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(-) Description

Title :  CRYSTAL STRUCTURE OF BETA-LACTAMASE OXY-1-1 FROM KLEBSIELLA OXYTOCA
 
Authors :  Y. -H. Liang, S. W. Wu, X. -D. Su
Date :  15 Jan 08  (Deposition) - 20 Jan 09  (Release) - 07 Nov 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.93
Chains :  Asym./Biol. Unit :  A
Keywords :  Multi-Domain Proteins (Alpha And Beta), Antibiotic Resistance, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. -H. Liang, R. Gao, X. -D. Su
Structural Insights Into The Broadened Substrate Profile Of The Extended-Spectrum Beta-Lactamase Oxy-1-1 From Klebsiell Oxytoca
Acta Crystallogr. , Sect. D V. 68 1460 2012
PubMed-ID: 23090395  |  Reference-DOI: 10.1107/S090744491203466X

(-) Compounds

Molecule 1 - BETA-LACTAMASE OXY-1
    Chains: A
    EC Number: 3.5.2.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQESW-9
    Expression System Strain: M15
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: KLEBSIELLA OXYTOCA
    Organism Taxid: 571
    Synonym: PENICILLINASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric/Biological Unit (2, 5)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2SO44Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:73 , SER A:133 , LYS A:237 , THR A:238 , GLY A:239 , ALA A:240 , HOH A:524 , HOH A:570BINDING SITE FOR RESIDUE SO4 A 301
2AC2SOFTWARESER A:231 , TRP A:232 , PRO A:254 , GLU A:255 , ASN A:256 , HIS A:257 , HOH A:557BINDING SITE FOR RESIDUE SO4 A 302
3AC3SOFTWAREARG A:97 , GLU A:124 , GLY A:221 , HOH A:560BINDING SITE FOR RESIDUE SO4 A 303
4AC4SOFTWAREARG A:68 , LYS A:102 , LYS A:180 , GLU A:255 , HOH A:474 , HOH A:520BINDING SITE FOR RESIDUE SO4 A 304
5AC5SOFTWAREARG A:181 , HOH A:596BINDING SITE FOR RESIDUE ACT A 305

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Glu A:169 -Pro A:170

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 2)

Asymmetric/Biological Unit (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_BLO1_KLEOX_001 *L262PBLO1_KLEOX  ---  ---AL262P
2UniProtVAR_BLO1_KLEOX_002 *E278KBLO1_KLEOX  ---  ---AE278K
   * ID not provided by source
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BETA_LACTAMASE_APS00146 Beta-lactamase class-A active site.BLO1_KLEOX69-84  1A:69-84

(-) Exons   (0, 0)

(no "Exon" information available for 3BYD)

(-) 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:261
 aligned with BLO1_KLEOX | P22391 from UniProtKB/Swiss-Prot  Length:291

    Alignment length:261
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290 
           BLO1_KLEOX    31 DAIQQKLADLEKRSGGRLGVALINTADDSQTLYRGDERFAMCSTGKVMAAAAVLKQSESNPEVVNKRLEIKKSDLVVWSPITEKHLQSGMTLAELSAAALQYSDNTAMNKMISYLGGPEKVTAFAQSIGDVTFRLDRTEPALNSAIPGDKRDTTTPLAMAESLRKLTLGNALGEQQRAQLVTWLKGNTTGGQSIRAGLPASWAVGDKTGAGDYGTTNDIAVIWPENHAPLVLVTYFTQPQQDAKSRKEVLAAAAKIVTEGL 291
               SCOP domains d3byda_ A: automated matches                                                                                                                                                                                                                                          SCOP domains
               CATH domains 3bydA00 A:31-291 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                                              CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhh.eeeeeeee.....eeee.....ee.hhhhhhhhhhhhhhhhhhh......ee..hhhhh.....hhhhh....eehhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhh........eehhhhhhhhhhhhhh....hhhhhhhhhhhhhh......hhhhhh....eeeeeeeee...eeeeeeeee......eeeeeeee........hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------P---------------K------------- SAPs(SNPs)
                    PROSITE --------------------------------------BETA_LACTAMASE_A--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3byd A  31 DAIQQKLADLEKRSGGRLGVALINTADDSQTLYRGDERFAMCSTGKVMAAAAVLKQSESNPEVVNKRLEIKKSDLVVWSPITEKHLQSGMTLAELSAAALQYSDNTAMNKMISYLGGPEKVTAFAQSIGDVTFRLDRTEPALNSAIPGDKRDTTTPLAMAESLRKLTLGNALGEQQRAQLVTWLKGNTTGGQSIRAGLPASWAVGDKTGAGDYGTTNDIAVIWPENHAPLVLVTYFTQPQQDAKSRKEVLAAAAKIVTEGL 291
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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, 1)

Asymmetric/Biological Unit
(-)
Class: Multi-domain proteins (alpha and beta) (2421)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (BLO1_KLEOX | P22391)
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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