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Protein

Invertebrate-type lysozyme

Gene
N/A
Organism
Ruditapes philippinarum (Japanese littleneck clam) (Venerupis philippinarum)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Bacteriolytic activity against Gram-positive bacterium M.luteus and thereby probably protects against bacterial infection (PubMed:9914527, PubMed:14523554, PubMed:15249048). Also has chitinase activity (PubMed:15249048, PubMed:9914527, PubMed:17631496, PubMed:14523554). May act as an ispopeptidase, cleaving isopeptide bonds between the side chains of Lys and Gln residues in proteins or in the cross-linking peptide of peptidoglycan in bacterial cell walls (PubMed:15249048, PubMed:14523554).4 Publications

Catalytic activityi

Hydrolysis of (1->4)-beta-linkages between N-acetylmuramic acid and N-acetyl-D-glucosamine residues in a peptidoglycan and between N-acetyl-D-glucosamine residues in chitodextrins.4 Publications

Enzyme regulationi

Chitinase activity is activated by high salt concentrations which cause the release of the monomer from the autoinhibited homodimer.1 Publication

Kineticsi

  1. KM=34 µM for p-nitrophenyl beta 1,4-linked pentamer of N-acetyl-D-glucosamine ((GlcNAc)5-PNP) at pH 5 and 40 degrees Celsius1 Publication

    pH dependencei

    Optimum pH is 4-5 at 40 degrees Celsius for chitinase activity.1 Publication

    Temperature dependencei

    Optimum temperature is 76 degrees Celsius.1 Publication

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Active sitei29Proton donor1 Publication1
    Active sitei41Nucleophile1 Publication1
    Binding sitei84SubstrateCombined sources1 Publication1
    Binding sitei92SubstrateCombined sources1 Publication1
    Binding sitei119SubstrateCombined sources1 Publication1

    GO - Molecular functioni

    • chitinase activity Source: UniProtKB
    • isopeptidase activity Source: UniProtKB
    • lysozyme activity Source: UniProtKB
    • protein homodimerization activity Source: UniProtKB

    GO - Biological processi

    Keywordsi

    Molecular functionAntibiotic, Antimicrobial, Bacteriolytic enzyme, Glycosidase, Hydrolase

    Protein family/group databases

    CAZyiGH22. Glycoside Hydrolase Family 22.
    MEROPSiS81.001.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Invertebrate-type lysozymeCurated (EC:3.2.1.174 Publications)
    Alternative name(s):
    1,4-beta-N-acetylmuramidaseCurated
    Destabilase1 Publication
    OrganismiRuditapes philippinarum (Japanese littleneck clam) (Venerupis philippinarum)Imported
    Taxonomic identifieri129788 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaLophotrochozoaMolluscaBivalviaHeteroconchiaEuheterodontaVeneroidaVeneroideaVeneridaeRuditapes

    Subcellular locationi

    Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

    Keywords - Cellular componenti

    Secreted

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Mutagenesisi29E → A: Loss of chitinase catalytic activity. 1 Publication1
    Mutagenesisi41D → A: Loss of chitinase catalytic activity. 1 Publication1

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Signal peptidei1 – 112 PublicationsAdd BLAST11
    ChainiPRO_000044009612 – 136Invertebrate-type lysozymeCuratedAdd BLAST125

    Amino acid modifications

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Disulfide bondi21 ↔ 98Combined sources1 Publication
    Disulfide bondi24 ↔ 130Combined sources1 Publication
    Disulfide bondi26 ↔ 33Combined sources1 Publication
    Disulfide bondi38 ↔ 47Combined sources1 Publication
    Disulfide bondi60 ↔ 80Combined sources1 Publication
    Disulfide bondi70 ↔ 76Combined sources1 Publication
    Glycosylationi75N-linked (GlcNAc...) asparaginePROSITE-ProRule annotation1
    Disulfide bondi94 ↔ 112Combined sources1 Publication

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Sitei134 – 135Cleavage3 Publications2

    Keywords - PTMi

    Disulfide bond, Glycoprotein

    Interactioni

    Subunit structurei

    Homodimer in its autoinhibited state. Active as monomer.1 Publication

    GO - Molecular functioni

    • protein homodimerization activity Source: UniProtKB

    Structurei

    Secondary structure

    1136
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Beta strandi15 – 17Combined sources3
    Helixi19 – 30Combined sources12
    Beta strandi38 – 41Combined sources4
    Beta strandi44 – 47Combined sources4
    Turni48 – 51Combined sources4
    Helixi54 – 59Combined sources6
    Beta strandi64 – 66Combined sources3
    Helixi67 – 71Combined sources5
    Helixi74 – 91Combined sources18
    Helixi98 – 107Combined sources10
    Helixi111 – 113Combined sources3
    Helixi115 – 117Combined sources3
    Helixi118 – 124Combined sources7

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    2DQAX-ray1.60A/B12-134[»]
    ProteinModelPortaliQ8IU26.
    SMRiQ8IU26.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ8IU26.

    Family & Domainsi

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Regioni53 – 59Substrate bindingCombined sources1 Publication7
    Regioni105 – 107Substrate bindingCombined sources1 Publication3

    Sequence similaritiesi

    Belongs to the lysozyme type I family.Curated

    Keywords - Domaini

    Signal

    Family and domain databases

    InterProiView protein in InterPro
    IPR008597. Invert_lysozyme.
    IPR023346. Lysozyme-like_dom_sf.
    PANTHERiPTHR11195. PTHR11195. 1 hit.
    PfamiView protein in Pfam
    PF05497. Destabilase. 1 hit.
    SUPFAMiSSF53955. SSF53955. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    Sequence processingi: The displayed sequence is further processed into a mature form.

    Q8IU26-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    METVSVEEGL DFAPGMVSQK CLLCMCKLES GGCKPIGCRM DVGSLSCGYF
    60 70 80 90 100
    QIKQPYWIDC GKPGKDWKSC SNDINCSSKC VQQYMKRYAT HYRCPLNCEG
    110 120 130
    FAREHNGGPN GCHSSRTLKY WELLQKIPGC KGVKFS
    Length:136
    Mass (Da):15,198
    Last modified:March 1, 2003 - v1
    Checksum:i78E0918E7A563876
    GO

    Experimental Info

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Sequence conflicti88Y → S in BAB33389 (Ref. 3) Curated1

    Mass spectrometryi

    Molecular mass is 13806 Da from positions 12 - 134. Determined by MALDI. 1 Publication

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AB091383 mRNA. Translation: BAC15553.1.
    AB055701 mRNA. Translation: BAB33389.1.

    Similar proteinsi

    Entry informationi

    Entry nameiLYS_RUDPH
    AccessioniPrimary (citable) accession number: Q8IU26
    Secondary accession number(s): Q9BLE0
    Entry historyiIntegrated into UniProtKB/Swiss-Prot: June 7, 2017
    Last sequence update: March 1, 2003
    Last modified: November 22, 2017
    This is version 48 of the entry and version 1 of the sequence. See complete history.
    Entry statusiReviewed (UniProtKB/Swiss-Prot)

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Direct protein sequencing

    Documents

    1. Glycosyl hydrolases
      Classification of glycosyl hydrolase families and list of entries
    2. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    3. SIMILARITY comments
      Index of protein domains and families