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(-) Description

Title :  LYSOZYME COMPLEX WITH 4-METHYL-UMBELLIFERYL CHITOTRIOSE
 
Authors :  V. B. Vollan, E. Hough, S. Karlsen
Date :  29 Apr 98  (Deposition) - 04 May 99  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase, N-Acetyl-Muramidase, Umbelliferone Glycosides (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. B. Vollan, E. Hough, S. Karlsen
Structural Studies On The Binding Of 4-Methylumbelliferone Glycosides Of Chitin To Rainbow Trout Lysozyme.
Acta Crystallogr. , Sect. D V. 55 60 1999
PubMed-ID: 10089395  |  Reference-DOI: 10.1107/S0907444998006623
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - LYSOZYME
    Chains: A
    EC Number: 3.2.1.17
    Organ: KIDNEY
    Organism Common: RAINBOW TROUT
    Organism Scientific: ONCORHYNCHUS MYKISS
    Organism Taxid: 8022
    Synonym: N-ACETYL-MURAMIDASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1UMG1Ligand/IonMETHYL-UMBELLIFERTL-N-ACETYL-CHITOTRIOSE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:46 , ASP A:52 , ILE A:58 , ASN A:59 , TYR A:62 , TRP A:63 , VAL A:75 , ARG A:97 , ASP A:101 , PRO A:102 , ASN A:103 , ALA A:107 , TRP A:108 , HOH A:149 , HOH A:151 , HOH A:219 , HOH A:237 , HOH A:259 , HOH A:261 , HOH A:273BINDING SITE FOR RESIDUE UMG A 130
2NULUNKNOWNGLU A:35 , ASP A:52CATALYTICALLY ACTIVE RESIDUES.

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:6 -A:127
2A:30 -A:115
3A:64 -A:80
4A:76 -A:94

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1BB6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1BB6)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LACTALBUMIN_LYSOZYME_2PS51348 Alpha-lactalbumin / lysozyme C family profile.LYSC2_ONCMY16-144  1A:1-129
2LACTALBUMIN_LYSOZYME_1PS00128 Alpha-lactalbumin / lysozyme C signature.LYSC2_ONCMY91-109  1A:76-94

(-) Exons   (0, 0)

(no "Exon" information available for 1BB6)

(-) 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:129
 aligned with LYSC2_ONCMY | P11941 from UniProtKB/Swiss-Prot  Length:144

    Alignment length:129
                                    25        35        45        55        65        75        85        95       105       115       125       135         
          LYSC2_ONCMY    16 KVYDRCELARALKASGMDGYAGNSLPNWVCLSKWESSYNTQATNRNTDGSTDYGIFQINSRYWCDDGRTPGAKNVCGIRCSQLLTADLTVAIRCAKRVVLDPNGIGAWVAWRLHCQNQDLRSYVAGCGV 144
               SCOP domains d1bb6a_ A: Lysozyme                                                                                                               SCOP domains
               CATH domains 1bb6A00 A:1-129  [code=1.10.530.10, no name defined]                                                                              CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhh.....hhh..hhhhhhhhhhhh......eee.....eee..........................hhhh.....hhhhhhhhhhhh...hhhh.hhhhhh......hhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) LACTALBUMIN_LYSOZYME_2  PDB: A:1-129 UniProt: 16-144                                                                              PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------LACTALBUMIN_LYSOZYM----------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1bb6 A   1 KVYDRCELARALKASGMDGYAGNSLPNWVCLSKWESSYNTQATNRNTDGSTDYGIFQINSRYWCDDGRTPGAKNVCGIRCSQLLTDDLTVAIRCAKRVVLDPNGIGAWVAWRLHCQNQDLRSYVAGCGV 129
                                    10        20        30        40        50        60        70        80        90       100       110       120
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1BB6)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (LYSC2_ONCMY | P11941)
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: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.
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.
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.

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 Related Entries

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

UniProtKB/Swiss-Prot
        LYSC2_ONCMY | P11941: 1bb7 1lmc 1lmn 1lmo 1lmp 1lmq

(-) Related Entries Specified in the PDB File

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