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(-) Description

Title :  THE CRYSTAL STRUCTURE OF THE LISTERIA MONOCYTOGENES BACTERIOPHAGE PSA ENDOLYSIN PLYPSA
 
Authors :  I. P. Korndoerfer, A. Skerra
Date :  07 Oct 04  (Deposition) - 18 Oct 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Alpha/Beta Hydrolase, Multi-Domain, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. P. Korndoerfer, J. Danzer, M. Schmelcher, M. Zimmer, A. Skerra, M. J. Loessner
The Crystal Structure Of The Bacteriophage Psa Endolysin Reveals A Unique Fold Responsible For Specific Recognition Of Listeria Cell Walls
J. Mol. Biol. V. 364 678 2006
PubMed-ID: 17010991  |  Reference-DOI: 10.1016/J.JMB.2006.08.069

(-) Compounds

Molecule 1 - PLY PROTEIN
    Chains: A
    EC Number: 3.5.1.28
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PSPLPSA
    Expression System Strain: JM83
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PLY
    Organism Scientific: LISTERIA PHAGE PSA
    Organism Taxid: 171618
    Other Details: HOST: LISTERIA MONOCYTOGENES
    Synonym: PLYPSA

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (6, 6)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2GLU1Mod. Amino AcidGLUTAMIC ACID
3LYS1Mod. Amino AcidLYSINE
4SO41Ligand/IonSULFATE ION
5TRS1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
6ZN1Ligand/IonZINC ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:10 , GLU A:23 , HIS A:79 , GLU A:2001BINDING SITE FOR RESIDUE ZN A 1001
2AC2SOFTWARELYS A:249 , ARG A:251 , LYS A:278 , TYR A:280 , TYR A:300 , HOH A:2212BINDING SITE FOR RESIDUE SO4 A 1002
3AC3SOFTWARETYR A:217 , ARG A:251BINDING SITE FOR RESIDUE CL A 1005
4AC4SOFTWAREHIS A:10 , ALA A:17 , GLU A:23 , HIS A:79 , LEU A:80 , GLU A:141 , ZN A:1001 , LYS A:2002 , HOH A:2307BINDING SITE FOR RESIDUE GLU A 2001
5AC5SOFTWAREGLN A:56 , LEU A:127 , GLU A:2001 , HOH A:2082 , HOH A:2307BINDING SITE FOR RESIDUE LYS A 2002
6AC6SOFTWARELYS A:84 , ARG A:119 , ARG A:147 , HOH A:2122 , HOH A:2249BINDING SITE FOR RESIDUE TRS A 1008

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1XOV)

(-) 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:317
 aligned with Q8W5Y8_9CAUD | Q8W5Y8 from UniProtKB/TrEMBL  Length:314

    Alignment length:317
                             1                                                                                                                                                                                                                                                                                                                      314  
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309    |  
        Q8W5Y8_9CAUD      - -MSNYSMSRGHSDKCVGAEDILSEIKEAEKVLNAASDELKREGHNVKTFIDRTSTTQSANLNKIVNWHNANPADVHISVHLNAGKGTGVEVWYYAGDEKGRKLAVEISAKMAKALGLPNRGAKATKDLRFLNSTKGTAVLLEVCFVDRKEDANAIHKSGMYDKLGIAIAEGLTGKTVAAKNPNRHSGAVVDSVPMLSKMDFKSSPIKMYKAGSSLLVYEHNKYWYKAYINDKLCYIYKSFCISNGKKDAKGRIKVRIKSAKDLRIPVWNNTKLNSGKIKWYSPGTKLSWYDNKKGYLELWYEKDGWYYTANYFLK--    -
               SCOP domains -d1xova2 A:1-180 Endolysin Ply, catalytic domain                                                                                                                                     d1xova1 A:181-314 Endolysin Ply, C-terminal domain                                                                                    -- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------Amidase_3-1xovA01 A:6-173                                                                                                                                               ----------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeee..........hhhhhhhhhhhhhhhhhhhh..eeeeeee....hhhhhhhhhhhhhhhh...eeeeeeee......eeeeee..hhhhhhhhhhhhhhhhhhhh..eeeeeee..hhhhhhh...eeeeeeee..hhhhhhhhh..hhhhhhhhhhhhhhhh.....hhh.eeeeee..eeeee........eeeeee...eeeeee....eeeeee..eeeeee...eee.........eeeee.......eeee.........eeee....eeeee......eeeee...eeeeehhh.ee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1xov A    0 AMSNYSMSRGHSDKCVGAEDILSEIKEAEKVLNAASDELKREGHNVKTFIDRTSTTQSANLNKIVNWHNANPADVHISVHLNAGKGTGVEVWYYAGDEKGRKLAVEISAKMAKALGLPNRGAKATKDLRFLNSTKGTAVLLEVCFVDRKEDANAIHKSGMYDKLGIAIAEGLTGKTVAAKNPNRHSGAVVDSVPMLSKMDFKSSPIKMYKAGSSLLVYEHNKYWYKAYINDKLCYIYKSFCISNGKKDAKGRIKVRIKSAKDLRIPVWNNTKLNSGKIKWYSPGTKLSWYDNKKGYLELWYEKDGWYYTANYFLKEK 2002
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309    || 
                                                                                                                                                                                                                                                                                                                                                    314| 
                                                                                                                                                                                                                                                                                                                                                    2001
   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  (2, 2)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: Peptidase_MH (119)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q8W5Y8_9CAUD | Q8W5Y8)
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:0004386    helicase activity    Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a DNA or RNA helix.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
biological process
    GO:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.
    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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