CAZyme Information: MGYG000003970_01083

Basic Information

• Lineage: Bacteria; Firmicutes_A; Clostridia; Lachnospirales; Lachnospiraceae
• CAZyme ID: MGYG000003970_01083
• CAZy Family: CE4
• CAZyme Description: hypothetical protein

CAZyme Property

Protein Length	CGC	Molecular Weight	Isoelectric Point
530		58814.79	5.9259

Genome Property

Genome Assembly ID	Genome Size	Genome Type	Country	Continent
MGYG000003970	3341610	MAG	United Kingdom	Europe

• Gene Location: Start: 4756; End: 6348 Strand: -

Full Sequence      

MSSKREKLRRQKRILGIIRIIVCMLCLVIAVLAIVFLTKVIRGSQPDSDPVSNITDNNTN
PKGNEPDKPDDPEPDDHVLTVCIDPGHGGKDGGTNSGSRLEKDDTLKLALQVASYFEEQN
IKVVMTRSDDTYPDLSERCRIANNAKADYLVSIHRNSGNGYGVETWISTSASKEEKDLAD
NIMSGLKDVGIQRDRGVKTGSQSNSTKNYSVNKNSNMPSCIIELGFINNSKDNQLYDNHL
ADYAKAIGKAVLDTFSKYHPDGLVSAPPSGSASDPENNPPVVQQPTTSTSHTMSNPQIDI
SSLSNKSEGWGPGTDCDEKNRPRSALSYQEKYGKYNANFIVPEGNKVYLTFDEGYENGCT
PAILDTLKAKNAKAVFFVTSQFTKQNPDLVQRMIDEGHMVGNHSVTHPSKGLPSQTIEKQ
QNEVMELHNYIKENFNYEMHLFRYPAGIFSEQSLAILNNCNYKSVFWSFAYLDYDTANQP
EPAKALEKVKSRLHPGAIYLLHAVSTTNTQILGDFIDYIRAEGYEVALFD

Enzyme Prediction     

No EC number prediction in MGYG000003970_01083.

CAZyme Signature Domains

Family	Start	End	Evalue	family coverage
CE4	344	464	9.8e-26	0.8923076923076924

CDD Domains     

Cdd ID	Domain	E-Value	qStart	qEnd	sStart	sEnd	Domain Description
cd10948	CE4_BsPdaA_like	8.64e-106	306	527	1	221	Catalytic NodB homology domain of Bacillus subtilis polysaccharide deacetylase PdaA, and its bacterial homologs. The Bacillus subtilis genome contains six polysaccharide deacetylase gene homologs: pdaA, pdaB (previously known as ybaN), yheN, yjeA, yxkH and ylxY. This family is represented by Bacillus subtilis pdaA gene encoding polysaccharide deacetylase BsPdaA, which is a member of the carbohydrate esterase 4 (CE4) superfamily. BsPdaA deacetylates peptidoglycan N-acetylmuramic acid (MurNAc) residues to facilitate the formation of muramic delta-lactam, which is required for recognition of germination lytic enzymes. BsPdaA deficiency leads to the absence of muramic delta-lactam residues in the spore cortex. Like other CE4 esterases, BsPdaA consists of a single catalytic NodB homology domain that appears to adopt a deformed (beta/alpha)8 barrel fold with a putative substrate binding groove harboring the majority of the conserved residues. It utilizes a general acid/base catalytic mechanism involving a tetrahedral transition intermediate, where a water molecule functions as the nucleophile tightly associated to the zinc cofactor.
TIGR02884	spore_pdaA	7.22e-75	328	530	19	221	delta-lactam-biosynthetic de-N-acetylase. Muramic delta-lactam is an unusual constituent of peptidoglycan, found only in bacterial spores in the peptidoglycan wall, or spore cortex. The proteins in this family are PdaA (yfjS), a member of a larger family of polysaccharide deacetylases, and are specificially involved in delta-lactam biosynthesis. PdaA acts immediately after CwlD, an N-acetylmuramoyl-L-alanine amidase and performs a de-N-acetylation. PdaA may also perform the following transpeptidation for lactam ring formation, as heterologous expression in E. coli of CwlD and PdaA together is sufficient for delta-lactam production. [Cell envelope, Biosynthesis and degradation of murein sacculus and peptidoglycan, Cellular processes, Sporulation and germination]
cd02696	MurNAc-LAA	2.56e-59	80	252	1	172	N-acetylmuramoyl-L-alanine amidase or MurNAc-LAA (also known as peptidoglycan aminohydrolase, NAMLA amidase, NAMLAA, Amidase 3, and peptidoglycan amidase; EC 3.5.1.28) is an autolysin that hydrolyzes the amide bond between N-acetylmuramoyl and L-amino acids in certain cell wall glycopeptides. These proteins are Zn-dependent peptidases with highly conserved residues involved in cation co-ordination. MurNAc-LAA in this family is one of several peptidoglycan hydrolases (PGHs) found in bacterial and bacteriophage or prophage genomes that are involved in the degradation of the peptidoglycan. In Escherichia coli, there are five MurNAc-LAAs present: AmiA, AmiB, AmiC and AmiD that are periplasmic, and AmpD that is cytoplasmic. Three of these (AmiA, AmiB and AmiC) belong to this family, the other two (AmiD and AmpD) do not. E. coli AmiA, AmiB and AmiC play an important role in cleaving the septum to release daughter cells after cell division. In general, bacterial MurNAc-LAAs are members of the bacterial autolytic system and carry a signal peptide in their N-termini that allows their transport across the cytoplasmic membrane. However, the bacteriophage MurNAc-LAAs are endolysins since these phage-encoded enzymes break down bacterial peptidoglycan at the terminal stage of the phage reproduction cycle. As opposed to autolysins, almost all endolysins have no signal peptides and their translocation through the cytoplasmic membrane is thought to proceed with the help of phage-encoded holin proteins. The amidase catalytic module is fused to another functional module (cell wall binding module or CWBM) either at the N- or C-terminus, which is responsible for high affinity binding of the protein to the cell wall.
pfam01520	Amidase_3	9.77e-51	81	251	1	172	N-acetylmuramoyl-L-alanine amidase. This enzyme domain cleaves the amide bond between N-acetylmuramoyl and L-amino acids in bacterial cell walls.
cd10917	CE4_NodB_like_6s_7s	1.82e-45	345	520	1	171	Catalytic NodB homology domain of rhizobial NodB-like proteins. This family belongs to the large and functionally diverse carbohydrate esterase 4 (CE4) superfamily, whose members show strong sequence similarity with some variability due to their distinct carbohydrate substrates. It includes many rhizobial NodB chitooligosaccharide N-deacetylase (EC 3.5.1.-)-like proteins, mainly from bacteria and eukaryotes, such as chitin deacetylases (EC 3.5.1.41), bacterial peptidoglycan N-acetylglucosamine deacetylases (EC 3.5.1.-), and acetylxylan esterases (EC 3.1.1.72), which catalyze the N- or O-deacetylation of substrates such as acetylated chitin, peptidoglycan, and acetylated xylan. All members of this family contain a catalytic NodB homology domain with the same overall topology and a deformed (beta/alpha)8 barrel fold with 6- or 7 strands. Their catalytic activity is dependent on the presence of a divalent cation, preferably cobalt or zinc, and they employ a conserved His-His-Asp zinc-binding triad closely associated with the conserved catalytic base (aspartic acid) and acid (histidine) to carry out acid/base catalysis. Several family members show diversity both in metal ion specificities and in the residues that coordinate the metal.

CAZyme Hits     

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End
VCV22796.1	5.25e-171	75	524	69	519
AEN96049.1	5.20e-160	75	524	64	548
QNK40789.1	1.78e-82	296	527	62	291
BBF42562.1	5.73e-82	275	529	58	314
ADU22848.1	5.79e-80	299	526	45	270

PDB Hits     

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End	Description
1W1A_1	1.14e-40	334	524	48	238	Structureof Bacillus subtilis PdaA in complex with NAG, a family 4 Carbohydrate esterase. [Bacillus subtilis],1W1A_2 Structure of Bacillus subtilis PdaA in complex with NAG, a family 4 Carbohydrate esterase. [Bacillus subtilis],1W1B_1 Structure of Bacillus subtilis PdaA with Cadmium, a family 4 Carbohydrate esterase. [Bacillus subtilis],1W1B_2 Structure of Bacillus subtilis PdaA with Cadmium, a family 4 Carbohydrate esterase. [Bacillus subtilis]
1W17_A	1.34e-40	334	524	54	244	Structureof Bacillus subtilis PdaA, a family 4 Carbohydrate esterase. [Bacillus subtilis],1W17_B Structure of Bacillus subtilis PdaA, a family 4 Carbohydrate esterase. [Bacillus subtilis]
1NY1_A	9.95e-40	334	524	31	221	CrystalStructure Of B. Subtilis Polysaccharide Deacetylase Northeast Structural Genomics Consortium Target Sr127. [Bacillus subtilis],1NY1_B Crystal Structure Of B. Subtilis Polysaccharide Deacetylase Northeast Structural Genomics Consortium Target Sr127. [Bacillus subtilis]
2J13_A	1.67e-39	336	530	44	239	Structureof a family 4 carbohydrate esterase from Bacillus anthracis [Bacillus anthracis str. Ames]
4RN7_A	2.68e-27	77	242	2	172	ChainA, N-acetylmuramoyl-L-alanine amidase [Clostridioides difficile 630]

Swiss-Prot Hits     

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End	Description
Q04729	4.03e-41	322	524	43	245	Uncharacterized 30.6 kDa protein in fumA 3'region OS=Geobacillus stearothermophilus OX=1422 PE=3 SV=1
O34928	7.33e-40	334	524	54	244	Peptidoglycan-N-acetylmuramic acid deacetylase PdaA OS=Bacillus subtilis (strain 168) OX=224308 GN=pdaA PE=1 SV=1
Q8Y9V5	1.34e-19	346	530	267	443	Peptidoglycan-N-acetylglucosamine deacetylase PgdA OS=Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e) OX=169963 GN=pgdA PE=1 SV=1
A0A0H3GDH9	1.34e-19	346	530	267	443	Peptidoglycan-N-acetylglucosamine deacetylase PgdA OS=Listeria monocytogenes serotype 1/2a (strain 10403S) OX=393133 GN=pgdA PE=2 SV=1
A0A3Q0NBH7	1.34e-19	346	530	267	443	Peptidoglycan-N-acetylglucosamine deacetylase PgdA OS=Listeria monocytogenes serotype 1/2a (strain EGD / Mackaness) OX=1334565 GN=pgdA PE=1 SV=1

SignalP and Lipop Annotations

This protein is predicted as OTHER

Other	SP_Sec_SPI	LIPO_Sec_SPII	TAT_Tat_SPI	TATLIP_Sec_SPII	PILIN_Sec_SPIII
1.000038	0.000003	0.000000	0.000000	0.000000	0.000000

TMHMM  Annotations     

start	end
13	35