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Protein

Glycyl-glycine endopeptidase LytM

Gene

lytM

Organism
Staphylococcus aureus (strain NCTC 8325)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Peptidoglycan hydrolase (autolysin) specifically acting on polyglycine interpeptide bridges of the cell wall peptidoglycan.2 Publications

Catalytic activityi

Hydrolysis of the -Gly-|-Gly- bond in the pentaglycine inter-peptide link joining staphylococcal cell wall peptidoglycans.

Cofactori

Zn2+Note: Binds 1 zinc ion per subunit.

Enzyme regulationi

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.1 Publication

pH dependencei

Optimum pH is 5-8.1 Publication

Temperature dependencei

Thermostable at 100 degrees Celsius for 15 minutes, but loses activity at the same temperature within 30 minutes.1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi117Zinc1
Metal bindingi210Zinc1
Metal bindingi214Zinc1
Metal bindingi293Zinc1

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Hydrolase, Metalloprotease, Protease

Keywords - Biological processi

Cell wall biogenesis/degradation, Virulence

Keywords - Ligandi

Metal-binding, Zinc

Protein family/group databases

MEROPSiM23.013.

Names & Taxonomyi

Protein namesi
Recommended name:
Glycyl-glycine endopeptidase LytM (EC:3.4.24.75)
Alternative name(s):
Autolysin LytM
Gene namesi
Name:lytM
Ordered Locus Names:SAOUHSC_00248
OrganismiStaphylococcus aureus (strain NCTC 8325)
Taxonomic identifieri93061 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesStaphylococcaceaeStaphylococcus
Proteomesi
  • UP000008816 Componenti: Chromosome

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Secreted

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi117N → A: Activates the enzyme. 1 Publication1
Mutagenesisi210H → A: Inactivates the enzyme. 1 Publication1
Mutagenesisi214D → A: Inactivates the enzyme. 1 Publication1
Mutagenesisi291H → A: Inactivates the enzyme. 1 Publication1
Mutagenesisi293H → A: Yields insoluble protein. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Signal peptidei1 – 251 PublicationAdd BLAST25
ChainiPRO_000002681926 – 316Glycyl-glycine endopeptidase LytMAdd BLAST291

Keywords - PTMi

Zymogen

Expressioni

Inductioni

Repressed by MgrA. More protein is secreted in a double secG/secY2 mutant (at protein level).1 Publication

Interactioni

Subunit structurei

Monomer.

Protein-protein interaction databases

STRINGi93061.SAOUHSC_00248.

Structurei

Secondary structure

1316
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi49 – 53Combined sources5
Beta strandi59 – 65Combined sources7
Helixi69 – 73Combined sources5
Beta strandi79 – 82Combined sources4
Beta strandi88 – 93Combined sources6
Helixi126 – 132Combined sources7
Helixi142 – 144Combined sources3
Helixi190 – 193Combined sources4
Beta strandi197 – 199Combined sources3
Beta strandi201 – 203Combined sources3
Beta strandi207 – 210Combined sources4
Beta strandi212 – 216Combined sources5
Beta strandi222 – 224Combined sources3
Beta strandi226 – 237Combined sources12
Turni238 – 241Combined sources4
Beta strandi242 – 249Combined sources8
Beta strandi252 – 264Combined sources13
Beta strandi277 – 280Combined sources4
Beta strandi288 – 302Combined sources15
Helixi303 – 305Combined sources3
Helixi310 – 313Combined sources4

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1QWYX-ray1.30A26-316[»]
2B0PX-ray1.50A/B185-316[»]
2B13X-ray1.55A/B185-316[»]
2B44X-ray1.83A/B185-316[»]
4ZYBX-ray1.50A/B/C/D185-316[»]
DisProtiDP00352.
ProteinModelPortaliO33599.
SMRiO33599.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiO33599.

Family & Domainsi

Sequence similaritiesi

Belongs to the peptidase M23B family.Curated

Keywords - Domaini

Signal

Phylogenomic databases

eggNOGiENOG41061JJ. Bacteria.
COG0739. LUCA.
COG3942. LUCA.
HOGENOMiHOG000279753.
KOiK08259.
OMAiGNGKINY.

Family and domain databases

InterProiIPR011055. Dup_hybrid_motif.
IPR016047. Peptidase_M23.
[Graphical view]
PfamiPF01551. Peptidase_M23. 1 hit.
[Graphical view]
SUPFAMiSSF51261. SSF51261. 1 hit.

Sequencei

Sequence statusi: Complete.

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

O33599-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKKLTAAAIA TMGFATFTMA HQADAAETTN TQQAHTQMST QSQDVSYGTY
60 70 80 90 100
YTIDSNGDYH HTPDGNWNQA MFDNKEYSYT FVDAQGHTHY FYNCYPKNAN
110 120 130 140 150
ANGSGQTYVN PATAGDNNDY TASQSQQHIN QYGYQSNVGP DASYYSHSNN
160 170 180 190 200
NQAYNSHDGN GKVNYPNGTS NQNGGSASKA TASGHAKDAS WLTSRKQLQP
210 220 230 240 250
YGQYHGGGAH YGVDYAMPEN SPVYSLTDGT VVQAGWSNYG GGNQVTIKEA
260 270 280 290 300
NSNNYQWYMH NNRLTVSAGD KVKAGDQIAY SGSTGNSTAP HVHFQRMSGG
310
IGNQYAVDPT SYLQSR
Length:316
Mass (Da):34,317
Last modified:June 27, 2006 - v3
Checksum:i9974F78A19522C09
GO

Sequence cautioni

The sequence AAB62278 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti25A → S in AAB62278 (PubMed:9171409).Curated1
Sequence conflicti182A → R in AAB62278 (PubMed:9171409).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L77194 Genomic DNA. Translation: AAB62278.1. Different initiation.
CP000253 Genomic DNA. Translation: ABD29423.1.
RefSeqiWP_000736798.1. NC_007795.1.
YP_498843.1. NC_007795.1.

Genome annotation databases

EnsemblBacteriaiABD29423; ABD29423; SAOUHSC_00248.
GeneIDi28379404.
3919268.
KEGGisao:SAOUHSC_00248.
PATRICi19578104. VBIStaAur99865_0228.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L77194 Genomic DNA. Translation: AAB62278.1. Different initiation.
CP000253 Genomic DNA. Translation: ABD29423.1.
RefSeqiWP_000736798.1. NC_007795.1.
YP_498843.1. NC_007795.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1QWYX-ray1.30A26-316[»]
2B0PX-ray1.50A/B185-316[»]
2B13X-ray1.55A/B185-316[»]
2B44X-ray1.83A/B185-316[»]
4ZYBX-ray1.50A/B/C/D185-316[»]
DisProtiDP00352.
ProteinModelPortaliO33599.
SMRiO33599.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi93061.SAOUHSC_00248.

Protein family/group databases

MEROPSiM23.013.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABD29423; ABD29423; SAOUHSC_00248.
GeneIDi28379404.
3919268.
KEGGisao:SAOUHSC_00248.
PATRICi19578104. VBIStaAur99865_0228.

Phylogenomic databases

eggNOGiENOG41061JJ. Bacteria.
COG0739. LUCA.
COG3942. LUCA.
HOGENOMiHOG000279753.
KOiK08259.
OMAiGNGKINY.

Miscellaneous databases

EvolutionaryTraceiO33599.

Family and domain databases

InterProiIPR011055. Dup_hybrid_motif.
IPR016047. Peptidase_M23.
[Graphical view]
PfamiPF01551. Peptidase_M23. 1 hit.
[Graphical view]
SUPFAMiSSF51261. SSF51261. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiLYTM_STAA8
AccessioniPrimary (citable) accession number: O33599
Secondary accession number(s): Q2G197
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 21, 2005
Last sequence update: June 27, 2006
Last modified: November 2, 2016
This is version 107 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.