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(-) Description

Title :  CRYSTAL STRUCTURE OF TUEKEY EGG LYSOZYME COMPLEX WITH DI-N-ACETYLCHITOBIOSE AT 1.19A RESOLUTION
 
Authors :  K. Harata, R. Kanai
Date :  22 Apr 02  (Deposition) - 05 Jun 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.19
Chains :  Asym./Biol. Unit :  A
Keywords :  Sugar Complex, Non-Productive Binding, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Harata, R. Kanai
Crystallographic Dissection Of The Thermal Motion Of Protein-Sugar Complex.
Proteins V. 48 53 2002
PubMed-ID: 12012337  |  Reference-DOI: 10.1002/PROT.10127
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - LYSOZYME C
    Chains: A
    EC Number: 3.2.1.17
    Organism Common: TURKEY
    Organism Scientific: MELEAGRIS GALLOPAVO
    Organism Taxid: 9103

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1CBS1Ligand/IonDI(N-ACETYL-D-GLUCOSAMINE)
2SO42Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:35 , ASP A:48 , SER A:50 , ASP A:52 , GLN A:57 , ILE A:58 , ASN A:59 , ARG A:61 , ALA A:107 , TRP A:108 , VAL A:109 , HOH A:241 , HOH A:280 , HOH A:290 , HOH A:322 , HOH A:328 , HOH A:336BINDING SITE FOR RESIDUE CBS A 130
2AC2SOFTWAREASN A:39 , HIS A:41 , HIS A:121 , ARG A:125 , HOH A:220 , HOH A:288 , HOH A:320 , HOH A:360BINDING SITE FOR RESIDUE SO4 A 132
3AC3SOFTWAREGLY A:22 , SER A:24 , ASN A:27 , THR A:43 , ARG A:45 , HIS A:121 , HOH A:373BINDING SITE FOR RESIDUE SO4 A 133

(-) 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 1LJN)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LACTALBUMIN_LYSOZYME_2PS51348 Alpha-lactalbumin / lysozyme C family profile.LYSC_MELGA19-147  1A:1-129
2LACTALBUMIN_LYSOZYME_1PS00128 Alpha-lactalbumin / lysozyme C signature.LYSC_MELGA94-112  1A:76-94

(-) Exons   (0, 0)

(no "Exon" information available for 1LJN)

(-) 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 LYSC_MELGA | P00703 from UniProtKB/Swiss-Prot  Length:147

    Alignment length:129
                                    28        38        48        58        68        78        88        98       108       118       128       138         
           LYSC_MELGA    19 KVYGRCELAAAMKRLGLDNYRGYSLGNWVCAAKFESNFNTHATNRNTDGSTDYGILQINSRWWCNDGRTPGSKNLCNIPCSALLSSDITASVNCAKKIASGGNGMNAWVAWRNRCKGTDVHAWIRGCRL 147
               SCOP domains d1ljna_ A: Lysozyme                                                                                                               SCOP domains
               CATH domains 1ljnA00 A:1-129  [code=1.10.530.10, no name defined]                                                                              CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.....eee.....eee....ee...................hhhhhhh..hhhhhhhhhhhhh..hhhhhhhhhhhhh...hhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) LACTALBUMIN_LYSOZYME_2  PDB: A:1-129 UniProt: 19-147                                                                              PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------LACTALBUMIN_LYSOZYM----------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ljn A   1 KVYGRCELAAAMKRLGLDNYRGYSLGNWVCAAKFESNFNTHATNRNTDGSTDYGILQINSRWWCNDGRTPGSKNLCNIPCSALLSSDITASVNCAKKIASGGNGMNAWVAWRNRCKGTDVHAWIRGCRL 129
                                    10        20        30        40        50        60        70        80        90       100       110       120
   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
(-)
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 1LJN)

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (LYSC_MELGA | P00703)
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:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    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.
    GO:0001895    retina homeostasis    A tissue homeostatic process involved in the maintenance of an internal equilibrium within the retina of the eye, including control of cellular proliferation and death and control of metabolic function.
cellular component
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    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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  1ljn
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  3.2.1.17
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 Related Entries

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

UniProtKB/Swiss-Prot
        LYSC_MELGA | P00703: 135l 1dzb 1jef 1jse 1jtp 1lz2 1lzy 1tew 1uac 1xft 2lz2 3lz2

(-) Related Entries Specified in the PDB File

1lzy 1LZY CONTAINS THE SAME PROTEIN AT 1.3 A