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(-) Description

Title :  CHOLINE BINDING DOMAIN OF THE MAJOR AUTOLYSIN (C-LYTA) FROM STREPTOCOCCUS PNEUMONIAE
 
Authors :  C. Fernandez-Tornero, R. Lopez, E. Garcia, G. Gimenez-Gallego, A. Romero
Date :  10 May 01  (Deposition) - 29 Nov 01  (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 (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Fernandez-Tornero, R. Lopez, E. Garcia, G. Gimenez-Gallego, A. Romero
A Novel Solenoid Fold In The Cell Wall Anchoring Domain Of The Pneumococcal Virulence Factor Lyta
Nat. Struct. Biol. V. 8 1020 2001
PubMed-ID: 11694890  |  Reference-DOI: 10.1038/NSB724
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MAJOR AUTOLYSIN
    Cellular Location: EXTRACELLULAR
    Chains: A, B
    EC Number: 3.5.1.28
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Cellular Location: CYTOPLASM
    Expression System Plasmid: PCE17
    Expression System Strain: RB791
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: CHOLINE-BINDING DOMAIN
    Gene: LYTA
    Organism Scientific: STREPTOCOCCUS PNEUMONIAE
    Organism Taxid: 1313
    Synonym: C-LYTA, CELL WALL BINDING DOMAIN

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric/Biological Unit (3, 8)
No.NameCountTypeFull Name
1CHT5Ligand/IonCHOLINE ION
2DDQ2Ligand/IonDECYLAMINE-N,N-DIMETHYL-N-OXIDE
3TPT1Ligand/Ion2,2':6',2''-TERPYRIDINE PLATINUM(II)

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP A:241 , TRP A:248 , TYR A:264 , TYR A:269 , ASP A:298 , TYR B:194 , HOH B:2003BINDING SITE FOR RESIDUE TPT A1319
2AC2SOFTWAREPHE A:199 , TRP A:206 , GLU A:254 , HOH A:2028BINDING SITE FOR RESIDUE CHT A1320
3AC3SOFTWARETRP A:220 , TRP A:228 , MET A:257 , LYS A:274 , GLU A:275BINDING SITE FOR RESIDUE CHT A1321
4AC4SOFTWARETRP A:261 , TRP A:268 , TYR A:293 , HOH A:2029 , THR B:224 , ASP B:225BINDING SITE FOR RESIDUE CHT A1323
5AC5SOFTWARELYS A:263 , ASP A:266 , PHE B:199 , HIS B:223 , TYR B:229 , GLU B:254BINDING SITE FOR RESIDUE DDQ B1319
6AC6SOFTWARETRP B:220 , ARG B:221 , LYS B:222 , TRP B:228 , GLU B:275 , PRO B:311BINDING SITE FOR RESIDUE DDQ B1320
7AC7SOFTWARETRP B:241 , TRP B:248 , TYR B:269BINDING SITE FOR RESIDUE CHT B1321
8AC8SOFTWAREASP A:312 , TRP B:261 , TRP B:268BINDING SITE FOR RESIDUE CHT B1322

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1HCX)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) 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 1HCX)

(-) 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:127
 aligned with ALYS_STRPN | P06653 from UniProtKB/Swiss-Prot  Length:318

    Alignment length:127
                                   201       211       221       231       241       251       261       271       281       291       301       311       
           ALYS_STRPN   192 GSYPKDKFEKINGTWYYFDSSGYMLADRWRKHTDGNWYWFDNSGEMATGWKKIADKWYYFNEEGAMKTGWVKYKDTWYYLDAKEGAMVSNAFIQSADGTGWYYLKPDGTLADKPEFTVEPDGLITVK 318
               SCOP domains d1hcxa_ A: Choline binding domain of autolysin C-LytA                                                                           SCOP domains
               CATH domains 1hcxA00 A:192-318 Cholin Binding                                                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeee..eeeee.........eeeee...eeeee........eeeee..eeeee........eeeee..eeeee..........eeeee....eeeee..........eeeee...eeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE CW -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
                 1hcx A 192 GSYPKDKFEKINGTWYYFDSSGYMLADRWRKHTDGNWYWFDNSGEMATGWKKIADKWYYFNEEGAMKTGWVKYKDTWYYLDAKEGAMVSNAFIQSADGTGWYYLKPDGTLADRPEFTVEPDGLITVK 318
                                   201       211       221       231       241       251       261       271       281       291       301       311       


Chain B from PDB  Type:PROTEIN  Length:127
 aligned with ALYS_STRPN | P06653 from UniProtKB/Swiss-Prot  Length:318

    Alignment length:127
                                   201       211       221       231       241       251       261       271       281       291       301       311       
           ALYS_STRPN   192 GSYPKDKFEKINGTWYYFDSSGYMLADRWRKHTDGNWYWFDNSGEMATGWKKIADKWYYFNEEGAMKTGWVKYKDTWYYLDAKEGAMVSNAFIQSADGTGWYYLKPDGTLADKPEFTVEPDGLITVK 318
               SCOP domains d1hcxb_ B: Choline binding domain of autolysin C-LytA                                                                           SCOP domains
               CATH domains 1hcxB00 B:192-318 Cholin Binding                                                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeee..eeeee.........eeeee...eeeee........eeeee..eeeee........eeeee..eeeee..........eeeee....eeeee..........eeeee...eeeee 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
                 1hcx B 192 GSYPKDKFEKINGTWYYFDSSGYMLADRWRKHTDGNWYWFDNSGEMATGWKKIADKWYYFNEEGAMKTGWVKYKDTWYYLDAKEGAMVSNAFIQSADGTGWYYLKPDGTLADRPEFTVEPDGLITVK 318
                                   201       211       221       231       241       251       261       271       281       291       301       311
   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 1HCX)

(-) 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 2bml 4ivv 4x36 5ctv

(-) Related Entries Specified in the PDB File

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