2AC2SOFTWAREASP B:66 , SER B:67 , KCX B:70 , GLY B:98 , MET B:99 , SER B:115 , VAL B:117 , LEU B:161 , LYS B:212 , THR B:213 , GLY B:214 , ALA B:215 , LEU B:255 , SER B:258 , HOH B:276 , HOH B:345 , HOH B:443BINDING SITE FOR RESIDUE DRW B 300
3AC3SOFTWAREILE B:82 , GLU B:122 , HOH B:347BINDING SITE FOR RESIDUE MPD B 400

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3ISG)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3ISG)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BETA_LACTAMASE_DPS00337 Beta-lactamase class-D active site.BLO1_ECOLX69-79
 
  2A:65-75
B:65-75
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BETA_LACTAMASE_DPS00337 Beta-lactamase class-D active site.BLO1_ECOLX69-79
 
  1A:65-75
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BETA_LACTAMASE_DPS00337 Beta-lactamase class-D active site.BLO1_ECOLX69-79
 
  1-
B:65-75

(-) Exons   (0, 0)

(no "Exon" information available for 3ISG)

(-) 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:249
 aligned with BLO1_ECOLX | P13661 from UniProtKB/Swiss-Prot  Length:276

    Alignment length:251
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275 
           BLO1_ECOLX    26 STDISTVASPLFEGTEGCFLLYDASTNAEIAQFNKAKCATQMAPDSTFKIALSLMAFDAEIIDQKTIFKWDKTPKGMEIWNSNHTPKTWMQFSVVWVSQEITQKIGLNKIKNYLKDFDYGNQDFSGDKERNNGLTEAWLESSLKISPEEQIQFLRKIINHNLPVKNSAIENTIENMYLQDLDNSTKLYGKTGAGFTANRTLQNGWFEGFIISKSGHKYVFVSALTGNLGSNLTSSIKAKKNAITILNTLNL 276
               SCOP domains d3isga_ A: Class D beta-lactamase                                                                                                                                                                                                                           SCOP domains
               CATH domains 3isgA00 A:18-274 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                                    CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eehhhhhhhhh..eeeeeeeee.....eeeeehhhhhh....hhhhhhhhhhhhhhhh.................hhhhh...hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh..........--..hhhhhh........hhhhhhhhhhhhhh.....hhhhhhhhhhhheeee.....eeeeeeeeee......eeeeeeeeee.....eeeeeeeeee......hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------BETA_LACTAM----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3isg A  18 STDISTVASPLFEGTEGCFLLYDASTNAEIAQFNKAKCATQMAPDSTFkIALSLMAFDAEIIDQKTIFKWDKTPKGMEIWNSNHTPKTWMQFSVVWVSQEITQKIGLNKIKNYLKDFDYGNQDFSGD--RNNGLTEAWLESSLKISPEEQIQFLRKIINHNLPVKNSAIENTIENMYLQDLDNSTKLYGKTGAGFTANRTLQNGWFEGFIISKSGHKYVFVSALTGNLGSNLTSSIKAKKNAITILNTLNL 274
                                    27  ||    39   ||   51        61        71        81 ||     92       102       112       122       132       142      |152       162       172       182       192       202       212    || 223       233       243       253       263       273 
                                       30|        43|                      70-KCX       83|                                                             149  |                                                              217|                                                       
                                        33         46                                    85                                                                152                                                               219                                                       

Chain B from PDB  Type:PROTEIN  Length:249
 aligned with BLO1_ECOLX | P13661 from UniProtKB/Swiss-Prot  Length:276

    Alignment length:251
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275 
           BLO1_ECOLX    26 STDISTVASPLFEGTEGCFLLYDASTNAEIAQFNKAKCATQMAPDSTFKIALSLMAFDAEIIDQKTIFKWDKTPKGMEIWNSNHTPKTWMQFSVVWVSQEITQKIGLNKIKNYLKDFDYGNQDFSGDKERNNGLTEAWLESSLKISPEEQIQFLRKIINHNLPVKNSAIENTIENMYLQDLDNSTKLYGKTGAGFTANRTLQNGWFEGFIISKSGHKYVFVSALTGNLGSNLTSSIKAKKNAITILNTLNL 276
               SCOP domains d3isgb_ B: Class D beta-lactamase                                                                                                                                                                                                                           SCOP domains
               CATH domains 3isgB00 B:18-274 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                                    CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eehhhhhhhhhh.eeeeeeeee.....eeeeehhhhhh....hhhhhhhhhhhhhhhh.................hhhhh...hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh..........--..hhhhhh........hhhhhhhhhhhhhh.....hhhhhhhhhhhheeee.....eeeeeeeeee......eeeeeeeeee.....eeeeeeeeee......hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------BETA_LACTAM----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3isg B  18 STDISTVASPLFEGTEGCFLLYDASTNAEIAQFNKAKCATQMAPDSTFkIALSLMAFDAEIIDQKTIFKWDKTPKGMEIWNSNHTPKTWMQFSVVWVSQEITQKIGLNKIKNYLKDFDYGNQDFSGD--RNNGLTEAWLESSLKISPEEQIQFLRKIINHNLPVKNSAIENTIENMYLQDLDNSTKLYGKTGAGFTANRTLQNGWFEGFIISKSGHKYVFVSALTGNLGSNLTSSIKAKKNAITILNTLNL 274
                                    27  ||    39   ||   51        61        71        81 ||     92       102       112       122       132       142      |152       162       172       182       192       202       212    || 223       233       243       253       263       273 
                                       30|        43|                      70-KCX       83|                                                             149  |                                                              217|                                                       
                                        33         46                                    85                                                                152                                                               219                                                       

   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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (BLO1_ECOLX | P13661)
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)

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        BLO1_ECOLX | P136611m6k 4mll

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