Reviewed, UniProtKB/Swiss-Prot O33599 (LYTM_STAA8)

Names and origin

Protein names

Recommended name:
    Glycyl-glycine endopeptidase lytM
    EC=3.4.24.75
Alternative name(s):
    Autolysin lytM

Gene names

Name:	lytM
Ordered Locus Names:	SAOUHSC_00248

Organism

Staphylococcus aureus (strain NCTC 8325) [Complete proteome] [HAMAP]

Taxonomic identifier

93061 [NCBI]

Taxonomic lineage

Bacteria › Firmicutes › Bacillales › Staphylococcus

Protein attributes

Sequence length	316 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level.

General annotation (Comments)

Function	Peptidoglycan hydrolase (autolysin) specifically acting on polyglycine interpeptide bridges of the cell wall peptidoglycan. Ref.3 Ref.4
Catalytic activity	Hydrolysis of the -Gly-|-Gly- bond in the pentaglycine inter-peptide link joining staphylococcal cell wall peptidoglycans.
Cofactor	Binds 1 zinc ion per subunit.
Enzyme regulation	Completely inhibited by DEPC, HgCl2, ammonium sulfate and glucosamine. Inhibited by 1,10-phenanthroline at concentrations as low as 1 mM. Glycine hydroxamate, Zn2+, Hg2+ and EDTA inhibit the activity at 10 mM. Sodium chloride (NaCl) and potassium chloride (KCl) inhibit protease activity at 100 mM. Ref.4
Subunit structure	Monomer.
Subcellular location	Secreted. Ref.4
Induction	Repressed by mgrA.
Sequence similarities	Belongs to the peptidase M23B family.
Biophysicochemical properties	pH dependence: Optimum pH is 5-8. Temperature dependence: Thermostable at 100 degrees Celsius for 15 minutes, but loses activity at the same temperature within 30 minutes.

Ontologies

Keywords
Biological process	Cell wall biogenesis/degradation Virulence
Cellular component	Secreted
Domain	Signal
Ligand	Metal-binding Zinc
Molecular function	Hydrolase Metalloprotease Protease
PTM	Zymogen
Technical term	3D-structure Complete proteome Direct protein sequencing
Gene Ontology (GO)
Biological process	cell wall organization Inferred from electronic annotation. Source: UniProtKB-KW pathogenesis Inferred from electronic annotation. Source: UniProtKB-KW proteolysis Inferred from electronic annotation. Source: InterPro
Cellular component	extracellular region Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular function	metalloendopeptidase activity Inferred from electronic annotation. Source: InterPro zinc ion binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Signal peptide

1 – 25

25

Ref.1

Chain

26 – 316

291

Glycyl-glycine endopeptidase lytM

PRO_0000026819

Sites

Metal binding

117

1

Zinc

Metal binding

210

1

Zinc

Metal binding

214

1

Zinc

Metal binding

293

1

Zinc

Experimental info

Mutagenesis

117

1

N → A: Activates the enzyme. Ref.6

Mutagenesis

210

1

H → A: Inactivates the enzyme. Ref.6

Mutagenesis

214

1

D → A: Inactivates the enzyme. Ref.6

Mutagenesis

291

1

H → A: Inactivates the enzyme. Ref.6

Mutagenesis

293

1

H → A: Yields insoluble protein. Ref.6

Sequence conflict

25

1

A → S in AAB62278. Ref.1

Sequence conflict

182

1

A → R in AAB62278. Ref.1

Secondary structure

1

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316

Helix Strand Turn

Details...

Beta strand

49 – 53

5

Beta strand

59 – 65

7

Helix

69 – 73

5

Beta strand

79 – 82

4

Beta strand

88 – 93

6

Helix

126 – 132

7

Helix

142 – 144

3

Helix

190 – 193

4

Beta strand

197 – 199

3

Beta strand

201 – 203

3

Beta strand

207 – 210

4

Beta strand

212 – 216

5

Beta strand

222 – 224

3

Beta strand

226 – 237

12

Turn

238 – 241

4

Beta strand

242 – 249

8

Beta strand

252 – 264

13

Beta strand

277 – 280

4

Beta strand

288 – 302

15

Helix

303 – 305

3

Helix

310 – 313

4

Sequences

	Sequence		Length	Mass (Da)
	O33599-1 [UniParc]. Last modified June 27, 2006. Version 3. Checksum: 9974F78A19522C09	FASTA	316	34,317
	10 20 30 40 50 60 MKKLTAAAIA TMGFATFTMA HQADAAETTN TQQAHTQMST QSQDVSYGTY YTIDSNGDYH 70 80 90 100 110 120 HTPDGNWNQA MFDNKEYSYT FVDAQGHTHY FYNCYPKNAN ANGSGQTYVN PATAGDNNDY 130 140 150 160 170 180 TASQSQQHIN QYGYQSNVGP DASYYSHSNN NQAYNSHDGN GKVNYPNGTS NQNGGSASKA 190 200 210 220 230 240 TASGHAKDAS WLTSRKQLQP YGQYHGGGAH YGVDYAMPEN SPVYSLTDGT VVQAGWSNYG 250 260 270 280 290 300 GGNQVTIKEA NSNNYQWYMH NNRLTVSAGD KVKAGDQIAY SGSTGNSTAP HVHFQRMSGG 310 IGNQYAVDPT SYLQSR

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Molecular cloning, sequencing, and expression of lytM, a unique autolytic gene of Staphylococcus aureus." Ramadurai L., Jayaswal R.K. J. Bacteriol. 179:3625-3631(1997) [PubMed: 9171409] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 26-40.
[2]	"The Staphylococcus aureus NCTC8325 genome." Gillaspy A.F., Worrell V., Orvis J., Roe B.A., Dyer D.W., Iandolo J.J. Submitted (JAN-2006) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[3]	"Isolation and characterization of autolysis-defective mutants of Staphylococcus aureus created by Tn917-lacZ mutagenesis." Mani N., Tobin P., Jayaswal R.K. J. Bacteriol. 175:1493-1499(1993) [PubMed: 8095258] [Abstract] Cited for: FUNCTION.
[4]	"Characterization of a chromosomally encoded glycylglycine endopeptidase of Staphylococcus aureus." Ramadurai L., Lockwood K.J., Nadakavukaren M.J., Jayaswal R.K. Microbiology 145:801-808(1999) [PubMed: 10220159] [Abstract] Cited for: FUNCTION, BIOPHYSICOCHEMICAL PROPERTIES, ENZYME REGULATION, SUBCELLULAR LOCATION.
[5]	"Characterization of RAT, an autolysis regulator in Staphylococcus aureus." Ingavale S.S., Van Wamel W., Cheung A.L. Mol. Microbiol. 48:1451-1466(2003) [PubMed: 12791130] [Abstract] Cited for: REGULATION BY MGRA.
[6]	"Latent LytM at 1.3A resolution." Odintsov S.G., Sabala I., Marcyjaniak M., Bochtler M. J. Mol. Biol. 335:775-785(2004) [PubMed: 14687573] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.3 ANGSTROMS) OF 26-316, MUTAGENESIS OF ASN-117; HIS-210; ASP-214; HIS-291 AND HIS-293.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBLGenBankDDBJ

L77194 Genomic DNA. Translation: AAB62278.1. Different initiation.
CP000253 Genomic DNA. Translation: ABD29423.1.

RefSeq

YP_498843.1.

3D structure databases

PDBPDBe

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1QWY	X-ray	1.30	A	26-316	[»]
2B0P	X-ray	1.50	A/B	185-316	[»]
2B13	X-ray	1.55	A/B	185-316	[»]
2B44	X-ray	1.83	A/B	185-316	[»]

DisProt

DP00352.

ModBase

Search...

Protein-protein interaction databases

STRING

O33599.

Genome annotation databases

GeneID

3919268.

GenomeReviews

Gene locus SAOUHSC_00248 in contig CP000253_GR.

KEGG

sao:SAOUHSC_00248.

Organism-specific databases

CMR

Search...

Phylogenomic databases

HOGENOM

O33599.

OMA

AYNSHNG.

Enzyme and pathway databases

BioCyc

SAUR93061:SAOUHSC_00248-MON.

Family and domain databases

InterPro

IPR016047. Peptidase_M23.
IPR002886. Peptidase_M23B.
[Graphical view]

PANTHER

PTHR21666:SF7. Peptidase_M23B. 1 hit.

Pfam

PF01551. Peptidase_M23. 1 hit.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

LYTM_STAA8

Accession

Primary (citable) accession number: O33599
Secondary accession number(s): Q2G197

Entry history

Integrated into UniProtKB/Swiss-Prot:	June 21, 2005
Last sequence update:	June 27, 2006
Last modified:	November 3, 2009
This is version 62 of the entry and version 3 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes)