CAZyme Information: MGYG000003687_05135

Basic Information

• Species: Paenibacillus polymyxa
• Lineage: Bacteria; Firmicutes; Bacilli; Paenibacillales; Paenibacillaceae; Paenibacillus; Paenibacillus polymyxa
• CAZyme ID: MGYG000003687_05135
• CAZy Family: CBM50
• CAZyme Description: 2',3'-cyclic-nucleotide 2'-phosphodiesterase/3'-nucleotidase

CAZyme Property

Protein Length	CGC	Molecular Weight	Isoelectric Point
322	MGYG000003687_33|CGC1	35678.52	4.9586

Genome Property

Genome Assembly ID	Genome Size	Genome Type	Country	Continent
MGYG000003687	5656034	Isolate	China	Asia

• Gene Location: Start: 14239; End: 15207 Strand: +

Full Sequence      

MLFRKNWFKGFTAAVVACSLLVFSAAPSWAASDSRDSATVNLRIMETTDIHGALMNYDYY
SDKETNEYGLVSTASLIQKARSETRNSMLFDNGDLLQGNPLGDYMARNKTFEKEGGVHPV
YKMMNLMGYDAATVGNHEFNYGLDFLDKSLKGADFPYVNANVYVDKGGEATKNYFTPYQI
LDKTVMDEKGEEHTLRVGVIGLVTPQIMQWDEANLKDKVVTKDIVETAKKFIPQMKTEGA
DIIVVLAHTGYEDVPQTPMMENAVKYLSQVDGINAILFGHAHKSFPSSDFKDMKGVDLDK
GTINGVPAVEASSWGKDLALLI

Enzyme Prediction     

No EC number prediction in MGYG000003687_05135.

CDD Domains     

Cdd ID	Domain	E-Value	qStart	qEnd	sStart	sEnd	Domain Description
PRK09420	cpdB	1.66e-165	12	320	6	299	bifunctional 2',3'-cyclic-nucleotide 2'-phosphodiesterase/3'-nucleotidase.
TIGR01390	CycNucDiestase	1.82e-135	40	321	1	277	2',3'-cyclic-nucleotide 2'-phosphodiesterase. 2',3'-cyclic-nucleotide 2'-phosphodiesterase is a bifunctional enzyme localized to the periplasm of Gram-negative bacteria. 2',3'-cyclic-nucleotide 2'-phosphodiesters are intermediates formed during the hydrolysis of RNA by the ribonuclease I, which is also found to the periplasm, and other enzymes of the RNAse T2 family. Bacteria are unable to transport 2',3'-cyclic-nucleotides into the cytoplasm. 2',3'-cyclic-nucleotide 2'-phosphodiesterase contains 2 active sites which catalyze the reactions that convert the 2',3'-cyclic-nucleotide into a 3'-nucleotide, which is then converted into nucleic acid and phosphate. Both final products can be transported into the cytoplasm. Thus, it has been suggested that 2',3'-cyclic-nucleotide 2'-phosphodiesterase has a 'scavenging' function. Experimental evidence indicates that 2',3'-cyclic-nucleotide 2'-phosphodiesterase enables Yersinia enterocolitica O:8 to grow on 2'3'-cAMP as a sole source of carbon and energy (). [Purines, pyrimidines, nucleosides, and nucleotides, Other]
PRK09419	PRK09419	1.21e-120	4	321	2	317	multifunctional 2',3'-cyclic-nucleotide 2'-phosphodiesterase/3'-nucleotidase/5'-nucleotidase.
cd07410	MPP_CpdB_N	4.11e-119	42	319	1	255	Escherichia coli CpdB and related proteins, N-terminal metallophosphatase domain. CpdB is a bacterial periplasmic protein with an N-terminal metallophosphatase domain and a C-terminal 3'-nucleotidase domain. This alignment model represents the N-terminal metallophosphatase domain, which has 2',3'-cyclic phosphodiesterase activity, hydrolyzing the 2',3'-cyclic phosphates of adenosine, guanosine, cytosine and uridine to yield nucleoside and phosphate. CpdB also hydrolyzes the chromogenic substrates p-nitrophenyl phosphate (PNPP), bis(PNPP) and p-nitrophenyl phosphorylcholine (NPPC). CpdB is thought to play a scavenging role during RNA hydrolysis by converting the non-transportable nucleotides produced by RNaseI to nucleosides which can easily enter a cell for use as a carbon source. This family also includes YfkN, a Bacillus subtilis nucleotide phosphoesterase with two copies of each of the metallophosphatase and 3'-nucleotidase domains. The N-terminal metallophosphatase domain belongs to a large superfamily of distantly related metallophosphatases (MPPs) that includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases). MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets. This domain is thought to allow for productive metal coordination.
PRK09418	PRK09418	7.76e-111	9	321	6	312	bifunctional 2',3'-cyclic-nucleotide 2'-phosphodiesterase/3'-nucleotidase.

CAZyme Hits     

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End
APO43595.1	3.93e-145	4	321	2	317
QZN77538.1	1.66e-144	5	321	5	319
QOS76560.1	3.51e-144	5	321	5	319
QLG37215.1	5.76e-144	5	321	5	319
QKS58250.1	2.64e-143	5	321	5	319

PDB Hits     

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End	Description
5EQV_A	1.81e-111	37	321	5	284	1.45Angstrom Crystal Structure of Bifunctional 2',3'-cyclic Nucleotide 2'-phosphodiesterase/3'-Nucleotidase Periplasmic Precursor Protein from Yersinia pestis with Phosphate bound to the Active site [Yersinia pestis CO92]
3JYF_A	2.48e-111	34	321	1	283	ChainA, 2',3'-cyclic nucleotide 2'-phosphodiesterase/3'-nucleotidase bifunctional periplasmic protein [Klebsiella pneumoniae subsp. pneumoniae MGH 78578],3JYF_B Chain B, 2',3'-cyclic nucleotide 2'-phosphodiesterase/3'-nucleotidase bifunctional periplasmic protein [Klebsiella pneumoniae subsp. pneumoniae MGH 78578]
3GVE_A	3.88e-98	40	321	10	290	Crystalstructure of calcineurin-like phosphoesterase YfkN from Bacillus subtilis [Bacillus subtilis subsp. subtilis str. 168],3GVE_B Crystal structure of calcineurin-like phosphoesterase YfkN from Bacillus subtilis [Bacillus subtilis subsp. subtilis str. 168]
3QFK_A	6.58e-27	41	252	19	211	ChainA, Uncharacterized protein [Staphylococcus aureus subsp. aureus NCTC 8325]
4Q7F_A	6.58e-27	41	252	19	211	ChainA, 5' nucleotidase family protein [Staphylococcus aureus subsp. aureus COL]

Swiss-Prot Hits     

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End	Description
P26265	2.85e-108	34	321	16	298	2',3'-cyclic-nucleotide 2'-phosphodiesterase/3'-nucleotidase OS=Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) OX=99287 GN=cpdB PE=3 SV=2
P08331	1.59e-107	34	321	16	298	2',3'-cyclic-nucleotide 2'-phosphodiesterase/3'-nucleotidase OS=Escherichia coli (strain K12) OX=83333 GN=cpdB PE=1 SV=2
P53052	7.19e-107	32	321	19	303	2',3'-cyclic-nucleotide 2'-phosphodiesterase/3'-nucleotidase OS=Yersinia enterocolitica OX=630 GN=cpdB PE=3 SV=1
O34313	1.07e-92	40	321	43	323	Trifunctional nucleotide phosphoesterase protein YfkN OS=Bacillus subtilis (strain 168) OX=224308 GN=yfkN PE=1 SV=1
P44764	3.51e-91	15	321	10	308	2',3'-cyclic-nucleotide 2'-phosphodiesterase/3'-nucleotidase OS=Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd) OX=71421 GN=cpdB PE=3 SV=1

SignalP and Lipop Annotations

This protein is predicted as SP

Other	SP_Sec_SPI	LIPO_Sec_SPII	TAT_Tat_SPI	TATLIP_Sec_SPII	PILIN_Sec_SPIII
0.000623	0.998003	0.000674	0.000252	0.000213	0.000187

TMHMM  Annotations     

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7	29