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(-) Description

Title :  DOUBLE MUTANT PBP2X T338A/M339F FROM STREPTOCOCCUS PNEUMONIAE STRAIN R6 AT 2.4 A RESOLUTION
 
Authors :  L. Chesnel, L. Pernot, D. Lemaire, D. Champelovier, J. Croize, O. Dideb T. Vernet, A. Zapun
Date :  09 Jul 03  (Deposition) - 30 Sep 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.42
Chains :  Asym./Biol. Unit :  A
Keywords :  Penicillin-Binding Protein, Antibiotic Resistance, Peptidoglycan Synthesis, Cell Wall, Transmembrane, Transpeptidase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Chesnel, L. Pernot, D. Lemaire, D. Champelovier, J. Croize, O. Dideberg, T. Vernet, A. Zapun
The Structural Modifications Induced By The M339F Substitution In Pbp2X From Streptococcus Pneumoniae Further Decreases The Susceptibility To Beta-Lactams Of Resistant Strains
J. Biol. Chem. V. 278 44448 2003
PubMed-ID: 12923202  |  Reference-DOI: 10.1074/JBC.M305948200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PENICILLIN-BINDING PROTEIN 2X
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX
    Expression System Strain: MC1061
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PBPX
    Mutation: YES
    Organism Scientific: STREPTOCOCCUS PNEUMONIAE
    Organism Taxid: 171101
    Strain: R6
    Synonym: PBP-2X, PBP2X

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 3)

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
1MPD1Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
2OSU1Ligand/IonN-OCTANOYLSUCROSE
3SO41Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:337 , SER A:395 , LYS A:547 , SER A:548 , GLY A:549 , THR A:550 , HOH A:848BINDING SITE FOR RESIDUE SO4 A 751
2AC2SOFTWAREALA A:369 , THR A:370 , ILE A:371 , ARG A:372 , TRP A:374 , ASP A:375 , VAL A:376 , GLN A:447 , PHE A:450 , GLN A:452 , GLN A:552 , TYR A:561 , HOH A:758 , HOH A:776 , HOH A:910BINDING SITE FOR RESIDUE OSU A 752
3AC3SOFTWAREASP A:414 , ASN A:735 , ALA A:737 , ASP A:740BINDING SITE FOR RESIDUE MPD A 753

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1PYY)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Arg A:307 -Pro A:308
2Ser A:576 -Pro A:577

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1PYY)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PASTAPS51178 PASTA domain profile.PBPX_STRR6632-691
692-750		  2A:632-691
A:692-750

(-) Exons   (0, 0)

(no "Exon" information available for 1PYY)

(-) 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 PBPX_STRR6 | P59676 from UniProtKB/Swiss-Prot  Length:750

    Alignment length:678
                                    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       692       702       712       722       732       742        
           PBPX_STRR6    73 PAKRGTIYDRNGVPIAEDATSYNVYAVIDENYKSATGKILYVEKTQFNKVAEVFHKYLDMEESYVREQLSQPNLKQVSFGAKGNGITYANMMSIKKELEAAEVKGIDFTTSPNRSYPNGQFASSFIGLAQLHENEDGSKSLLGTSGMESSLNSILAGTDGIITYEKDRLGNIVPGTEQVSQRTMDGKDVYTTISSPLQSFMETQMDAFQEKVKGKYMTATLVSAKTGEILATTQRPTFDADTKEGITEDFVWRDILYQSNYEPGSTMKVMMLAAAIDNNTFPGGEVFNSSELKIADATIRDWDVNEGLTGGRMMTFSQGFAHSSNVGMTLLEQKMGDATWLDYLNRFKFGVPTRFGLTDEYAGQLPADNIVNIAQSSFGQGISVTQTQMIRAFTAIANDGVMLEPKFISAIYDPNDQTARKSQKEIVGNPVSKDAASLTRTNMVLVGTDPVYGTMYNHSTGKPTVTVPGQNVALKSGTAQIADEKNGGYLVGLTDYIFSAVSMSPAENPDFILYVTVQQPEHYSGIQLGEFANPILERASAMKDSLNLQTTAKALEQVSQQSPYPMPSVKDISPGDLAEELRRNLVQPIVVGTGTKIKNSSAEEGKNLAPNQQVLILSDKAEEVPDMYGWTKETAETLAKWLNIELEFQGSGSTVQKQDVRANTAIKDIKKITLTLGD 750
               SCOP domains d1pyya3 A:73-263 Penicilli                     n-binding protein 2x (       pbp-2x), N-termi                  nal domain                                                                       d1pyya4 A:264-631 Penicillin-binding protein 2x (pbp-2x), transpeptidase domain                                                                                                                                                                                                                                                                                                 d1pyya1 A:632-692                                            d1pyya2 A:693-750                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains PBP_dimer-1pyyA03 A:73-231                                                                                                                                                              --------------------------------Transpeptidase-1pyyA01 A:289-609                                                                                                                                                                                                                                                                                                 ------------------------------------------------------------------------------------PASTA-1pyyA02 A:694-750                                   Pfam domains
         Sec.struct. author ......ee.....eeeee..ee....---------------------.hhhhhhhhhh..hhhhhhhh.-------.........ee.....------------------...ee......hhhhhh.eeeee.....eeeee.hhhhhhhhhhhhh..-------------------------...eeee..hhhhhhhhhhhhhhhhhhhh..eeeeeeee.....eeeeeee..................hhhhhh...hhhhhhhhhhhhhhhh.......eee...eee..eee..ee...ee....eeehhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh.....................hhhhhhhhhhh.....hhhhhhhhhhhhhh...ee....eeeeeehhhheeee....eee...hhhhhhhhhhhhhhhhhh......ee....ee.........eeeeeeee...............eeeeeeeee......eeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhh.........................hhhhhhhhhhhh..eeeee.....eeee............eeeeee............hhhhhhhhhhhh..eeeee....eeeee......hhhhh.eeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PASTA  PDB: A:632-691 UniProt: 632-691                      PASTA  PDB: A:692-750 UniProt: 692-750                      PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1pyy A  73 PAKRGTIYDRNGVPIAEDATSYNVYA---------------------NKVAEVFHKYLDMEESYVREQL-------VSFGAKGNGITYANMM------------------SPNRSYPNGQFASSFIGLAQLHENEDGSKSLLGTSGMESSLNSILAGTD-------------------------DGKDVYTTISSPLQSFMETQMDAFQEKVKGKYMTATLVSAKTGEILATTQRPTFDADTKEGITEDFVWRDILYQSNYEPGSAFKVMMLAAAIDNNTFPGGEVFNSSELKIADATIRDWDVNEGLTGGRMMTFSQGFAHSSNVGMTLLEQKMGDATWLDYLNRFKFGVPTRFGLTDEYAGQLPADNIVNIAQSSFGQGISVTQTQMIRAFTAIANDGVMLEPKFISAIYDPNDQTARKSQKEIVGNPVSKDAASLTRTNMVLVGTDPVYGTMYNHSTGKPTVTVPGQNVALKSGTAQIADEKNGGYLVGLTDYIFSAVSMSPAENPDFILYVTVQQPEHYSGIQLGEFANPILERASAMKDSLNLQTTAKALEQVSQQSPYPMPSVKDISPGDLAEELRRNLVQPIVVGTGTKIKNSSAEEGKNLAPNQQVLILSDKAEEVPDMYGWTKETAETLAKWLNIELEFQGSGSTVQKQDVRANTAIKDIKKITLTLGD 750
                                    82        92     |   -         -       122       132        |-      |152       162 |       -         -|      192       202       212       222        |-         -         -    |  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       692       702       712       722       732       742        
                                                    98                   120                  141     149            164                183                                             231                       257
   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  (3, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Multi-domain proteins (alpha and beta) (2421)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1PYY)

(-) Pfam Domains  (3, 3)

Asymmetric/Biological Unit
(-)
Clan: Beta-lactamase (210)
(-)
Clan: no clan defined [family: PASTA] (12)
(-)
Clan: no clan defined [family: PBP_dimer] (15)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PBPX_STRR6 | P59676)
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:0007049    cell cycle    The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
    GO:0051301    cell division    The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.
    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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 Related Entries

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

UniProtKB/Swiss-Prot
        PBPX_STRR6 | P59676: 2z2l 2z2m 2zc3 2zc4

(-) Related Entries Specified in the PDB File

1k25 PBP2X FROM A HIGHLY PENICILLIN-RESISTANT STREPTOCOCCUS PNEUMONIAE CLINICAL ISOLATE
1pmd PENICILLIN-BINDING PROTEIN 2X (PBP-2X)
1qme PENICILLIN-BINDING PROTEIN 2X (PBP-2X)
1qmf PENICILLIN-BINDING PROTEIN 2X (PBP-2X): ACYL-ENZYME COMPLEX