dbCAN-seq: a database of CAZyme sequence and annotation

Basic Information help

Species

HGM12619 sp900753195

Lineage

Bacteria; Firmicutes_A; Clostridia; Oscillospirales; UBA644; HGM12619; HGM12619 sp900753195

CAZyme ID

MGYG000001869_01004

CAZy Family

CBM50

CAZyme Description

Gamma-D-glutamyl-L-diamino acid endopeptidase 1

CAZyme Property

Protein Length	CGC	Molecular Weight	Isoelectric Point
435	MGYG000001869_12\|CGC1	47336.01	6.6845

Genome Property

Genome Assembly ID	Genome Size	Genome Type	Country	Continent
MGYG000001869	1750418	MAG	Denmark	Europe

Gene Location

Start: 12452; End: 13759 Strand: -

Enzyme Prediction help

No EC number prediction in MGYG000001869_01004.

CDD Domains download full data without filtering help

Cdd ID	Domain	E-Value	qStart	qEnd	sStart	sEnd	Domain Description
cd06229	M14_Endopeptidase_I	1.19e-97	176	419	1	237	Peptidase M14 carboxypeptidase family-like domain of Endopeptidase I. Peptidase M14-like domain of Gamma-D-glutamyl-L-diamino acid endopeptidase 1 (also known as Gamma-D-glutamyl-meso-diaminopimelate peptidase I, and Endopeptidase I (ENP1); EC 3.4.19.11). ENP1 is a member of the M14 family of metallocarboxypeptidases (MCPs), and is classified as belonging to subfamily C. However it has an exceptional type of activity of hydrolyzing the gamma-D-Glu-(L)meso-diaminopimelic acid (gamma-D-Glu-Dap) bond of L-Ala-gamma-D-Glu-(L)meso-diaminopimelic acid and L-Ala-gamma-D-Glu-(L)meso-diaminopimelic acid(L)-D-Ala peptides. ENP1 has a different substrate specificity and cellular role than MpaA (MpaA does not belong to this group). ENP1 hydrolyzes the gamma-D-Glu-Dap bond of MurNAc-tripeptide and MurNAc-tetrapeptide, as well as the amide bond of free tripeptide and tetrapeptide. ENP1 is active on spore cortex peptidoglycan, and is produced at stage IV of sporulation in forespore and spore integuments.
smart00631	Zn_pept	1.40e-49	130	413	2	277	Zn_pept domain.
cd00596	Peptidase_M14_like	1.18e-38	176	420	1	216	M14 family of metallocarboxypeptidases and related proteins. The M14 family of metallocarboxypeptidases (MCPs), also known as funnelins, are zinc-binding carboxypeptidases (CPs) which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. Two major subfamilies of the M14 family, defined based on sequence and structural homology, are the A/B and N/E subfamilies. Enzymes belonging to the A/B subfamily are normally synthesized as inactive precursors containing preceding signal peptide, followed by an N-terminal pro-region linked to the enzyme; these proenzymes are called procarboxypeptidases. The A/B enzymes can be further divided based on their substrate specificity; Carboxypeptidase A-like (CPA-like) enzymes favor hydrophobic residues while carboxypeptidase B-like (CPB-like) enzymes only cleave the basic residues lysine or arginine. The A forms have slightly different specificities, with Carboxypeptidase A1 (CPA1) preferring aliphatic and small aromatic residues, and CPA2 preferring the bulky aromatic side chains. Enzymes belonging to the N/E subfamily enzymes are not produced as inactive precursors and instead rely on their substrate specificity and subcellular compartmentalization to prevent inappropriate cleavage. They contain an extra C-terminal transthyretin-like domain, thought to be involved in folding or formation of oligomers. MCPs can also be classified based on their involvement in specific physiological processes; the pancreatic MCPs participate only in alimentary digestion and include carboxypeptidase A and B (A/B subfamily), while others, namely regulatory MCPs or the N/E subfamily, are involved in more selective reactions, mainly in non-digestive tissues and fluids, acting on blood coagulation/fibrinolysis, inflammation and local anaphylaxis, pro-hormone and neuropeptide processing, cellular response and others. Another MCP subfamily, is that of succinylglutamate desuccinylase /aspartoacylase, which hydrolyzes N-acetyl-L-aspartate (NAA), and deficiency in which is the established cause of Canavan disease. Another subfamily (referred to as subfamily C) includes an exceptional type of activity in the MCP family, that of dipeptidyl-peptidase activity of gamma-glutamyl-(L)-meso-diaminopimelate peptidase I which is involved in bacterial cell wall metabolism.
pfam00246	Peptidase_M14	1.80e-36	135	416	1	284	Zinc carboxypeptidase.
cd03859	M14_CPT	4.15e-36	135	417	10	289	Peptidase M14 Carboxypeptidase T subfamily. Peptidase M14-like domain of carboxypeptidase (CP) T (CPT), CPT belongs to the M14 family of metallocarboxypeptidases (MCPs). The M14 family are zinc-binding CPs which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. CPT has moderate similarity to CPA and CPB, and exhibits dual-substrate specificity by cleaving C-terminal hydrophobic amino acid residues like CPA and C-terminal positively charged residues like CPB. CPA and CPB are M14 family peptidases but do not belong to this CPT group. The substrate specificity difference between CPT and CPA and CPB is ascribed to a few amino acid substitutions at the substrate-binding pocket while the spatial organization of the binding site remains the same as in all Zn-CPs. CPT has increased thermal stability in presence of Ca2+ ions, and two disulfide bridges which give an additional stabilization factor.

CAZyme Hits help

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End
QWT55181.1	1.32e-160	1	421	1	420
CDZ24839.1	3.77e-144	7	425	7	422
AUS95891.1	3.90e-144	7	416	7	413
AUM98842.1	7.03e-142	4	423	4	420
APQ78488.1	7.03e-142	4	423	4	420

PDB Hits download full data without filtering help

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End	Description
7RUM_A	5.00e-13	1	101	22	119	ChainA, Endolysin [Salmonella phage GEC_vB_GOT],7RUM_B Chain B, Endolysin [Salmonella phage GEC_vB_GOT]
5MRV_A	5.26e-11	110	345	37	252	Crystalstructure of human carboxypeptidase O in complex with NvCI [Homo sapiens],5MRV_B Crystal structure of human carboxypeptidase O in complex with NvCI [Homo sapiens]
5TV7_A	1.09e-10	4	70	109	174	ChainA, Putative peptidoglycan-binding/hydrolysing protein [Clostridioides difficile 630],5TV7_B Chain B, Putative peptidoglycan-binding/hydrolysing protein [Clostridioides difficile 630]
3BKH_A	2.13e-10	4	113	12	121	ChainA, lytic transglycosylase [Pseudomonas phage phiKZ],3BKV_A Chain A, lytic transglycosylase [Pseudomonas phage phiKZ]
5K2L_A	2.01e-09	75	118	5	48	Crystalstructure of LysM domain from Volvox carteri chitinase [Volvox carteri f. nagariensis],5YZK_A Solution structure of LysM domain from a chitinase derived from Volvox carteri [Volvox carteri f. nagariensis]

Swiss-Prot Hits download full data without filtering help

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End	Description
Q03415	2.44e-66	129	419	109	389	Gamma-D-glutamyl-L-diamino acid endopeptidase 1 OS=Lysinibacillus sphaericus OX=1421 PE=1 SV=1
P54497	8.35e-50	86	420	48	368	Uncharacterized protein YqgT OS=Bacillus subtilis (strain 168) OX=224308 GN=yqgT PE=3 SV=1
P19223	2.82e-12	153	396	142	376	Carboxypeptidase B OS=Rattus norvegicus OX=10116 GN=Cpb1 PE=1 SV=1
P00732	5.06e-12	154	408	145	393	Carboxypeptidase B OS=Bos taurus OX=9913 GN=CPB1 PE=1 SV=2
Q0II73	3.17e-11	135	345	57	247	Carboxypeptidase O OS=Bos taurus OX=9913 GN=CPO PE=2 SV=1

SignalP and Lipop Annotations help

This protein is predicted as OTHER

Other	SP_Sec_SPI	LIPO_Sec_SPII	TAT_Tat_SPI	TATLIP_Sec_SPII	PILIN_Sec_SPIII
0.999946	0.000074	0.000000	0.000000	0.000000	0.000000

TMHMM Annotations help

There is no transmembrane helices in MGYG000001869_01004.

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