LYTM_STAA8
ID LYTM_STAA8 Reviewed; 316 AA.
AC O33599; Q2G197;
DT 21-JUN-2005, integrated into UniProtKB/Swiss-Prot.
DT 27-JUN-2006, sequence version 3.
DT 03-AUG-2022, entry version 132.
DE RecName: Full=Glycyl-glycine endopeptidase LytM;
DE EC=3.4.24.75;
DE AltName: Full=Autolysin LytM;
DE Flags: Precursor;
GN Name=lytM; OrderedLocusNames=SAOUHSC_00248;
OS Staphylococcus aureus (strain NCTC 8325 / PS 47).
OC Bacteria; Firmicutes; Bacilli; Bacillales; Staphylococcaceae;
OC Staphylococcus.
OX NCBI_TaxID=93061;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND PROTEIN SEQUENCE OF 26-40.
RX PubMed=9171409; DOI=10.1128/jb.179.11.3625-3631.1997;
RA Ramadurai L., Jayaswal R.K.;
RT "Molecular cloning, sequencing, and expression of lytM, a unique autolytic
RT gene of Staphylococcus aureus.";
RL J. Bacteriol. 179:3625-3631(1997).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=NCTC 8325 / PS 47;
RA Gillaspy A.F., Worrell V., Orvis J., Roe B.A., Dyer D.W., Iandolo J.J.;
RT "The Staphylococcus aureus NCTC 8325 genome.";
RL (In) Fischetti V., Novick R., Ferretti J., Portnoy D., Rood J. (eds.);
RL Gram positive pathogens, 2nd edition, pp.381-412, ASM Press, Washington
RL D.C. (2006).
RN [3]
RP FUNCTION.
RX PubMed=8095258; DOI=10.1128/jb.175.5.1493-1499.1993;
RA Mani N., Tobin P., Jayaswal R.K.;
RT "Isolation and characterization of autolysis-defective mutants of
RT Staphylococcus aureus created by Tn917-lacZ mutagenesis.";
RL J. Bacteriol. 175:1493-1499(1993).
RN [4]
RP FUNCTION, BIOPHYSICOCHEMICAL PROPERTIES, ACTIVITY REGULATION, AND
RP SUBCELLULAR LOCATION.
RX PubMed=10220159; DOI=10.1099/13500872-145-4-801;
RA Ramadurai L., Lockwood K.J., Nadakavukaren M.J., Jayaswal R.K.;
RT "Characterization of a chromosomally encoded glycylglycine endopeptidase of
RT Staphylococcus aureus.";
RL Microbiology 145:801-808(1999).
RN [5]
RP REGULATION BY MGRA.
RX PubMed=12791130; DOI=10.1046/j.1365-2958.2003.03503.x;
RA Ingavale S.S., Van Wamel W., Cheung A.L.;
RT "Characterization of RAT, an autolysis regulator in Staphylococcus
RT aureus.";
RL Mol. Microbiol. 48:1451-1466(2003).
RN [6]
RP IDENTIFICATION BY MASS SPECTROMETRY, SUBCELLULAR LOCATION, AND INDUCTION.
RC STRAIN=RN4220;
RX PubMed=20472795; DOI=10.1128/jb.01452-09;
RA Sibbald M.J., Winter T., van der Kooi-Pol M.M., Buist G., Tsompanidou E.,
RA Bosma T., Schafer T., Ohlsen K., Hecker M., Antelmann H., Engelmann S.,
RA van Dijl J.M.;
RT "Synthetic effects of secG and secY2 mutations on exoproteome biogenesis in
RT Staphylococcus aureus.";
RL J. Bacteriol. 192:3788-3800(2010).
RN [7] {ECO:0007744|PDB:1QWY}
RP X-RAY CRYSTALLOGRAPHY (1.3 ANGSTROMS) OF 26-316 IN COMPLEX WITH ZINC,
RP COFACTOR, AND MUTAGENESIS OF ASN-117; HIS-210; ASP-214; HIS-291 AND
RP HIS-293.
RX PubMed=14687573; DOI=10.1016/j.jmb.2003.11.009;
RA Odintsov S.G., Sabala I., Marcyjaniak M., Bochtler M.;
RT "Latent LytM at 1.3A resolution.";
RL J. Mol. Biol. 335:775-785(2004).
CC -!- FUNCTION: Peptidoglycan hydrolase (autolysin) specifically acting on
CC polyglycine interpeptide bridges of the cell wall peptidoglycan.
CC {ECO:0000269|PubMed:10220159, ECO:0000269|PubMed:8095258}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=Hydrolysis of the -Gly-|-Gly- bond in the pentaglycine inter-
CC peptide link joining staphylococcal cell wall peptidoglycans.;
CC EC=3.4.24.75;
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000269|PubMed:14687573};
CC Note=Binds 1 zinc ion per subunit. {ECO:0000269|PubMed:14687573};
CC -!- ACTIVITY REGULATION: Completely inhibited by DEPC, HgCl(2), ammonium
CC sulfate and glucosamine. Inhibited by 1,10-phenanthroline at
CC concentrations as low as 1 mM. Glycine hydroxamate, Zn(2+), Hg(2+) and
CC EDTA inhibit the activity at 10 mM. Sodium chloride (NaCl) and
CC potassium chloride (KCl) inhibit protease activity at 100 mM.
CC {ECO:0000269|PubMed:10220159}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC pH dependence:
CC Optimum pH is 5-8. {ECO:0000269|PubMed:10220159};
CC Temperature dependence:
CC Thermostable at 100 degrees Celsius for 15 minutes, but loses
CC activity at the same temperature within 30 minutes.
CC {ECO:0000269|PubMed:10220159};
CC -!- SUBUNIT: Monomer.
CC -!- SUBCELLULAR LOCATION: Secreted {ECO:0000269|PubMed:10220159,
CC ECO:0000269|PubMed:20472795}.
CC -!- INDUCTION: Repressed by MgrA. More protein is secreted in a double
CC secG/secY2 mutant (at protein level). {ECO:0000269|PubMed:20472795}.
CC -!- SIMILARITY: Belongs to the peptidase M23B family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAB62278.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};
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DR EMBL; L77194; AAB62278.1; ALT_INIT; Genomic_DNA.
DR EMBL; CP000253; ABD29423.1; -; Genomic_DNA.
DR RefSeq; WP_000736798.1; NZ_LS483365.1.
DR RefSeq; YP_498843.1; NC_007795.1.
DR PDB; 1QWY; X-ray; 1.30 A; A=26-316.
DR PDB; 2B0P; X-ray; 1.50 A; A/B=185-316.
DR PDB; 2B13; X-ray; 1.55 A; A/B=185-316.
DR PDB; 2B44; X-ray; 1.83 A; A/B=185-316.
DR PDB; 4ZYB; X-ray; 1.50 A; A/B/C/D=185-316.
DR PDBsum; 1QWY; -.
DR PDBsum; 2B0P; -.
DR PDBsum; 2B13; -.
DR PDBsum; 2B44; -.
DR PDBsum; 4ZYB; -.
DR AlphaFoldDB; O33599; -.
DR SMR; O33599; -.
DR STRING; 1280.SAXN108_0256; -.
DR MEROPS; M23.013; -.
DR EnsemblBacteria; ABD29423; ABD29423; SAOUHSC_00248.
DR GeneID; 3919268; -.
DR KEGG; sao:SAOUHSC_00248; -.
DR PATRIC; fig|93061.5.peg.228; -.
DR eggNOG; COG0739; Bacteria.
DR HOGENOM; CLU_073067_0_0_9; -.
DR OMA; ANGHMHY; -.
DR EvolutionaryTrace; O33599; -.
DR PRO; PR:O33599; -.
DR Proteomes; UP000008816; Chromosome.
DR GO; GO:0005576; C:extracellular region; IEA:UniProtKB-SubCell.
DR GO; GO:0050897; F:cobalt ion binding; IMP:CAFA.
DR GO; GO:0030145; F:manganese ion binding; IMP:CAFA.
DR GO; GO:0004222; F:metalloendopeptidase activity; IMP:CAFA.
DR GO; GO:0016151; F:nickel cation binding; IMP:CAFA.
DR GO; GO:0008270; F:zinc ion binding; IMP:CAFA.
DR GO; GO:0071555; P:cell wall organization; IEA:UniProtKB-KW.
DR GO; GO:0043171; P:peptide catabolic process; IMP:CAFA.
DR GO; GO:0006508; P:proteolysis; IEA:UniProtKB-KW.
DR DisProt; DP00352; -.
DR Gene3D; 2.70.70.10; -; 1.
DR InterPro; IPR011055; Dup_hybrid_motif.
DR InterPro; IPR016047; Peptidase_M23.
DR Pfam; PF01551; Peptidase_M23; 1.
DR SUPFAM; SSF51261; SSF51261; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cell wall biogenesis/degradation; Direct protein sequencing;
KW Hydrolase; Metal-binding; Metalloprotease; Protease; Reference proteome;
KW Secreted; Signal; Virulence; Zinc; Zymogen.
FT SIGNAL 1..25
FT /evidence="ECO:0000269|PubMed:9171409"
FT CHAIN 26..316
FT /note="Glycyl-glycine endopeptidase LytM"
FT /id="PRO_0000026819"
FT REGION 133..189
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 133..180
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 117
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000269|PubMed:14687573,
FT ECO:0007744|PDB:1QWY"
FT BINDING 210
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000269|PubMed:14687573,
FT ECO:0007744|PDB:1QWY"
FT BINDING 214
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000269|PubMed:14687573,
FT ECO:0007744|PDB:1QWY"
FT BINDING 293
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000269|PubMed:14687573,
FT ECO:0007744|PDB:1QWY"
FT MUTAGEN 117
FT /note="N->A: Activates the enzyme."
FT /evidence="ECO:0000269|PubMed:14687573"
FT MUTAGEN 210
FT /note="H->A: Inactivates the enzyme."
FT /evidence="ECO:0000269|PubMed:14687573"
FT MUTAGEN 214
FT /note="D->A: Inactivates the enzyme."
FT /evidence="ECO:0000269|PubMed:14687573"
FT MUTAGEN 291
FT /note="H->A: Inactivates the enzyme."
FT /evidence="ECO:0000269|PubMed:14687573"
FT MUTAGEN 293
FT /note="H->A: Yields insoluble protein."
FT /evidence="ECO:0000269|PubMed:14687573"
FT CONFLICT 25
FT /note="A -> S (in Ref. 1; AAB62278)"
FT /evidence="ECO:0000305"
FT CONFLICT 182
FT /note="A -> R (in Ref. 1; AAB62278)"
FT /evidence="ECO:0000305"
FT STRAND 49..53
FT /evidence="ECO:0007829|PDB:1QWY"
FT STRAND 59..65
FT /evidence="ECO:0007829|PDB:1QWY"
FT HELIX 69..73
FT /evidence="ECO:0007829|PDB:1QWY"
FT STRAND 79..82
FT /evidence="ECO:0007829|PDB:1QWY"
FT STRAND 88..93
FT /evidence="ECO:0007829|PDB:1QWY"
FT HELIX 126..132
FT /evidence="ECO:0007829|PDB:1QWY"
FT HELIX 142..144
FT /evidence="ECO:0007829|PDB:1QWY"
FT HELIX 190..193
FT /evidence="ECO:0007829|PDB:1QWY"
FT STRAND 197..199
FT /evidence="ECO:0007829|PDB:1QWY"
FT STRAND 201..203
FT /evidence="ECO:0007829|PDB:1QWY"
FT STRAND 207..210
FT /evidence="ECO:0007829|PDB:1QWY"
FT STRAND 212..216
FT /evidence="ECO:0007829|PDB:1QWY"
FT STRAND 222..224
FT /evidence="ECO:0007829|PDB:1QWY"
FT STRAND 226..237
FT /evidence="ECO:0007829|PDB:1QWY"
FT TURN 238..241
FT /evidence="ECO:0007829|PDB:1QWY"
FT STRAND 242..249
FT /evidence="ECO:0007829|PDB:1QWY"
FT STRAND 252..264
FT /evidence="ECO:0007829|PDB:1QWY"
FT STRAND 277..280
FT /evidence="ECO:0007829|PDB:1QWY"
FT STRAND 288..302
FT /evidence="ECO:0007829|PDB:1QWY"
FT HELIX 303..305
FT /evidence="ECO:0007829|PDB:1QWY"
FT HELIX 310..313
FT /evidence="ECO:0007829|PDB:1QWY"
SQ SEQUENCE 316 AA; 34317 MW; 9974F78A19522C09 CRC64;
MKKLTAAAIA TMGFATFTMA HQADAAETTN TQQAHTQMST QSQDVSYGTY YTIDSNGDYH
HTPDGNWNQA MFDNKEYSYT FVDAQGHTHY FYNCYPKNAN ANGSGQTYVN PATAGDNNDY
TASQSQQHIN QYGYQSNVGP DASYYSHSNN NQAYNSHDGN GKVNYPNGTS NQNGGSASKA
TASGHAKDAS WLTSRKQLQP YGQYHGGGAH YGVDYAMPEN SPVYSLTDGT VVQAGWSNYG
GGNQVTIKEA NSNNYQWYMH NNRLTVSAGD KVKAGDQIAY SGSTGNSTAP HVHFQRMSGG
IGNQYAVDPT SYLQSR
