CAZyme Information: MGYG000002520_04964

Basic Information

• Species: Pluralibacter gergoviae
• Lineage: Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales; Enterobacteriaceae; Pluralibacter; Pluralibacter gergoviae
• CAZyme ID: MGYG000002520_04964
• CAZy Family: CBM50
• CAZyme Description: Murein hydrolase activator NlpD

CAZyme Property

Protein Length	CGC	Molecular Weight	Isoelectric Point
234		24943.63	10.6703

Genome Property

Genome Assembly ID	Genome Size	Genome Type	Country	Continent
MGYG000002520	5408082	Isolate	United States	North America

• Gene Location: Start: 5369262; End: 5369966 Strand: -

Full Sequence      

MKNRLNLILCLTLGLLLVGCAGRSSDATYTVKRGDTLYGISRQTGTSVRELARLNGISPP
YIIEVGQTLRTGGKATKKTAGSASTRTAKVVPSSAVPPSSWPPVGQRCWRWPASGKVILP
YSTANGGNKGIDIAGSLGQPVYAAGAGKVVYAGNQLRGYGNLIMIKHGEDYITAYAHNAR
ILVSNGQSVRIGQQIATMGNSDADSVRLHFQIRYRATAIDPQRYLPPQSSKPKC

Enzyme Prediction     

No EC number prediction in MGYG000002520_04964.

CDD Domains     

Cdd ID	Domain	E-Value	qStart	qEnd	sStart	sEnd	Domain Description
PRK10871	nlpD	3.03e-68	22	226	56	317	murein hydrolase activator NlpD.
COG0739	NlpD	1.34e-46	28	234	3	273	Murein DD-endopeptidase MepM and murein hydrolase activator NlpD, contain LysM domain [Cell wall/membrane/envelope biogenesis].
pfam01551	Peptidase_M23	1.18e-38	126	221	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	5.10e-30	128	212	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	1.88e-29	70	225	263	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
AVR05828.1	6.62e-166	1	234	1	234
AIR00002.1	2.70e-165	1	234	1	234
ALR78975.1	9.22e-128	1	234	1	237
ADO47138.1	4.63e-127	2	234	8	243
QIR26081.1	2.04e-125	9	234	1	231

PDB Hits     

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End	Description
6UE4_A	4.85e-12	128	233	266	372	ShyAEndopeptidase from Vibrio cholerae (Closed form) [Vibrio cholerae O1 biovar El Tor str. N16961],6UE4_B ShyA Endopeptidase from Vibrio cholerae (Closed form) [Vibrio cholerae O1 biovar El Tor str. N16961]
6U2A_A	4.88e-12	128	233	263	369	ShyAendopeptidase from Vibrio cholera (open form) [Vibrio cholerae]
5J1L_A	1.61e-10	113	224	50	163	Crystalstructure of Csd1-Csd2 dimer I [Helicobacter pylori 26695],5J1L_C Crystal structure of Csd1-Csd2 dimer I [Helicobacter pylori 26695],5J1M_A Crystal structure of Csd1-Csd2 dimer II [Helicobacter pylori 26695],5J1M_C Crystal structure of Csd1-Csd2 dimer II [Helicobacter pylori 26695]
2B44_A	2.81e-10	111	225	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	2.87e-10	111	225	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]

Swiss-Prot Hits     

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End	Description
Q46798	2.37e-118	2	234	8	251	Uncharacterized lipoprotein YgeR OS=Escherichia coli (strain K12) OX=83333 GN=ygeR PE=3 SV=2
P45682	1.06e-54	25	226	65	295	Lipoprotein NlpD/LppB homolog OS=Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) OX=208964 GN=PA3623 PE=3 SV=1
P0ADA4	6.33e-54	22	226	116	377	Murein hydrolase activator NlpD OS=Shigella flexneri OX=623 GN=nlpD PE=3 SV=1
P0ADA3	6.33e-54	22	226	116	377	Murein hydrolase activator NlpD OS=Escherichia coli (strain K12) OX=83333 GN=nlpD PE=1 SV=1
Q56131	3.04e-53	24	226	112	371	Murein hydrolase activator NlpD OS=Salmonella typhi OX=90370 GN=nlpD PE=3 SV=2

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	0.000000	1.000049	0.000000	0.000000	0.000000

TMHMM  Annotations     

There is no transmembrane helices in MGYG000002520_04964.