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(-) Description

Title :  PENICILLIN-BINDING PROTEIN 2B (PBP-2B) FROM STREPTOCOCCUS PNEUMONIAE (STRAIN 5204)
 
Authors :  C. Contreras-Martel, C. Dahout-Gonzalez, A. Dos-Santos-Martins, M. A. Dessen
Date :  05 Feb 09  (Deposition) - 24 Feb 09  (Release) - 19 Feb 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.26
Chains :  Asym./Biol. Unit :  A
Keywords :  Peptidoglycan Synthesis, Penicillin-Binding Protein, Transmembrane, Antibiotic Resistance, Cell Shape, Peptidoglycan, Cell Membrane, Cell Wall Biogenesis/Degradation, Membrane, Infection, Resistance, Antibiotic, Peptide Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Contreras-Martel, C. Dahout-Gonzalez, A. Dos-Santos-Martins, M. Kotnik, A. Dessen
Pbp Active Site Flexibility As The Key Mechanism For Beta-Lactam Resistance In Pneumococci
J. Mol. Biol. V. 387 899 2009
PubMed-ID: 19233207  |  Reference-DOI: 10.1016/J.JMB.2009.02.024
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PENICILLIN-BINDING PROTEIN 2B
    Chains: A
    EC Number: 3.4.-.-
    Organism Scientific: STREPTOCOCCUS PNEUMONIAE
    Organism Taxid: 1313
    Strain: 5204

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1ZN1Ligand/IonZINC ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:284 , HIS A:286 , GLU A:297BINDING SITE FOR RESIDUE ZN A1680

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ala A:638 -Pro A:639

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2WAE)

(-) 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:607
 aligned with B0B6I9_STREE | B0B6I9 from UniProtKB/TrEMBL  Length:685

    Alignment length:632
                                    62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642       652       662       672       682  
         B0B6I9_STREE    53 SASQTKVTTSSARGEIYDASGKPLVENTLKQVVSFTRSNKMTATDLKEIAKKLLTYVSISSPNLTERQLADYYLADPEIYKKTVEALPSEKRLDSDGNRLSESELYNNAVDSVPTSQLNYTEDEKKEIYLFSQLNAVGNFATGTIATDPLNDSQVAVIASISKEMPGISISTSWDRKILETSLSSIVGSVSSEKAGLPAEEAEAYLKKGYSLNDRVGTSYLEKQYEETLQGKRSVKEIHLDKYGNMESVDTIEEGSKGNNIKLTIDLAFQDSVDALLKSYFNSELGNGGAKYSEGVYAVALNPKTGAVLSMSGLKHDLKTGELTPDSLGTVTNVFVPGSVVKAATISSGWENGVLSGNQTLTDQPIVFQGSAPIYSWYKLAYGSFPITAVEALEYSSNAYVVQTALGIMGQTYQPNMFVGTSNLESAMGKLRSTFGEYGLGSATGIDLPDESTGLVPKEYNFANFITNAFGQFDNYTPMQLAQYVATIANNGVRLAPHIVEGIYDNNDKGGLGELIQAIDTKEINKVNISESDMAILHQGFYQVSHGTSPLTTGRAFSDGATVSISGKTGTGESYVAGGQEANNTNAVAYAPTENPQIAVAVVFPHNTNLTKNVGPAIARDIINLYNQHHPM 684
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------PBP_dimer-2waeA02 A:55-298                                                                                                                                                                                                                          --------------------------------------------Transpeptidase-2waeA01 A:343-671                                                                                                                                                                                                                                                                                                         -------- Pfam domains
         Sec.struct. author ..eeeeee.......ee.......eeeeeeeeeeee.....hhhhhhhhhhhhh..........hhhhhhhhhh.hhhhhhhhh....--------------.hhhhhhh............hhhhhhhhhhhhhh.....eee......hhhhhhhhhhhhhhh..eeeeeeeeeee....hhhhhh.........hhhhhhhhhh...........hhhhhhhhhhhh....eeeeee.....eeeeeeee......eeee..hhhhhhhhhhhhhhhhhhhhhh.......eeeeeee......eeeeeeeee......eee..hhhhhh...hhhhhhhhhhhhhhhh........eee.....................eeehhhhhhhh.hhhhhhhhhhhhh.............hhhhhhhhhhhhhhhh......................hhhhhhhhhh......hhhhhhhhhhhhhh..eee....eeeeeee.....eeeeeee....eeee...hhhhhhhhhhhhhhhhhh......hhhhh.......eeee..-----------....eeeee......eeeeee.........hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wae A  48 SASQTKVTTSSARGEIYDASGKPLVENTLKQVVSFTRSNKMTATDLKEIAKKLLTYVSISSPNLTERQLADYYLADPEIYKKTVEALP--------------SELYNNAVDSVPTSQLNYTEDEKKEIYLFSQLNAVGNFATGTIATDPLNDSQVAVIASISKEMPGISISTSWDRKILETSLSSIVGSVSSEKAGLPAEEAESYLKKGYSLNDRVGTSYLEKQYEEVLQGKRPVKEIHLDKHGDMESVENIEEGSKGKNIKLTIDLAFQDSVDALLKSYFNSELGNGGAKYSEGVYAVALNPQTGAVLSMSGLKHDLKTGELTPDSLGTVTNVFVPGSVVKAATISSGWENGVLSGNQTLTDQPIVFQGSAPIYSWYKLAYGSFPITAVEALEYSSNAYVVQTALGIMGQTYQPNMFVGTSNLESAMGKLRSTFGEYGLGSATGIDLPDESTGLVPKEYNFANFITNAFGQFDNYTPMQLAQYVATIANNGVRLAPHIVEGIYDNNDKGGLGELIQAIDTKEINKVNISESDMAILHQGFYQVSHGTSPLTTGRAFSDGATVSISGKTGT-----------NNTNAVAYAPTENPQIAVAVVFPHNTNLTKNVGPAIARDIINLYNQHHPM 679
                                    57        67        77        87        97       107       117       127       | -         -  |    157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577       587       597       607       617|        -  |    637       647       657       667       677  
                                                                                                                 135            150                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 618         630                                                 


Chain A from PDB  Type:PROTEIN  Length:607
 aligned with PBP2_STRR6 | P0A3M6 from UniProtKB/Swiss-Prot  Length:680

    Alignment length:632
                                    57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577       587       597       607       617       627       637       647       657       667       677  
           PBP2_STRR6    48 SASQTKITSSSARGEIYDASGKPLVENTLKQVVSFTRSNKMTATDLKETAKKLLTYVSISSPNLTERQLADYYLADPEIYKKIVEALPSEKRLDSDGNRLSESELYNNAVDSVQTSQLNYTEDEKKEIYLFSQLNAVGNFATGTIATDPLNDSQVAVIASISKEMPGISISTSWDRKVLETSLSSIVGSVSSEKAGLPAEEAEAYLKKGYSLNDRVGTSYLEKQYEETLQGKRSVKEIHLDKYGNMESVDTIEEGSKGNNIKLTIDLAFQDSVDALLKSYFNSELENGGAKYSEGVYAVALNPKTGAVLSMSGIKHDLKTGELTPDSLGTVTNVFVPGSVVKAATISSGWENGVLSGNQTLTDQSIVFQGSAPINSWYTQAYGSFPITAVQALEYSSNTYMVQTALGLMGQTYQPNMFVGTSNLESAMEKLRSTFGEYGLGTATGIDLPDESTGFVPKEYSFANYITNAFGQFDNYTPMQLAQYVATIANNGVRVAPRIVEGIYGNNDKGGLGDLIQQLQPTEMNKVNISDSDMSILHQGFYQVAHGTSGLTTGRAFSNGALVSISGKTGTAESYVADGQQATNTNAVAYAPSDNPQIAVAVVFPHNTNLTNGVGPSIARDIINLYQKYHPM 679
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------PBP_dimer-2waeA02 A:55-298                                                                                                                                                                                                                          --------------------------------------------Transpeptidase-2waeA01 A:343-671                                                                                                                                                                                                                                                                                                         -------- Pfam domains
         Sec.struct. author ..eeeeee.......ee.......eeeeeeeeeeee.....hhhhhhhhhhhhh..........hhhhhhhhhh.hhhhhhhhh....--------------.hhhhhhh............hhhhhhhhhhhhhh.....eee......hhhhhhhhhhhhhhh..eeeeeeeeeee....hhhhhh.........hhhhhhhhhh...........hhhhhhhhhhhh....eeeeee.....eeeeeeee......eeee..hhhhhhhhhhhhhhhhhhhhhh.......eeeeeee......eeeeeeeee......eee..hhhhhh...hhhhhhhhhhhhhhhh........eee.....................eeehhhhhhhh.hhhhhhhhhhhhh.............hhhhhhhhhhhhhhhh......................hhhhhhhhhh......hhhhhhhhhhhhhh..eee....eeeeeee.....eeeeeee....eeee...hhhhhhhhhhhhhhhhhh......hhhhh.......eeee..-----------....eeeee......eeeeee.........hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wae A  48 SASQTKVTTSSARGEIYDASGKPLVENTLKQVVSFTRSNKMTATDLKEIAKKLLTYVSISSPNLTERQLADYYLADPEIYKKTVEALP--------------SELYNNAVDSVPTSQLNYTEDEKKEIYLFSQLNAVGNFATGTIATDPLNDSQVAVIASISKEMPGISISTSWDRKILETSLSSIVGSVSSEKAGLPAEEAESYLKKGYSLNDRVGTSYLEKQYEEVLQGKRPVKEIHLDKHGDMESVENIEEGSKGKNIKLTIDLAFQDSVDALLKSYFNSELGNGGAKYSEGVYAVALNPQTGAVLSMSGLKHDLKTGELTPDSLGTVTNVFVPGSVVKAATISSGWENGVLSGNQTLTDQPIVFQGSAPIYSWYKLAYGSFPITAVEALEYSSNAYVVQTALGIMGQTYQPNMFVGTSNLESAMGKLRSTFGEYGLGSATGIDLPDESTGLVPKEYNFANFITNAFGQFDNYTPMQLAQYVATIANNGVRLAPHIVEGIYDNNDKGGLGELIQAIDTKEINKVNISESDMAILHQGFYQVSHGTSPLTTGRAFSDGATVSISGKTGT-----------NNTNAVAYAPTENPQIAVAVVFPHNTNLTKNVGPAIARDIINLYNQHHPM 679
                                    57        67        77        87        97       107       117       127       | -         -  |    157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577       587       597       607       617|        -  |    637       647       657       667       677  
                                                                                                                 135            150                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 618         630
   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  (0, 0)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: Beta-lactamase (210)
(-)
Clan: no clan defined [family: PBP_dimer] (15)

(-) Gene Ontology  (8, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (B0B6I9_STREE | B0B6I9)
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.

Chain A   (PBP2_STRR6 | P0A3M6)
molecular function
    GO:0008658    penicillin binding    Interacting selectively and non-covalently with penicillin, any antibiotic that contains the condensed beta-lactamthiazolidine ring system.
biological process
    GO:0071555    cell wall organization    A process that results in the assembly, arrangement of constituent parts, or disassembly of the cell wall, the rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis.
    GO:0009252    peptidoglycan biosynthetic process    The chemical reactions and pathways resulting in the formation of peptidoglycans, any of a class of glycoconjugates found in bacterial cell walls.
    GO:0008360    regulation of cell shape    Any process that modulates the surface configuration of a cell.
    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.
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.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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  2wae
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 Related Entries

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

UniProtKB/Swiss-Prot
        PBP2_STRR6 | P0A3M6: 2wad 2waf
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(-) Related Entries Specified in the PDB File

2wad PENICILLIN-BINDING PROTEIN 2B (PBP-2B) FROM STREPTOCOCCUS PNEUMONIAE (STRAIN 5204)
2waf PENICILLIN-BINDING PROTEIN 2B (PBP-2B) FROM STREPTOCOCCUS PNEUMONIAE (STRAIN 5204)