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(-) Description

Title :  CATALYTIC DOMAIN OF LYTA, THE MAJOR AUTOLYSIN OF STREPTOCOCCUS PNEUMONIAE, (C60A, H133A, C136A MUTANT) COMPLEXED WITH PEPTIDOGLYCAN FRAGMENT
 
Authors :  A. Achour, T. Sandalova, P. Mellroth
Date :  24 Jul 15  (Deposition) - 15 Jun 16  (Release) - 14 Sep 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.05
Chains :  Asym./Biol. Unit :  A,C,E
Keywords :  Lyta, Pneumococci, Autolysis, Amidase, Peptidoglycan Complex, Antibiotics, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Sandalova, M. Lee, B. Henriques-Normark, D. Hesek, S. Mobashery, P. Mellroth, A. Achour
The Crystal Structure Of The Major Pneumococcal Autolysin Lyta In Complex With A Large Peptidoglycan Fragment Reveals The Pivotal Role Of Glycans For Lytic Activity.
Mol. Microbiol. V. 101 954 2016
PubMed-ID: 27273793  |  Reference-DOI: 10.1111/MMI.13435

(-) Compounds

Molecule 1 - AUTOLYSIN
    Chains: A
    EC Number: 3.5.1.28
    Engineered: YES
    Expression System: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'
    Expression System Taxid: 866768
    Fragment: UNP RESIDUES 1-180
    Gene: LYTA, SP_1937
    Mutation: YES
    Organism Scientific: STREPTOCOCCUS PNEUMONIAE SEROTYPE 4
    Organism Taxid: 170187
    Strain: ATCC BAA-334 / TIGR4
    Synonym: CELL WALL HYDROLASE,MUCOPEPTIDE AMINOHYDROLASE,MUREIN HYDROLASE,N-ACETYLMURAMOYL-L-ALANINE AMIDASE
 
Molecule 2 - FRAGMENT OF PEPTIDOGLYCAN
    Chains: C, E
    Engineered: YES
    Organism Scientific: STREPTOCOCCUS PNEUMONIAE
    Organism Taxid: 1313
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ACE

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 7)

Asymmetric/Biological Unit (4, 7)
No.NameCountTypeFull Name
1AMV2Ligand/IonMETHYL 2-(ACETYLAMINO)-3-O-[(1R)-1-CARBOXYETHYL]-2-DEOXY-BETA-D-GLUCOPYRANOSIDE
2DAL1Mod. Amino AcidD-ALANINE
3DGL2Mod. Amino AcidD-GLUTAMIC ACID
4NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:26 , SER A:27 , THR A:28 , ASN A:30 , ASN A:37 , GLU A:38 , TYR A:41 , ARG A:44 , LEU A:49 , ASP A:73 , GLU A:87 , THR A:124 , GLY A:125 , ASP A:146 , HIS A:147 , VAL A:148 , ASP A:149 , HOH A:228 , HOH A:249 , HOH A:320 , DGL C:13 , HOH C:201 , HOH C:204 , HOH C:205 , HOH C:207 , HOH C:209 , HOH C:212 , HOH C:213 , HOH C:214 , HOH E:201 , HOH E:202 , HOH E:203binding site for Poly-Saccharide residues ALA C 12 through NAG C 103
2AC2SOFTWAREHIS A:26 , SER A:27 , THR A:28 , ASN A:30 , ASN A:37 , GLU A:38 , TYR A:41 , ARG A:44 , GLU A:87 , THR A:124 , GLY A:125 , ASP A:146 , HIS A:147 , VAL A:148 , ASP A:149 , HOH A:228 , HOH A:249 , HOH A:320 , ALA C:12 , HOH C:204 , HOH C:205 , HOH C:207 , HOH C:209 , HOH C:212 , HOH C:213 , HOH C:214 , ALA E:23 , DGL E:24 , HOH E:201 , HOH E:202 , HOH E:203binding site for Di-Saccharide NAG C 103 and AMV E 101

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5CTV)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Gln A:18 -Pro A:19
2Asp A:149 -Pro A:150

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5CTV)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5CTV)

(-) Exons   (0, 0)

(no "Exon" information available for 5CTV)

(-) 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:176
                                                                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......................eeeeee......hhhhhhhhhhhhhhhhh...eeee..eeee............hhhhh.eeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhh...........eeeehhhhhhhh.........hhhhhhhh..hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ctv A  -1 ASMEINVSKLRTDLPQVGVQPYRQVHAHSTGNPHSTVQNEADYHWRKDPELGFFSHIVGNGAIMQVGPVDNGAWDVGGGWNAETYAAVELIESHSTKEEFMTDYRLYIELLRNLADEAGLPKTLDTGSLAGIKTAEYATNNQPNNHSDHVDPYPYLAKWGISREQFKHDIENGLTI 174
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168      


Chain C from PDB  Type:PROTEIN  Length:4
                                    
               SCOP domains ---- SCOP domains
               CATH domains ---- CATH domains
               Pfam domains ---- Pfam domains
         Sec.struct. author .... Sec.struct. author
                 SAPs(SNPs) ---- SAPs(SNPs)
                    PROSITE ---- PROSITE
                 Transcript ---- Transcript
                 5ctv C  12 AxKx  15
                             | |
                            13-DGL
                              15-DAL


Chain E from PDB  Type:PROTEIN  Length:2
                                  
               SCOP domains -- SCOP domains
               CATH domains -- CATH domains
               Pfam domains -- Pfam domains
         Sec.struct. author .. Sec.struct. author
                 SAPs(SNPs) -- SAPs(SNPs)
                    PROSITE -- PROSITE
                 Transcript -- Transcript
                 5ctv E  23 Ax  24
                             |
                             |
                            24-DGL
   Legend:   → Mismatch (orange background)
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    → 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 5CTV)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5CTV)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5CTV)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        ALYS_STRPN | P06653: 1gvm 1h8g 1hcx 2bml 4ivv 4x36

(-) Related Entries Specified in the PDB File

4ivv 4IVV - THE SAME PROTEIN (DIFFERENT MUTANT) WITHOUT SUBSTRATE