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(-) Description

Title :  OFLOXACIN-LIKE ANTIBIOTICS INHIBIT PNEUMOCOCCAL CELL WALL DEGRADING VIRULENCE FACTORS
 
Authors :  C. Fernandez-Tornero, G. Gimenez-Gallego, A. Romero, E. Garcia, B. D. Pascual-Teresa, R. Lopez
Date :  15 Mar 05  (Deposition) - 30 Mar 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Choline-Binding Domain, Cell Wall Attachment, Ofloxacin- Like Antibiotics (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Fernandez-Tornero, E. Garcia, R. Lopez, B. D. Pascual-Teresa, G. Gimenez-Gallego, A. Romero
Ofloxacin-Like Antibiotics Inhibit Pneumococcal Cell Wall-Degrading Virulence Factors
J. Biol. Chem. V. 280 19948 2005
PubMed-ID: 15769740  |  Reference-DOI: 10.1074/JBC.M501236200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - AUTOLYSIN
    Chains: A, B
    EC Number: 3.5.1.28
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PCE17
    Expression System Strain: RB791
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: CHOLINE-BINDING DOMAIN, RESIDUES 193-318
    Organism Scientific: STREPTOCOCCUS PNEUMONIAE
    Organism Taxid: 1313
    Synonym: N-ACETYLMURAMOYL-L-ALANINE AMIDASE, MUREIN, HYDROLASE, MUCOPEPTIDE AMINOHYDROLASE, CELL WALL HYDROLASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 9)

Asymmetric/Biological Unit (5, 9)
No.NameCountTypeFull Name
1P6G2Ligand/IonHEXAETHYLENE GLYCOL
2PG41Ligand/IonTETRAETHYLENE GLYCOL
3SO43Ligand/IonSULFATE ION
4TRS2Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
5XED1Ligand/IonDEXTROFLOXACINE

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:201 , TRP A:206 , LYS B:243 , TRP B:248 , P6G B:1320 , HOH B:2028 , HOH B:2033 , HOH B:2034 , HOH B:2035BINDING SITE FOR RESIDUE SO4 B1322
2AC2SOFTWARELYS A:243 , TRP A:248 , LYS B:201 , TRP B:206BINDING SITE FOR RESIDUE SO4 B1323
3AC3SOFTWAREGLN A:285 , ASN B:281 , HOH B:2036BINDING SITE FOR RESIDUE SO4 B1324
4AC4SOFTWARETRP A:220 , GLU A:275BINDING SITE FOR RESIDUE TRS A1319
5AC5SOFTWARETRP A:261 , TRP A:268 , TYR A:293 , LEU A:301BINDING SITE FOR RESIDUE TRS A1320
6AC6SOFTWARETRP A:241 , TRP A:248 , TYR A:269 , MET A:278 , ASP A:298BINDING SITE FOR RESIDUE P6G A1321
7AC7SOFTWARESER B:212 , GLY B:213 , TYR B:214 , MET B:215 , TRP B:220 , TRP B:228 , GLU B:275 , HOH B:2009BINDING SITE FOR RESIDUE XED B1319
8AC8SOFTWAREPHE A:199 , TRP A:206 , TYR A:229 , GLU A:254 , TRP B:241 , TRP B:248 , TYR B:264 , TYR B:269 , ASP B:298 , SO4 B:1322 , HOH B:2030BINDING SITE FOR RESIDUE P6G B1320
9AC9SOFTWARETYR A:207 , MET A:215 , TRP B:261 , TRP B:268 , HOH B:2032BINDING SITE FOR RESIDUE PG4 B1321

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2BML)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 10)

Asymmetric/Biological Unit (1, 10)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CWPS51170 Cell wall-binding repeat profile.ALYS_STRPN175-194
196-215
 
217-237
 
238-257
 
258-277
 
280-301
 		  10-
A:196-215
B:196-215
A:217-237
B:217-237
A:238-257
B:238-257
A:258-277
B:258-277
A:280-301
B:280-301

(-) Exons   (0, 0)

(no "Exon" information available for 2BML)

(-) 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:125
 aligned with ALYS_STRPN | P06653 from UniProtKB/Swiss-Prot  Length:318

    Alignment length:125
                                   203       213       223       233       243       253       263       273       283       293       303       313     
           ALYS_STRPN   194 YPKDKFEKINGTWYYFDSSGYMLADRWRKHTDGNWYWFDNSGEMATGWKKIADKWYYFNEEGAMKTGWVKYKDTWYYLDAKEGAMVSNAFIQSADGTGWYYLKPDGTLADKPEFTVEPDGLITVK 318
               SCOP domains d2bmla_ A: automated matches                                                                                                  SCOP domains
               CATH domains 2bmlA00 A:194-318 Cholin Binding                                                                                              CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee..eeeee.........eeee.....eeee........eeee....eeee........eeee....eeee..........eeee......eeee...........eee.....eee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE C-CW  PDB: A:196-215  -CW  PDB: A:217-237   CW  PDB: A:238-257  CW  PDB: A:258-277  --CW  PDB: A:280-301    ----------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bml A 194 YPKDKFEKINGTWYYFDSSGYMLADRWRKHTDGNWYWFDNSGEMATGWKKIADKWYYFNEEGAMKTGWVKYKDTWYYLDAKEGAMVSNAFIQSADGTGWYYLKPDGTLADRPEFTVEPDGLITVK 318
                                   203       213       223       233       243       253       263       273       283       293       303       313     


Chain B from PDB  Type:PROTEIN  Length:126
 aligned with ALYS_STRPN | P06653 from UniProtKB/Swiss-Prot  Length:318

    Alignment length:126
                                   202       212       222       232       242       252       262       272       282       292       302       312      
           ALYS_STRPN   193 SYPKDKFEKINGTWYYFDSSGYMLADRWRKHTDGNWYWFDNSGEMATGWKKIADKWYYFNEEGAMKTGWVKYKDTWYYLDAKEGAMVSNAFIQSADGTGWYYLKPDGTLADKPEFTVEPDGLITVK 318
               SCOP domains d2bmlb_ B: automated matches                                                                                                   SCOP domains
               CATH domains 2bmlB00 B:193-318 Cholin Binding                                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeeee..eeeee.........eeee.....eeee........eeee....eeee........eeeee..eeeee..........eeee......eeee...........eee.....eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE CW-CW  PDB: B:196-215  -CW  PDB: B:217-237   CW  PDB: B:238-257  CW  PDB: B:258-277  --CW  PDB: B:280-301    ----------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2bml B 193 SYPKDKFEKINGTWYYFDSSGYMLADRWRKHTDGNWYWFDNSGEMATGWKKIADKWYYFNEEGAMKTGWVKYKDTWYYLDAKEGAMVSNAFIQSADGTGWYYLKPDGTLADRPEFTVEPDGLITVK 318
                                   202       212       222       232       242       252       262       272       282       292       302       312
   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  (1, 2)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (ALYS_STRPN | P06653)
molecular function
    GO:0008745    N-acetylmuramoyl-L-alanine amidase activity    Catalysis of the hydrolysis of the link between N-acetylmuramoyl residues and L-amino acid residues in certain bacterial cell-wall glycopeptides.
    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: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:0030420    establishment of competence for transformation    The process in which a naturally transformable bacterium acquires the ability to take up exogenous DNA. This term should be applied only to naturally transformable bacteria, and should not be used in the context of artificially induced bacterial transformation.
    GO:0009253    peptidoglycan catabolic process    The chemical reactions and pathways resulting in the breakdown of peptidoglycans, any of a class of glycoconjugates found in bacterial cell walls.
    GO:0030435    sporulation resulting in formation of a cellular spore    The process in which a relatively unspecialized cell acquires the specialized features of a cellular spore, a cell form that can be used for dissemination, for survival of adverse conditions because of its heat and dessication resistance, and/or for reproduction.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

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 Related Entries

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

UniProtKB/Swiss-Prot
        ALYS_STRPN | P06653: 1gvm 1h8g 1hcx 4ivv 4x36 5ctv

(-) Related Entries Specified in the PDB File

1gvm CHOLINE BINDING DOMAIN OF THE MAJOR AUTOLYSIN (C-LYTA) FROM STREPTOCOCCUS PNEUMONIAE
1h8g C-TERMINAL DOMAIN OF THE MAJOR AUTOLYSIN ( C-LYTA) FROM STREPTOCOCCUS PNEUMONIAE
1hcx CHOLINE BINDING DOMAIN OF THE MAJOR AUTOLYSIN FROM STREPTOCOCCUS PNEUMONIAE