CAZyme Information: MGYG000003137_05049

Basic Information

• Species: Bradyrhizobium sp000015165
• Lineage: Bacteria; Proteobacteria; Alphaproteobacteria; Rhizobiales; Xanthobacteraceae; Bradyrhizobium; Bradyrhizobium sp000015165
• CAZyme ID: MGYG000003137_05049
• CAZy Family: CE4
• CAZyme Description: hypothetical protein

CAZyme Property

Protein Length	CGC	Molecular Weight	Isoelectric Point
475	MGYG000003137_26|CGC1	53530.49	6.2692

Genome Property

Genome Assembly ID	Genome Size	Genome Type	Country	Continent
MGYG000003137	8388709	MAG	United States	North America

• Gene Location: Start: 60187; End: 61614 Strand: -

Full Sequence      

MSADIYPRDMVGYGRTPPHPRWPGDARIAVQFVINYEEGGENNILHGDAASEAFLSEIVG
AAPWPGQRHMNMESIYEFGARAGFWRLWRMFTARKLPVTVFAIATAMARNPDAVAAMKEA
GWEIASHGLKWIDYRDFSEAEERAHIEQAIRLHTELTGARPLGFYQGRTSEHTLDIVLNE
QGFLYSADSYADELPYWIQGPHGPQLIVPYTLDANDMRFATPQGFNSGDQFFAYLKDSFD
TLYAEGTDAPRMMSVGLHCRLVGRPGRAAALARFLDYIMSHDKVWVATRLDIARHWIKTH
PPDGTWRPSQMSRVLFVERYGDIFEHSPEIADRAYRAGLSAFDDAADALHTTLMNVVRGM
SRDEKLKLVRAHPELAGREALAGEMTTDSIGEQGRLGFTSLSRAEFERVADINRRYRDKF
GMPLIVALALHADRASVIAEMERRISNDLDTEIANAVDQIGHITRARLARKFEQG

Enzyme Prediction     

No EC number prediction in MGYG000003137_05049.

CDD Domains     

Cdd ID	Domain	E-Value	qStart	qEnd	sStart	sEnd	Domain Description
TIGR03212	uraD_N-term-dom	0.0	6	302	1	297	putative urate catabolism protein. This model represents a protein that is predominantly found just upstream of the UraD protein (OHCU decarboxylase) and in a number of instances as a N-terminal fusion with it. UraD itself catalyzes the last step in the catabolism of urate to allantoate. The function of this protein is presently unknown. It shows homology with the pfam01522 polysaccharide deacetylase domain family.
cd10977	CE4_PuuE_SpCDA1	6.17e-164	22	295	1	273	Catalytic domain of bacterial PuuE allantoinases, Schizosaccharomyces pombe chitin deacetylase 1 (SpCDA1), and similar proteins. Allantoinase (EC 3.5.2.5) can hydrolyze allantoin((2,5-dioxoimidazolidin-4-yl)urea), one of the most important nitrogen carrier for some plants, soil animals, and microorganisms, to allantoate. DAL1 gene from Saccharomyces cerevisiae encodes an allantoinase. However, some organisms possess allantoinase activity but lack DAL1 allantoinase. In those organisms, a defective allantoinase gene, named puuE (purine utilization E), encodes an allantoinase that specifically catalyzes the hydrolysis of (S)-allantoin into allantoic acid. PuuE allantoinase is related to polysaccharide deacetylase (DCA), one member of the carbohydrate esterase 4 (CE4) superfamily, that removes N-linked or O-linked acetyl groups of cell wall polysaccharides, and lacks sequence similarity with the known DAL1 allantoinase that belongs to the amidohydrolase superfamily. PuuE allantoinase functions as a homotetramer. Its monomer is composed of a 7-stranded barrel with detectable sequence similarity to the 6-stranded barrel NodB homology domain of DCAs. It appears to be metal-independent and acts on a small substrate molecule, which is distinct from the common features of DCAs that are normally metal ion dependent and recognize multimeric substrates. This family also includes a chitin deacetylase 1 (SpCDA1) encoded by the Schizosaccharomyces pombe cda1 gene. Although the general function of chitin deacetylase (CDA) is the synthesis of chitosan from chitin, a polymer of N-acetyl glucosamine, to build up the proper ascospore wall, the actual function of SpCDA1 might involve allantoin hydrolysis. It is likely orthologous to PuuE allantoinase, whereas it is more distantly related to the CDAs found in other fungi, such as Saccharomyces cerevisiae and Mucor rouxii. Those CDAs are similar with rizobial NodB protein and are not included in this family.
cd10980	CE4_SpCDA1	3.06e-107	22	301	1	296	Putative catalytic domain of Schizosaccharomyces pombe chitin deacetylase 1 (SpCDA1), and similar proteins. This family is represented by Schizosaccharomyces pombe chitin deacetylase 1 (SpCDA1), encoded by the cda1 gene. The general function of chitin deacetylase (CDA) is the synthesis of chitosan from chitin, a polymer of N-acetyl glucosamine, to build up the proper ascospore wall. The actual function of SpCDA1 might be involved in allantoin hydrolysis. It is likely an ortholog to bacterial PuuE allantoinase, whereas it is more distantly related to the CDAs found in other fungi, such as Saccharomyces cerevisiae and Mucor rouxii. Those CDAs are similar with rizobial NodB protein and are not included in this family.
cd10916	CE4_PuuE_HpPgdA_like	1.79e-67	29	295	1	247	Catalytic domain of bacterial PuuE allantoinases, Helicobacter pylori peptidoglycan deacetylase (HpPgdA), and similar proteins. This family is a member of the very large and functionally diverse carbohydrate esterase 4 (CE4) superfamily. It contains bacterial PuuE (purine utilization E) allantoinases, a peptidoglycan deacetylase from Helicobacter pylori (HpPgdA), Escherichia coli ArnD, and many uncharacterized homologs from all three kingdoms of life. PuuE allantoinase appears to be metal-independent and specifically catalyzes the hydrolysis of (S)-allantoin into allantoic acid. Different from PuuE allantoinase, HpPgdA has the ability to bind a metal ion at the active site and is responsible for a peptidoglycan modification that counteracts the host immune response. Both PuuE allantoinase and HpPgdA function as a homotetramer. The monomer is composed of a 7-stranded barrel with detectable sequence similarity to the 6-stranded barrel NodB homology domain of polysaccharide deacetylase (DCA)-like proteins in the CE4 superfamily, which removes N-linked or O-linked acetyl groups from cell wall polysaccharides. However, in contrast with the typical DCAs, PuuE allantoinase and HpPgdA might not exhibit a solvent-accessible polysaccharide binding groove and only recognize a small substrate molecule. ArnD catalyzes the deformylation of 4-deoxy-4-formamido-L-arabinose-phosphoundecaprenol to 4-amino-4-deoxy-L-arabinose-phosphoundecaprenol.
cd10979	CE4_PuuE_like	6.90e-57	18	299	10	281	Putative catalytic domain of uncharacterized prokaryotic polysaccharide deacetylases similar to bacterial PuuE allantoinases. The family includes a group of uncharacterized prokaryotic polysaccharide deacetylases (DCAs) that show high sequence similarity to the catalytic domain of bacterial PuuE (purine utilization E) allantoinases. PuuE allantoinase specifically catalyzes the hydrolysis of (S)-allantoin into allantoic acid. It functions as a homotetramer. Its monomer is composed of a 7-stranded barrel with detectable sequence similarity to the 6-stranded barrel NodB homology domain of DCA-like proteins in the CE4 superfamily, which removes N-linked or O-linked acetyl groups from cell wall polysaccharides. PuuE allantoinase appears to be metal-independent and acts on a small substrate molecule, which is distinct from the common feature of DCAs which are normally metal ion dependent and recognize multimeric substrates.

CAZyme Hits     

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End
ABQ39079.1	0.0	1	475	1	475
SMX55682.1	0.0	1	474	1	473
CAL74786.1	0.0	1	474	1	474
BAM92733.1	0.0	1	475	1	475
QFU16137.1	4.76e-237	1	468	1	465

PDB Hits     

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End	Description
3CL6_A	1.50e-141	1	304	1	305	Crystalstructure of Puue Allantoinase [Pseudomonas fluorescens],3CL6_B Crystal structure of Puue Allantoinase [Pseudomonas fluorescens],3CL7_A Crystal structure of Puue Allantoinase in complex with Hydantoin [Pseudomonas fluorescens],3CL7_B Crystal structure of Puue Allantoinase in complex with Hydantoin [Pseudomonas fluorescens],3CL8_A Crystal structure of Puue Allantoinase complexed with ACA [Pseudomonas fluorescens],3CL8_B Crystal structure of Puue Allantoinase complexed with ACA [Pseudomonas fluorescens]
1Z7A_A	1.97e-134	2	301	2	302	Crystalstructure of probable Polysaccharide deacetylase from Pseudomonas aeruginosa PAO1 [Pseudomonas aeruginosa PAO1],1Z7A_B Crystal structure of probable Polysaccharide deacetylase from Pseudomonas aeruginosa PAO1 [Pseudomonas aeruginosa PAO1],1Z7A_C Crystal structure of probable Polysaccharide deacetylase from Pseudomonas aeruginosa PAO1 [Pseudomonas aeruginosa PAO1],1Z7A_D Crystal structure of probable Polysaccharide deacetylase from Pseudomonas aeruginosa PAO1 [Pseudomonas aeruginosa PAO1],1Z7A_E Crystal structure of probable Polysaccharide deacetylase from Pseudomonas aeruginosa PAO1 [Pseudomonas aeruginosa PAO1],1Z7A_F Crystal structure of probable Polysaccharide deacetylase from Pseudomonas aeruginosa PAO1 [Pseudomonas aeruginosa PAO1],1Z7A_G Crystal structure of probable Polysaccharide deacetylase from Pseudomonas aeruginosa PAO1 [Pseudomonas aeruginosa PAO1],1Z7A_H Crystal structure of probable Polysaccharide deacetylase from Pseudomonas aeruginosa PAO1 [Pseudomonas aeruginosa PAO1]
3S6O_A	7.59e-130	6	301	11	310	Crystalstructure of a Polysaccharide deacetylase family protein from Burkholderia pseudomallei [Burkholderia pseudomallei],3S6O_B Crystal structure of a Polysaccharide deacetylase family protein from Burkholderia pseudomallei [Burkholderia pseudomallei],3S6O_C Crystal structure of a Polysaccharide deacetylase family protein from Burkholderia pseudomallei [Burkholderia pseudomallei],3S6O_D Crystal structure of a Polysaccharide deacetylase family protein from Burkholderia pseudomallei [Burkholderia pseudomallei]
2O8I_A	7.57e-32	311	475	2	165	ChainA, Hypothetical protein Atu2327 [Agrobacterium fabrum str. C58]
2O70_A	5.95e-17	316	468	14	162	Structureof OHCU decarboxylase from zebrafish [Danio rerio],2O70_B Structure of OHCU decarboxylase from zebrafish [Danio rerio],2O70_C Structure of OHCU decarboxylase from zebrafish [Danio rerio],2O70_D Structure of OHCU decarboxylase from zebrafish [Danio rerio],2O70_E Structure of OHCU decarboxylase from zebrafish [Danio rerio],2O70_F Structure of OHCU decarboxylase from zebrafish [Danio rerio],2O73_A Structure of OHCU decarboxylase in complex with allantoin [Danio rerio],2O73_B Structure of OHCU decarboxylase in complex with allantoin [Danio rerio],2O73_C Structure of OHCU decarboxylase in complex with allantoin [Danio rerio],2O73_D Structure of OHCU decarboxylase in complex with allantoin [Danio rerio],2O73_E Structure of OHCU decarboxylase in complex with allantoin [Danio rerio],2O73_F Structure of OHCU decarboxylase in complex with allantoin [Danio rerio],2O74_A Structure of OHCU decarboxylase in complex with guanine [Danio rerio],2O74_B Structure of OHCU decarboxylase in complex with guanine [Danio rerio],2O74_C Structure of OHCU decarboxylase in complex with guanine [Danio rerio],2O74_D Structure of OHCU decarboxylase in complex with guanine [Danio rerio],2O74_E Structure of OHCU decarboxylase in complex with guanine [Danio rerio],2O74_F Structure of OHCU decarboxylase in complex with guanine [Danio rerio]

Swiss-Prot Hits     

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End	Description
O13842	1.05e-78	8	301	5	317	Putative polysaccharide deacetylase OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) OX=284812 GN=cda1 PE=1 SV=1
D4GPU8	8.82e-24	316	472	17	165	2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase OS=Haloferax volcanii (strain ATCC 29605 / DSM 3757 / JCM 8879 / NBRC 14742 / NCIMB 2012 / VKM B-1768 / DS2) OX=309800 GN=HVO_B0301 PE=3 SV=1
D8JBB8	1.12e-17	309	468	10	161	2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase OS=Halalkalicoccus jeotgali (strain DSM 18796 / CECT 7217 / JCM 14584 / KCTC 4019 / B3) OX=795797 GN=HacjB3_16066 PE=3 SV=1
Q283N4	5.56e-17	316	468	14	162	2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase OS=Mus musculus OX=10090 GN=Urad PE=1 SV=1
A1L259	3.26e-16	316	468	14	162	2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase OS=Danio rerio OX=7955 GN=urad 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
1.000043	0.000002	0.000000	0.000000	0.000000	0.000000

TMHMM  Annotations     

There is no transmembrane helices in MGYG000003137_05049.