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(-) Description

Title :  CRYSTAL STRUCTURE OF PENI BETA-LACTAMASE FROM BURKHOLDERIA PSEUDOMALLEI AT PH9.5
 
Authors :  M. Nukaga, N. Ohuchi, K. M. Papp-Wallace, M. A. Taracila, R. A. Bonomo
Date :  10 Jan 13  (Deposition) - 15 May 13  (Release) - 04 Sep 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.18
Chains :  Asym./Biol. Unit :  A
Keywords :  Beta-Lactamase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. M. Papp-Wallace, M. A. Taracila, J. A. Gatta, N. Ohuchi, R. A. Bonomo M. Nukaga
Insights Into Beta-Lactamases From Burkholderia Species, Tw Phylogenetically Related Yet Distinct Resistance Determinants
J. Biol. Chem. V. 288 19090 2013
PubMed-ID: 23658015  |  Reference-DOI: 10.1074/JBC.M113.458315

(-) Compounds

Molecule 1 - BETA-LACTAMASE
    Chains: A
    EC Number: 3.5.2.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET24A(+)
    Expression System Strain: ORIGAMI 2 (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 31-295
    Gene: BPSS0946, PENA, PENI
    Organism Scientific: BURKHOLDERIA PSEUDOMALLEI
    Organism Taxid: 272560
    Strain: K96243

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2NHE1Ligand/Ion2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:25 , ARG A:83 , LEU A:90 , ARG A:93 , LEU A:141 , HOH A:587 , HOH A:610 , HOH A:758 , HOH A:764BINDING SITE FOR RESIDUE NHE A 301
2AC2SOFTWARELEU A:212 , ARG A:222 , ARG A:230 , VAL A:231 , ASN A:271 , HOH A:514 , HOH A:531 , HOH A:620BINDING SITE FOR RESIDUE GOL A 302

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3W4O)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Glu A:166 -Pro A:167

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3W4O)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3W4O)

(-) Exons   (0, 0)

(no "Exon" information available for 3W4O)

(-) 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:266
 aligned with H7C785_BURPS | H7C785 from UniProtKB/TrEMBL  Length:295

    Alignment length:266
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289      
         H7C785_BURPS    30 AKNVAAAERQLRELESTFDGRLGFVALDTATGARIAHRGDERFPFCSTSKMMLCAAVLARSAGEPALLQRRIAYAKGDLIRYSPITEQHVGAGMSVAELCAATLQYSDNTAANLLIALLGGPQTVTAYARSIGDATFRLDRREPELNTALPGDERDTTTPAAMAASVHRLLVGDALGAAQRAQLNAWMLGNKTGDARIRAGVPADWRVADKTGTGDYGTANDIGVAYPPNRAPIVFIVYTTMRNPNAQARDDVIASATRIAARAFA 295
               SCOP domains d3w4oa_ A: automated matches                                                                                                                                                                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhh...eeeeeeeee.....eeee.....ee...hhhhhhhhhhhhhhh.hhhhhh.ee..hhhhh.....hhhhhh...eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhh........eehhhhhhhhhhhhhh....hhhhhhhhhhhhhh......hhhhhh....eeeeeeee.....eeeeeeee......eeeeeeeee........hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3w4o A  24 MKNVAAAERQLRELESTFDGRLGFVALDTATGARIAHRGDERFPFCSTSKMMLCAAVLARSAGEPALLQRRIAYAKGDLIRYSPITEQHVGAGMSVAELCAATLQYSDNTAANLLIALLGGPQTVTAYARSIGDATFRLDRREPELNTALPGDERDTTTPAAMAASVHRLLVGDALGAAQRAQLNAWMLGNKTGDARIRAGVPADWRVADKTGTGDYGTANDIGVAYPPNRAPIVFIVYTTMRNPNAQARDDVIASATRIAARAFA 291
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233    || 244       255       265       275       285      
                                                                                                                                                                                                                                                238|         252|                                     
                                                                                                                                                                                                                                                 240          254
   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  (0, 0)

(no "CATH Domain" information available for 3W4O)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3W4O)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (H7C785_BURPS | H7C785)
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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 Related Entries

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

UniProtKB/TrEMBL
        H7C785_BURPS | H7C785: 3w4p

(-) Related Entries Specified in the PDB File

2ov5 BETA-LACTAMASE WITH SIMILAR SUBSTRATE SPECIFICITY
3w4p
3w4q