CAZyme Information: MGYG000001394_01798

Basic Information

• Species: Yokenella regensburgei
• Lineage: Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales; Enterobacteriaceae; Yokenella; Yokenella regensburgei
• CAZyme ID: MGYG000001394_01798
• CAZy Family: CBM50
• CAZyme Description: Murein hydrolase activator NlpD

CAZyme Property

Protein Length	CGC	Molecular Weight	Isoelectric Point
249		26438.12	10.5772

Genome Property

Genome Assembly ID	Genome Size	Genome Type	Country	Continent
MGYG000001394	4680112	Isolate	not provided	not provided

• Gene Location: Start: 398030; End: 398779 Strand: +

Full Sequence      

MRAGRLNNIHFSLILCLLAGLMLAGCSSNKSGSSGGSSGPTYTVKRGDTLYRISRTTGTS
VQDLARLNGISPPYTIEVGQRLKINGSSGSTKKTGSSKSTQTAKVTPSAAVPQSSWPPVG
QRCWRWPTSGKVVLPYSTADGGNKGIDIAGQRGQPIYAAGAGKVVYVGNQLRGYGNLIMI
KHSEDYITAYAHNDKMMVNNGQSVKIGQQIATMGSSDASGVQLHFQIRYRATAIDPLRYL
PPQGSKPKC

Enzyme Prediction     

No EC number prediction in MGYG000001394_01798.

CDD Domains     

Cdd ID	Domain	E-Value	qStart	qEnd	sStart	sEnd	Domain Description
PRK10871	nlpD	3.00e-73	41	241	62	317	murein hydrolase activator NlpD.
COG0739	NlpD	3.01e-50	41	249	3	273	Murein DD-endopeptidase MepM and murein hydrolase activator NlpD, contain LysM domain [Cell wall/membrane/envelope biogenesis].
pfam01551	Peptidase_M23	9.18e-39	141	236	1	96	Peptidase family M23. Members of this family are zinc metallopeptidases with a range of specificities. The peptidase family M23 is included in this family, these are Gly-Gly endopeptidases. Peptidase family M23 are also endopeptidases. This family also includes some bacterial lipoproteins for which no proteolytic activity has been demonstrated. This family also includes leukocyte cell-derived chemotaxin 2 (LECT2) proteins. LECT2 is a liver-specific protein which is thought to be linked to hepatocyte growth although the exact function of this protein is unknown.
cd12797	M23_peptidase	5.09e-30	143	227	1	85	M23 family metallopeptidase, also known as beta-lytic metallopeptidase, and similar proteins. This model describes the metallopeptidase M23 family, which includes beta-lytic metallopeptidase and lysostaphin. Members of this family are zinc endopeptidases that lyse bacterial cell wall peptidoglycans; they cleave either the N-acylmuramoyl-Ala bond between the cell wall peptidoglycan and the cross-linking peptide (e.g. beta-lytic endopeptidase) or a bond within the cross-linking peptide (e.g. stapholysin, and lysostaphin). Beta-lytic metallopeptidase, formerly known as beta-lytic protease, has a preference for cleavage of Gly-X bonds and favors hydrophobic or apolar residues on either side. It inhibits growth of sensitive organisms and may potentially serve as an antimicrobial agent. Lysostaphin, produced by Staphylococcus genus, cleaves pentaglycine cross-bridges of cell wall peptidoglycan, acting as autolysins to maintain cell wall metabolism or as toxins and weapons against competing strains. Staphylolysin (also known as LasA) is implicated in a range of processes related to Pseudomonas virulence, including stimulating shedding of the ectodomain of cell surface heparan sulphate proteoglycan syndecan-1, and elastin degradation in connective tissue. Its active site is less constricted and contains a five-coordinate zinc ion with trigonal bipyramidal geometry and two metal-bound water molecules, possibly contributing to its activity against a wider range of substrates than those used by related lytic enzymes, consistent with its multiple roles in Pseudomonas virulence. The family includes members that do not appear to have the conserved zinc-binding site and might be lipoproteins lacking proteolytic activity.
COG4942	EnvC	4.59e-27	88	240	267	418	Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, cell division, chromosome partitioning].

CAZyme Hits     

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End
QIU90327.1	1.21e-164	1	249	1	249
ADO47138.1	1.75e-135	1	249	1	243
QKN80598.1	7.65e-135	1	249	1	245
ALR78975.1	5.49e-133	11	249	5	237
ANO79422.1	2.12e-131	1	249	1	251

PDB Hits     

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End	Description
2GU1_A	4.98e-13	127	238	224	327	Crystalstructure of a zinc containing peptidase from vibrio cholerae [Vibrio cholerae]
4BH5_A	3.17e-12	126	240	23	140	LytMdomain of EnvC, an activator of cell wall amidases in Escherichia coli [Escherichia coli K-12],4BH5_B LytM domain of EnvC, an activator of cell wall amidases in Escherichia coli [Escherichia coli K-12],4BH5_C LytM domain of EnvC, an activator of cell wall amidases in Escherichia coli [Escherichia coli K-12],4BH5_D LytM domain of EnvC, an activator of cell wall amidases in Escherichia coli [Escherichia coli K-12]
2B44_A	1.84e-11	126	240	8	130	TruncatedS. aureus LytM, P 32 2 1 crystal form [Staphylococcus aureus],2B44_B Truncated S. aureus LytM, P 32 2 1 crystal form [Staphylococcus aureus]
2B0P_A	1.88e-11	126	240	9	131	truncatedS. aureus LytM, P212121 crystal form [Staphylococcus aureus],2B0P_B truncated S. aureus LytM, P212121 crystal form [Staphylococcus aureus],2B13_A Truncated S. aureus LytM, P41 crystal form [Staphylococcus aureus],2B13_B Truncated S. aureus LytM, P41 crystal form [Staphylococcus aureus],4ZYB_A Chain A, Glycyl-glycine endopeptidase LytM [Staphylococcus aureus subsp. aureus NCTC 8325],4ZYB_B Chain B, Glycyl-glycine endopeptidase LytM [Staphylococcus aureus subsp. aureus NCTC 8325],4ZYB_C Chain C, Glycyl-glycine endopeptidase LytM [Staphylococcus aureus subsp. aureus NCTC 8325],4ZYB_D Chain D, Glycyl-glycine endopeptidase LytM [Staphylococcus aureus subsp. aureus NCTC 8325]
6TPI_A	3.70e-11	126	240	267	384	EnvCbound to the FtsX periplasmic domain [Escherichia coli K-12]

Swiss-Prot Hits     

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End	Description
Q46798	1.41e-130	1	249	1	251	Uncharacterized lipoprotein YgeR OS=Escherichia coli (strain K12) OX=83333 GN=ygeR PE=3 SV=2
Q56131	1.49e-55	39	241	114	371	Murein hydrolase activator NlpD OS=Salmonella typhi OX=90370 GN=nlpD PE=3 SV=2
P40827	1.64e-55	39	241	118	375	Murein hydrolase activator NlpD OS=Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) OX=99287 GN=nlpD PE=3 SV=2
P39700	1.64e-55	39	241	118	375	Murein hydrolase activator NlpD OS=Salmonella dublin OX=98360 GN=nlpD PE=2 SV=2
P0ADA4	1.72e-55	35	241	116	377	Murein hydrolase activator NlpD OS=Shigella flexneri OX=623 GN=nlpD PE=3 SV=1

SignalP and Lipop Annotations

This protein is predicted as LIPO

Other	SP_Sec_SPI	LIPO_Sec_SPII	TAT_Tat_SPI	TATLIP_Sec_SPII	PILIN_Sec_SPIII
0.000000	0.000003	1.000052	0.000000	0.000000	0.000000

TMHMM  Annotations     

There is no transmembrane helices in MGYG000001394_01798.