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(-) Description

Title :  STRUCTURAL AND MECHANISTIC BASIS OF PENICILLIN BINDING PROTEIN INHIBITION BY LACTIVICINS
 
Authors :  P. Macheboeuf, D. S. Fisher, T. J. Brown, A. Zervosen, A. Luxen, B. Joris, A. Dessen, C. J. Schofield
Date :  23 Dec 06  (Deposition) - 14 Aug 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A
Keywords :  Peptidoglycan Synthesis Multifunctional Enzyme, Cell Wall, Peptidoglycan, Gamma Lactam Antibiotics, Binding Protein, Drug-Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Macheboeuf, D. S. Fisher, T. J. Brown, A. Zervosen, A. Luxen, B. Joris, A. Dessen, C. J. Schofield
Structural And Mechanistic Basis Of Penicillin- Binding Protein Inhibition By Lactivicins
Nat. Chem. Biol. V. 3 565 2007
PubMed-ID: 17676039  |  Reference-DOI: 10.1038/NCHEMBIO.2007.21

(-) Compounds

Molecule 1 - PENICILLIN-BINDING PROTEIN 1B
    Atcc: BAA-255
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX4T1
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Fragment: RESIDUES 72-791
    Mutation: YES
    Organism Scientific: STREPTOCOCCUS PNEUMONIAE
    Organism Taxid: 171101
    Strain: R6

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (4, 4)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2EDO1Ligand/Ion1,2-ETHANEDIOL
3PL71Ligand/Ion(2E)-2-({(2S)-2-CARBOXY-2-[(PHENOXYACETYL)AMINO]ETHOXY}IMINO)PENTANEDIOIC ACID
4SO41Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:459 , SER A:460 , TYR A:498 , SER A:516 , ASN A:518 , THR A:652 , GLY A:653 , THR A:654 , ASN A:656 , ASP A:658 , HOH A:2147BINDING SITE FOR RESIDUE PL7 A1793
2AC2SOFTWARETHR A:563 , LYS A:583 , HOH A:2144 , HOH A:2145 , HOH A:2146BINDING SITE FOR RESIDUE SO4 A1790
3AC3SOFTWARESER A:634BINDING SITE FOR RESIDUE CL A1791
4AC4SOFTWARESER A:626 , ARG A:627 , VAL A:628BINDING SITE FOR RESIDUE EDO A1792

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2JCH)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Thr A:371 -Gln A:372

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2JCH)

(-) Exons   (0, 0)

(no "Exon" information available for 2JCH)

(-) 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:461
 aligned with O70038_STREE | O70038 from UniProtKB/TrEMBL  Length:821

    Alignment length:684
                                   115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695       705       715       725       735       745       755       765       775       785    
         O70038_STREE   106 SEITYSDGTVIASIESDLLRTSISSEQISENLKKAIIATEDEHFKEHKGVVPKAVIRATLGKFVGLGSSSGGSTLTQQLIKQQVVGDAPTLARKAAEIVDALALERAMNKDEILTTYLNVAPFGRNNKGQNIAGARQAAEGIFGVDASQLTVPQAAFLAGLPQSPITYSPYENTGELKSDEDLEIGLRRAKAVLYSMYRTGALSKDEYSQYKDYDLKQDFLPSGTVTGISRDYLYFTTLAEAQERMYDYLAQRDNVSAKELKNEATQKFYRDLAAKEIENGGYKITTTIDQKIHSAMQSAVADYGYLLDDGTGRVEVGNVLMDNQTGAILGFVGGRNYQENQNNHAFDTKRSPASTTKPLLAYGIAIDQGLMGSETILSNYPTNFANGNPIMYANSKGTGMMTLGEALNYSWNIPAYWTYRMLRENGVDVKGYMEKMGYEIPEYGIESLPMGGGIEVTVAQHTNGYQTLANNGVYHQKHVISKIEAADGRVVYEYQDKPVQVYSKATATIMQGLLREVLSSRVTTTFKSNLTSLNPTLANADWIGKTGTTNQDENMWLMLSTPRLTLGGWIGHDDNHSLSRRAGYSNNSNYMAHLVNAIQQASPSIWGNERFALDPSVVKSEVLKSTGQKPGKVSVEGKEVEVTGSTVTSYWANKSGAPATSYRFAIGGSDADYQNAWSSIVGS 789
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eee.....eeee.-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------hhhhhhhhhhhhhhhhhhhh.......------...hhhhhhhhhhhhhh..eeee..hhhhhhhhhhhhhhhhhhhh......eeeeeeee.....eeeee.......................hhhhhhhhhhhhh.......eee.....................eeehhhhhhhh.hhhhhhhhhhhhhh..hhhhhhhhh..........hhhhh.....hhhhhhhhhhhhhh..ee.....eeeee.....eeee.....ee..hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh...eeeeee.....eeeeeee...eeeeeeee.............hhhhhhhhhhhhhhhhh................eeeeee.......eee......eee...eeeeee.................hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2jch A 106 SEITYSDGTVIASI-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DYLYFTTLAEAQERMYDYLAQRDNVSA------ATQKFYRDLAAKEIENGGYKITTTIDQKIHSAMQSAVADYGYLLDDGTGRVEVGNVLMDNQTGAILGFVGGRNYQENQNNHAFDTKRSPASTTKPLLAYGIAIDQGLMGSETILSNYPTNFANGNPIMYANSKGTGMMTLGEALNYSWNIPAYWTYRMLRENGVDVKGYMEKMGYEIPEYGIESLPMGGGIEVTVAQHTNGYQTLANNGVYHQKHVISKIEAADGRVVYEYQDKPVQVYSKATATIMQGLLREVLSSRVTTTFKSNLTSLNPTLANADWIGKTGTTNQDENMWLMLSTPRLTLGGWIGHDDNHSLSQQAGYSNNSNYMAHLVNAIQQASPSIWGNERFALDPSVVKSEVLKSTGQKPGKVSVEGKEVEVTGSTVTSYWANKSGAPATSYRFAIGGSDADYQNAWSSIVGS 789
                                   115   |     -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         - |     345       355       | -    |  375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695       705       715       725       735       745       755       765       775       785    
                                       119                                                                                                                                                                                                                       337                       363    370
   Legend:   → Mismatch (orange background)
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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  (0, 0)

(no "SCOP Domain" information available for 2JCH)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2JCH)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (O70038_STREE | O70038)
molecular function
    GO:0008658    penicillin binding    Interacting selectively and non-covalently with penicillin, any antibiotic that contains the condensed beta-lactamthiazolidine ring system.
cellular component
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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 Related Entries

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

UniProtKB/TrEMBL
        O70038_STREE | O70038: 2bg1 2fff 2je5

(-) Related Entries Specified in the PDB File

2bg1 ACTIVE SITE RESTRUCTURING REGULATES LIGAND RECOGNITION IN CLASSA PENICILLIN-BINDING PROTEINS (PBPS)
2bg3 ACTIVE SITE RESTRUCTURING REGULATES LIGAND RECOGNITION IN CLASSA PENICILLIN-BINDING PROTEINS (PBPS)
2bg4 ACTIVE SITE RESTRUCTURING REGULATES LIGAND RECOGNITION IN CLASSA PENICILLIN-BINDING PROTEINS (PBPS)
2fff OPEN FORM OF A CLASS A TRANSPEPTIDASE DOMAIN
2jci STRUCTURAL INSIGHTS INTO THE CATALYTIC MECHANISM AND THE ROLE OF STREPTOCOCCUS PNEUMONIAE PBP1B