CAZyme Information: MGYG000003736_00522

Basic Information

• Species: Cupriavidus metallidurans
• Lineage: Bacteria; Proteobacteria; Gammaproteobacteria; Burkholderiales; Burkholderiaceae; Cupriavidus; Cupriavidus metallidurans
• CAZyme ID: MGYG000003736_00522
• CAZy Family: CBM50
• CAZyme Description: Murein hydrolase activator NlpD

CAZyme Property

Protein Length	CGC	Molecular Weight	Isoelectric Point
239	MGYG000003736_4|CGC1	25542	10.8567

Genome Property

Genome Assembly ID	Genome Size	Genome Type	Country	Continent
MGYG000003736	3680628	MAG	Canada	North America

• Gene Location: Start: 123404; End: 124123 Strand: +

Full Sequence      

MNRTHHANLQTRRRALGALGSLAAISLSALLAACGTTPTEPAPDGFYRVERGDTLYSIAR
RNKRSVSELARWNNMSNTNQIEVGQLIRVRPPGGASTSAAAPQSDKPARPVQDMPSAKPP
ASSISLQWPADGRVSGRFAPPAEKGMRIEVPAGGKVRAAAPGWAIHVGTLRGYGMLVIVK
HNDDWLTVYGNLDKPLVKEGDRVTAGQEIGSMAQAAELHFEVRGNGRPLNPANYLPSRG

Enzyme Prediction     

No EC number prediction in MGYG000003736_00522.

CDD Domains     

Cdd ID	Domain	E-Value	qStart	qEnd	sStart	sEnd	Domain Description
pfam01551	Peptidase_M23	3.22e-31	144	231	4	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.
PRK10871	nlpD	4.49e-31	22	238	13	319	murein hydrolase activator NlpD.
COG0739	NlpD	8.12e-28	47	239	4	268	Murein DD-endopeptidase MepM and murein hydrolase activator NlpD, contain LysM domain [Cell wall/membrane/envelope biogenesis].
COG4942	EnvC	4.09e-27	107	235	279	418	Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, cell division, chromosome partitioning].
cd12797	M23_peptidase	3.77e-26	144	222	2	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.

CAZyme Hits     

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End
AVA33206.1	6.34e-169	1	239	1	240
QGS27787.1	2.58e-168	1	239	1	240
QBP09217.1	7.40e-168	1	239	1	240
QWC89629.1	7.40e-168	1	239	1	240
QWE95267.1	3.77e-119	12	239	18	247

PDB Hits     

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End	Description
4BH5_A	1.41e-11	128	235	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]
6TPI_A	1.41e-10	128	235	267	384	EnvCbound to the FtsX periplasmic domain [Escherichia coli K-12]
5J1L_A	5.55e-07	148	234	78	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]
6UE4_A	6.29e-06	134	230	259	358	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	6.31e-06	134	230	256	355	ShyAendopeptidase from Vibrio cholera (open form) [Vibrio cholerae]

Swiss-Prot Hits     

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End	Description
Q46798	1.16e-33	19	239	11	246	Uncharacterized lipoprotein YgeR OS=Escherichia coli (strain K12) OX=83333 GN=ygeR PE=3 SV=2
P45682	6.12e-28	7	238	11	297	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
P44833	4.95e-22	47	236	147	403	Outer membrane antigenic lipoprotein B OS=Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd) OX=71421 GN=lppB PE=3 SV=1
P36685	3.12e-20	47	223	120	330	Outer membrane antigenic lipoprotein B (Fragment) OS=Histophilus somni OX=731 GN=lppB PE=3 SV=2
Q56131	3.27e-20	118	238	239	373	Murein hydrolase activator NlpD OS=Salmonella typhi OX=90370 GN=nlpD PE=3 SV=2

SignalP and Lipop Annotations

This protein is predicted as TATLIPO

Other	SP_Sec_SPI	LIPO_Sec_SPII	TAT_Tat_SPI	TATLIP_Sec_SPII	PILIN_Sec_SPIII
0.000003	0.000045	0.053106	0.000197	0.946657	0.000000

TMHMM  Annotations     

start	end
17	39