LYS_RUDPH
ID LYS_RUDPH Reviewed; 136 AA.
AC Q8IU26; Q9BLE0;
DT 07-JUN-2017, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2003, sequence version 1.
DT 03-AUG-2022, entry version 65.
DE RecName: Full=Invertebrate-type lysozyme {ECO:0000305};
DE EC=3.2.1.17 {ECO:0000269|PubMed:14523554, ECO:0000269|PubMed:15249048, ECO:0000269|PubMed:17631496, ECO:0000269|PubMed:9914527};
DE AltName: Full=1,4-beta-N-acetylmuramidase {ECO:0000305};
DE AltName: Full=Destabilase {ECO:0000303|PubMed:14523554};
DE Flags: Precursor;
OS Ruditapes philippinarum (Japanese littleneck clam) (Venerupis
OS philippinarum).
OC Eukaryota; Metazoa; Spiralia; Lophotrochozoa; Mollusca; Bivalvia;
OC Autobranchia; Heteroconchia; Euheterodonta; Imparidentia; Neoheterodontei;
OC Venerida; Veneroidea; Veneridae; Ruditapes.
OX NCBI_TaxID=129788 {ECO:0000312|EMBL:BAC15553.1};
RN [1] {ECO:0000312|EMBL:BAC15553.1}
RP NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, AND CATALYTIC ACTIVITY.
RX PubMed=15249048; DOI=10.1016/j.pep.2004.05.001;
RA Takeshita K., Hashimoto Y., Thujihata Y., So T., Ueda T., Iomoto T.;
RT "Determination of the complete cDNA sequence, construction of expression
RT systems, and elucidation of fibrinolytic activity for Tapes japonica
RT lysozyme.";
RL Protein Expr. Purif. 36:254-262(2004).
RN [2] {ECO:0000305}
RP PROTEIN SEQUENCE OF 12-134, FUNCTION, CATALYTIC ACTIVITY, AND
RP BIOPHYSICOCHEMICAL PROPERTIES.
RX PubMed=9914527; DOI=10.1046/j.1432-1327.1999.00064.x;
RA Ito Y., Yoshikawa A., Hotani T., Fukuda S., Sugimura K., Imoto T.;
RT "Amino acid sequences of lysozymes newly purified from invertebrates imply
RT wide distribution of a novel class in the lysozyme family.";
RL Eur. J. Biochem. 259:456-461(1999).
RN [3] {ECO:0000312|EMBL:BAB33389.1}
RP NUCLEOTIDE SEQUENCE [MRNA] OF 12-134.
RA Takeshita K., Hashimoto Y., Imoto T.;
RT "Tapes japonica lysozyme.";
RL Submitted (FEB-2001) to the EMBL/GenBank/DDBJ databases.
RN [4] {ECO:0000305}
RP FUNCTION, CATALYTIC ACTIVITY, AND MASS SPECTROMETRY.
RX PubMed=14523554; DOI=10.1007/s00018-003-3082-z;
RA Takeshita K., Hashimoto Y., Ueda T., Imoto T.;
RT "A small chimerically bifunctional monomeric protein: Tapes japonica
RT lysozyme.";
RL Cell. Mol. Life Sci. 60:1944-1951(2003).
RN [5] {ECO:0007744|PDB:2DQA}
RP X-RAY CRYSTALLOGRAPHY (1.60 ANGSTROMS) OF 12-134 IN COMPLEX WITH
RP N-ACETYLGLUCOSAMINE TRISACCHARIDE, FUNCTION, CATALYTIC ACTIVITY, ACTIVITY
RP REGULATION, SUBUNIT, ACTIVE SITE, DISULFIDE BONDS, AND MUTAGENESIS OF
RP GLU-29 AND ASP-41.
RX PubMed=17631496; DOI=10.1074/jbc.m704555200;
RA Goto T., Abe Y., Kakuta Y., Takeshita K., Imoto T., Ueda T.;
RT "Crystal structure of Tapes japonica Lysozyme with substrate analogue:
RT structural basis of the catalytic mechanism and manifestation of its
RT chitinase activity accompanied by quaternary structural change.";
RL J. Biol. Chem. 282:27459-27467(2007).
CC -!- FUNCTION: Bacteriolytic activity against Gram-positive bacterium
CC M.luteus and thereby probably protects against bacterial infection
CC (PubMed:9914527, PubMed:14523554, PubMed:15249048). Also has chitinase
CC activity (PubMed:15249048, PubMed:9914527, PubMed:17631496,
CC PubMed:14523554). May act as an ispopeptidase, cleaving isopeptide
CC bonds between the side chains of Lys and Gln residues in proteins or in
CC the cross-linking peptide of peptidoglycan in bacterial cell walls
CC (PubMed:15249048, PubMed:14523554). {ECO:0000269|PubMed:14523554,
CC ECO:0000269|PubMed:15249048, ECO:0000269|PubMed:17631496,
CC ECO:0000269|PubMed:9914527}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=Hydrolysis of (1->4)-beta-linkages between N-acetylmuramic
CC acid and N-acetyl-D-glucosamine residues in a peptidoglycan and
CC between N-acetyl-D-glucosamine residues in chitodextrins.;
CC EC=3.2.1.17; Evidence={ECO:0000269|PubMed:14523554,
CC ECO:0000269|PubMed:15249048, ECO:0000269|PubMed:17631496,
CC ECO:0000269|PubMed:9914527};
CC -!- ACTIVITY REGULATION: Chitinase activity is activated by high salt
CC concentrations which cause the release of the monomer from the
CC autoinhibited homodimer. {ECO:0000269|PubMed:17631496}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=34 uM for p-nitrophenyl beta 1,4-linked pentamer of N-acetyl-D-
CC glucosamine ((GlcNAc)5-PNP) at pH 5 and 40 degrees Celsius
CC {ECO:0000269|PubMed:9914527};
CC pH dependence:
CC Optimum pH is 4-5 at 40 degrees Celsius for chitinase activity.
CC {ECO:0000269|PubMed:9914527};
CC Temperature dependence:
CC Optimum temperature is 76 degrees Celsius.
CC {ECO:0000269|PubMed:9914527};
CC -!- SUBUNIT: Homodimer in its autoinhibited state. Active as monomer.
CC {ECO:0000269|PubMed:17631496}.
CC -!- SUBCELLULAR LOCATION: Secreted {ECO:0000250|UniProtKB:P83673}.
CC -!- MASS SPECTROMETRY: Mass=13806; Method=MALDI;
CC Evidence={ECO:0000269|PubMed:14523554};
CC -!- SIMILARITY: Belongs to the glycosyl hydrolase 22 family. Type-I
CC lysozyme subfamily. {ECO:0000255|PROSITE-ProRule:PRU01257}.
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DR EMBL; AB091383; BAC15553.1; -; mRNA.
DR EMBL; AB055701; BAB33389.1; -; mRNA.
DR PDB; 2DQA; X-ray; 1.60 A; A/B=12-134.
DR PDBsum; 2DQA; -.
DR AlphaFoldDB; Q8IU26; -.
DR SMR; Q8IU26; -.
DR CAZy; GH22; Glycoside Hydrolase Family 22.
DR MEROPS; S81.001; -.
DR EvolutionaryTrace; Q8IU26; -.
DR GO; GO:0005576; C:extracellular region; IEA:UniProtKB-SubCell.
DR GO; GO:0004568; F:chitinase activity; IDA:UniProtKB.
DR GO; GO:0070122; F:isopeptidase activity; IDA:UniProtKB.
DR GO; GO:0003796; F:lysozyme activity; IDA:UniProtKB.
DR GO; GO:0008233; F:peptidase activity; IDA:UniProtKB.
DR GO; GO:0042803; F:protein homodimerization activity; IDA:UniProtKB.
DR GO; GO:0019835; P:cytolysis; IEA:UniProtKB-KW.
DR GO; GO:0042742; P:defense response to bacterium; IEA:UniProtKB-KW.
DR GO; GO:0008152; P:metabolic process; IEA:UniProtKB-KW.
DR CDD; cd16890; lyz_i; 1.
DR InterPro; IPR008597; Invert_lysozyme.
DR InterPro; IPR023346; Lysozyme-like_dom_sf.
DR PANTHER; PTHR11195; PTHR11195; 1.
DR Pfam; PF05497; Destabilase; 1.
DR SUPFAM; SSF53955; SSF53955; 1.
DR PROSITE; PS51909; LYSOZYME_I; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Antibiotic; Antimicrobial; Bacteriolytic enzyme;
KW Direct protein sequencing; Disulfide bond; Glycoprotein; Glycosidase;
KW Hydrolase; Secreted; Signal.
FT SIGNAL 1..11
FT /evidence="ECO:0000269|PubMed:14523554,
FT ECO:0000269|PubMed:9914527"
FT CHAIN 12..136
FT /note="Invertebrate-type lysozyme"
FT /evidence="ECO:0000305"
FT /id="PRO_0000440096"
FT DOMAIN 14..130
FT /note="I-type lysozyme"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01257"
FT ACT_SITE 29
FT /note="Proton donor"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01257,
FT ECO:0000269|PubMed:17631496"
FT ACT_SITE 41
FT /note="Nucleophile"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01257,
FT ECO:0000269|PubMed:17631496"
FT BINDING 53..59
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:17631496,
FT ECO:0007744|PDB:2DQA"
FT BINDING 84
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:17631496,
FT ECO:0007744|PDB:2DQA"
FT BINDING 92
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:17631496,
FT ECO:0007744|PDB:2DQA"
FT BINDING 105..107
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:17631496,
FT ECO:0007744|PDB:2DQA"
FT BINDING 119
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:17631496,
FT ECO:0007744|PDB:2DQA"
FT SITE 134..135
FT /note="Cleavage"
FT /evidence="ECO:0000305|PubMed:14523554,
FT ECO:0000305|PubMed:15249048, ECO:0000305|PubMed:9914527"
FT CARBOHYD 75
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00498"
FT DISULFID 21..98
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01257,
FT ECO:0000269|PubMed:17631496, ECO:0007744|PDB:2DQA"
FT DISULFID 24..130
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01257,
FT ECO:0000269|PubMed:17631496, ECO:0007744|PDB:2DQA"
FT DISULFID 26..33
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01257,
FT ECO:0000269|PubMed:17631496, ECO:0007744|PDB:2DQA"
FT DISULFID 38..47
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01257,
FT ECO:0000269|PubMed:17631496, ECO:0007744|PDB:2DQA"
FT DISULFID 60..80
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01257,
FT ECO:0000269|PubMed:17631496, ECO:0007744|PDB:2DQA"
FT DISULFID 70..76
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01257,
FT ECO:0000269|PubMed:17631496, ECO:0007744|PDB:2DQA"
FT DISULFID 94..112
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01257,
FT ECO:0000269|PubMed:17631496, ECO:0007744|PDB:2DQA"
FT MUTAGEN 29
FT /note="E->A: Loss of chitinase catalytic activity."
FT /evidence="ECO:0000269|PubMed:17631496"
FT MUTAGEN 41
FT /note="D->A: Loss of chitinase catalytic activity."
FT /evidence="ECO:0000269|PubMed:17631496"
FT CONFLICT 88
FT /note="Y -> S (in Ref. 3; BAB33389)"
FT /evidence="ECO:0000305"
FT STRAND 15..17
FT /evidence="ECO:0007829|PDB:2DQA"
FT HELIX 19..30
FT /evidence="ECO:0007829|PDB:2DQA"
FT STRAND 38..41
FT /evidence="ECO:0007829|PDB:2DQA"
FT STRAND 44..47
FT /evidence="ECO:0007829|PDB:2DQA"
FT TURN 48..51
FT /evidence="ECO:0007829|PDB:2DQA"
FT HELIX 54..59
FT /evidence="ECO:0007829|PDB:2DQA"
FT STRAND 64..66
FT /evidence="ECO:0007829|PDB:2DQA"
FT HELIX 67..71
FT /evidence="ECO:0007829|PDB:2DQA"
FT HELIX 74..91
FT /evidence="ECO:0007829|PDB:2DQA"
FT HELIX 98..107
FT /evidence="ECO:0007829|PDB:2DQA"
FT HELIX 111..113
FT /evidence="ECO:0007829|PDB:2DQA"
FT HELIX 115..117
FT /evidence="ECO:0007829|PDB:2DQA"
FT HELIX 118..124
FT /evidence="ECO:0007829|PDB:2DQA"
SQ SEQUENCE 136 AA; 15198 MW; 78E0918E7A563876 CRC64;
METVSVEEGL DFAPGMVSQK CLLCMCKLES GGCKPIGCRM DVGSLSCGYF QIKQPYWIDC
GKPGKDWKSC SNDINCSSKC VQQYMKRYAT HYRCPLNCEG FAREHNGGPN GCHSSRTLKY
WELLQKIPGC KGVKFS
