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(-) Description

Title :  STRUCTURE OF PLYL
 
Authors :  L. Y. Low, C. Yang, M. Perego, A. Osterman, R. C. Liddington
Date :  18 Dec 04  (Deposition) - 23 Aug 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.86
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  N-Acetylmuramoyl-L-Alanine Amidase, Plyl, E. C. 3. 5. 1. 28, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Y. Low, C. Yang, M. Perego, A. Osterman, R. C. Liddington
Structure And Lytic Activity Of A Bacillus Anthracis Prophage Endolysin
J. Biol. Chem. V. 280 35433 2005
PubMed-ID: 16103125  |  Reference-DOI: 10.1074/JBC.M502723200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROPHAGE LAMBDABA02, N-ACETYLMURAMOYL-L-ALANINE AMIDASE, FAMILY 2
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET22
    Expression System Strain: BL21DE3
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: BACILLUS ANTHRACIS
    Organism Taxid: 1392

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric/Biological Unit (2, 6)
No.NameCountTypeFull Name
1PO43Ligand/IonPHOSPHATE ION
2ZN3Ligand/IonZINC ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:29 , HIS A:129 , CYS A:137 , PO4 A:161BINDING SITE FOR RESIDUE ZN A 160
2AC2SOFTWAREHIS A:29 , ASN A:30 , GLU A:90 , HIS A:129 , LYS A:135 , CYS A:137 , ZN A:160 , HOH A:164 , HOH A:253BINDING SITE FOR RESIDUE PO4 A 161
3AC3SOFTWAREHIS B:29 , HIS B:129 , CYS B:137 , PO4 B:1161BINDING SITE FOR RESIDUE ZN B 160
4AC4SOFTWAREHIS B:29 , ALA B:74 , GLU B:90 , HIS B:129 , LYS B:135 , CYS B:137 , ZN B:160 , HOH B:1168 , HOH B:1180 , HOH B:1233 , HOH B:1255 , HOH B:1261BINDING SITE FOR RESIDUE PO4 B 1161
5AC5SOFTWAREHIS C:29 , HIS C:129 , CYS C:137 , PO4 C:2161BINDING SITE FOR RESIDUE ZN C 160
6AC6SOFTWAREHIS C:29 , ASN C:30 , ALA C:74 , GLU C:90 , HIS C:129 , LYS C:135 , CYS C:137 , ZN C:160BINDING SITE FOR RESIDUE PO4 C 2161

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1YB0)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Cys A:137 -Pro A:138
2Cys B:137 -Pro B:138
3Cys C:137 -Pro C:138

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1YB0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1YB0)

(-) Exons   (0, 0)

(no "Exon" information available for 1YB0)

(-) 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:157
 aligned with Q81WA9_BACAN | Q81WA9 from UniProtKB/TrEMBL  Length:234

    Alignment length:157
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       
         Q81WA9_BACAN     1 MEIRKKLVVPSKYGTKCPYTMKPKYITVHNTYNDAPAENEVNYMITNNNEVSFHVAVDDKQAIQGIPWERNAWACGDGNGPGNRESISVEICYSKSGGDRYYKAENNAVDVVRQLMSMYNIPIENVRTHQSWSGKYCPHRMLAEGRWGAFIQKVKSG 157
               SCOP domains d1yb0a1 A:1-157 N-acetylmuramoyl-L-alanine amidase PlyG                                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee...hhhhhhhhh.......eeeeee.....hhhhhhhhhhhh.......eee....eee...............hhhhhheeeeee.....hhhhhhhhhhhhhhhhhhhhhhhh.hhh.eeehhhhhh...hhhhhhh.hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yb0 A   1 MEIRKKLVVPSKYGTKCPYTMKPKYITVHNTYNDAPAENEVNYMITNNNEVSFHVAVDDKQAIQGIPWERNAWACGDGNGPGNRESISVEICYSKSGGDRYYKAENNAVDVVRQLMSMYNIPIENVRTHQSWSGKYCPHRMLAEGRWGAFIQKVKSG 157
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       


Chain B from PDB  Type:PROTEIN  Length:159
 aligned with Q81WA9_BACAN | Q81WA9 from UniProtKB/TrEMBL  Length:234

    Alignment length:159
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150         
         Q81WA9_BACAN     1 MEIRKKLVVPSKYGTKCPYTMKPKYITVHNTYNDAPAENEVNYMITNNNEVSFHVAVDDKQAIQGIPWERNAWACGDGNGPGNRESISVEICYSKSGGDRYYKAENNAVDVVRQLMSMYNIPIENVRTHQSWSGKYCPHRMLAEGRWGAFIQKVKSGNV 159
               SCOP domains d1yb0b_ B: N-acetylmuramoyl-L-alanine amidase PlyG                                                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee...hhhhhhhhh.......eeeeee.....hhhhhhhhhhhh.......eee....eee...............hhhhhheeeeee......hhhhhhhhhhhhhhhhhhhhhhh.hhh.eeehhhhhh...hhhhhhh.hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yb0 B   1 MEIRKKLVVPSKYGTKCPYTMKPKYITVHNTYNDAPAENEVNYMITNNNEVSFHVAVDDKQAIQGIPWERNAWACGDGNGPGNRESISVEICYSKSGGDRYYKAENNAVDVVRQLMSMYNIPIENVRTHQSWSGKYCPHRMLAEGRWGAFIQKVKSGNV 159
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150         


Chain C from PDB  Type:PROTEIN  Length:157
 aligned with Q81WA9_BACAN | Q81WA9 from UniProtKB/TrEMBL  Length:234

    Alignment length:157
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       
         Q81WA9_BACAN     1 MEIRKKLVVPSKYGTKCPYTMKPKYITVHNTYNDAPAENEVNYMITNNNEVSFHVAVDDKQAIQGIPWERNAWACGDGNGPGNRESISVEICYSKSGGDRYYKAENNAVDVVRQLMSMYNIPIENVRTHQSWSGKYCPHRMLAEGRWGAFIQKVKSG 157
               SCOP domains d1yb0c_ C: N-acetylmuramoyl-L-alanine amidase PlyG                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --------------Amidase_2-1yb0C01 C:15-141                                                                                                     ---------------- Pfam domains (1)
           Pfam domains (2) --------------Amidase_2-1yb0C02 C:15-141                                                                                                     ---------------- Pfam domains (2)
           Pfam domains (3) --------------Amidase_2-1yb0C03 C:15-141                                                                                                     ---------------- Pfam domains (3)
         Sec.struct. author ..eee...hhhhhhhhh.......eeeeee.....hhhhhhhhhhhh.......eee....eee...............hhhhhheeeeee......hhhhhhhhhhhhhhhhhhhhhhh.hhh.eeehhhhhh...hhhhhhh.hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yb0 C   1 MEIRKKLVVPSKYGTKCPYTMKPKYITVHNTYNDAPAENEVNYMITNNNEVSFHVAVDDKQAIQGIPWERNAWACGDGNGPGNRESISVEICYSKSGGDRYYKAENNAVDVVRQLMSMYNIPIENVRTHQSWSGKYCPHRMLAEGRWGAFIQKVKSG 157
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150
   Legend:   → Mismatch (orange background)
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  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, 3)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1YB0)

(-) Pfam Domains  (1, 3)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: Amidase_2] (23)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C   (Q81WA9_BACAN | Q81WA9)
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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    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.

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UniProtKB/TrEMBL
        Q81WA9_BACAN | Q81WA9: 2ar3

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