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(-) Description

Title :  CRYSTAL STRUCTURE OF ACTIVE FORM OF P1 PHAGE ENDOLYSIN LYZ
 
Authors :  A. Arockiasamy, J. C. Sacchettini
Date :  24 Sep 04  (Deposition) - 11 Jan 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym./Biol. Unit :  A
Keywords :  Open Conformation, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Xu, A. Arulandu, D. K. Struck, S. Swanson, J. C. Sacchettini, R. Young
Disulfide Isomerization After Membrane Release Of Its Sar Domain Activates P1 Lysozyme.
Science V. 307 113 2005
PubMed-ID: 15637279  |  Reference-DOI: 10.1126/SCIENCE.1105143
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - LYSOZYME
    ChainsA
    EC Number3.2.1.17
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)SLYD-, B834(DE3)
    Expression System Taxid562
    Expression System Vector TypePET11A
    Gene17, LYSA, LYZ
    Organism ScientificENTEROBACTERIA PHAGE P1
    Organism Taxid10678
    SynonymLYSIS PROTEIN, MURAMIDASE, ENDOLYSIN, PROTEIN GP17

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 10)

Asymmetric/Biological Unit (2, 10)
No.NameCountTypeFull Name
1CIT2Ligand/IonCITRIC ACID
2MSE8Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:21 , GLN A:94 , HIS A:95 , ARG A:122 , HIS A:138 , GLN A:142 , HOH A:334 , HOH A:378 , HOH A:379 , HOH A:386BINDING SITE FOR RESIDUE CIT A 192
2AC2SOFTWARETYR A:124 , THR A:135 , SER A:136 , ASP A:155 , HOH A:285 , HOH A:354BINDING SITE FOR RESIDUE CIT A 250

(-) SS Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1A:13 -A:44
2A:91 -A:118
3A:150 -A:178

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1XJT)

(-) 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:178
 aligned with LYS_BPP1 | Q37875 from UniProtKB/Swiss-Prot  Length:185

    Alignment length:178
                                                                                                                                                                                                          185 
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178      | 
             LYS_BPP1     9 GGAICAIAVMITIVMGNGNVRTNQAGLELIGNAEGCRRDPYMCPAGVWTDGIGNTHGVTPGVRKTDQQIAADWEKNILIAERCINQHFRGKDMPDNAFSAMTSAAFNMGCNSLRTYYSKARGMRVETSIHKWAQKGEWVNMCNHLPDFVNSNGVPLRGLKIRREKERQLCLTGLVNE-   -
               SCOP domains d1xjta_ A: Endolysin Lyz                                                                                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------Phage_lysozyme-1xjtA01 A:55-173                                                                                        ------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhh....hhhhhhhhhhhhh.eeeeee.....eeee.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheeee....eeeehhhhhhhhh.hhhhhhhhhhhh.ee..eehhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xjt A   9 GGAICAIAVmITIVmGNGNVRTNQAGLELIGNAEGCRRDPYmCPAGVWTDGIGNTHGVTPGVRKTDQQIAADWEKNILIAERCINQHFRGKDmPDNAFSAmTSAAFNmGCNSLRTYYSKARGmRVETSIHKWAQKGEWVNmCNHLPDFVNSNGVPLRGLKIRREKERQLCLTGLVNEH 186
                                    18    |   28        38        48 |      58        68        78        88        98  |    108|      118       128  |    138       148|      158       168       178        
                                    18-MSE|                         50-MSE                                            101-MSE 109-MSE  |            131-MSE           149-MSE                                 
                                         23-MSE                                                                                      116-MSE                                                                  

   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, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: Lysozyme (266)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (LYS_BPP1 | Q37875)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    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.
    GO:0016798    hydrolase activity, acting on glycosyl bonds    Catalysis of the hydrolysis of any glycosyl bond.
    GO:0003796    lysozyme activity    Catalysis of the hydrolysis of the beta-(1->4) linkages between N-acetylmuramic acid and N-acetyl-D-glucosamine residues in a peptidoglycan.
biological process
    GO:0016998    cell wall macromolecule catabolic process    The chemical reactions and pathways resulting in the breakdown of macromolecules that form part of a cell wall.
    GO:0019835    cytolysis    The rupture of cell membranes and the loss of cytoplasm.
    GO:0042742    defense response to bacterium    Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    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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 Related Entries

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

UniProtKB/Swiss-Prot
        LYS_BPP1 | Q378751xju

(-) Related Entries Specified in the PDB File

1xju P1 PHAGE ENDOLYSIN LYZ (SECRETED INACTIVE FORM)