CAZyme Information: CC1G_02937-t26_1-p1

Basic Information

• Species: Coprinopsis cinerea
• Lineage: Basidiomycota; Agaricomycetes; ; Psathyrellaceae; Coprinopsis; Coprinopsis cinerea
• CAZyme ID: CC1G_02937-t26_1-p1
• CAZy Family: AA8|AA3
• CAZyme Description: rhamnogalacturonase B

CAZyme Property

Protein Length	CGC	Molecular Weight	Isoelectric Point
372	AACS02000008|CGC5	40421.03	9.0503

Genome Property

Genome Version/Assembly ID	Genes	Strain NCBI Taxon ID	Non Protein Coding Genes	Protein Coding Genes
FungiDB-61_Ccinereaokay7-130	13657	240176	301	13356

• Gene Location: location=AACS02000008:1319809-1322428(+)

Full Sequence      

MKLILALIVVLPTAFAAFGVVRSGNNFVVDSGAGLVTTINANNGDITSLNYNGKQLQDQS
KFTHLSSGLGSASVTTLGEQQHRCNHYPNQHDYAFQVLFEHINNQGGDQQELYWYMNSGH
YQTESWRTGFFGPYALVITNGQAPSPDLDVSFFEDLNLQGYVRASQRGTVTGSFSGVLPG
QPVVIGFKNAAAQYWVEASGSGSGSFTRNMMKPGTYDVTLFQGELEAGAGRVTVNAGQTT
AINLSSNLSRPNVIWSIGTPDGTPRGFLNADKIEIMHPHAVPTYSSTLQVNNPTRVQWNA
NSSQIGARTLRIRTTGAFAGGRPQIYVNGRWTSHAPPEGKGSVGFVTRGTWRRDNQVYAV
IQMTSTYHLASW

Enzyme Prediction     

EC	4.2.2.23:4

CAZyme Signature Domains

Family	Start	End	Evalue	family coverage
PL4	99	361	6.5e-84	0.56312625250501

CDD Domains     

Cdd ID	Domain	E-Value	qStart	qEnd	sStart	sEnd	Domain Description
401282	RhgB_N	5.64e-46	18	160	1	251	Rhamnogalacturonan lyase B, N-terminal. Members of this family are found in both fungi, bacteria and wood-eating arthropods. The domain is found at the N-terminus of rhamnogalacturonase B, a member of the polysaccharide lyase family 4. The domain adopts a structure consisting of a beta super-sandwich, with eighteen strands in two beta-sheets. The three domains of the whole protein rhamnogalacturonan lyase (RGL4), are involved in the degradation of rhamnogalacturonan-I, RG-I, an important pectic plant cell-wall polysaccharide. The active-site residues are a lysine at position 169 in UniProtKB:Q00019 and a histidine at 229, Lys169 is likely to be a proton abstractor, His229 a proton donor in the mechanism. The substrate is a disaccharide, and RGL4, in contrast to other rhamnogalacturonan hydrolases, cleaves the alpha-1,4 linkages of RG-I between Rha and GalUA through a beta-elimination resulting in a double bond in the nonreducing GalUA residue, and is thus classified as a polysaccharide lyase (PL).
405384	CBM-like	1.57e-23	253	353	1	114	Polysaccharide lyase family 4, domain III. CBM-like is domain III of rhamnogalacturonan lyase (RG-lyase). The full-length protein specifically recognizes and cleaves alpha-1,4 glycosidic bonds between l-rhamnose and d-galacturonic acids in the backbone of rhamnogalacturonan-I, a major component of the plant cell wall polysaccharide, pectin. This domain possesses a jelly roll beta-sandwich fold structurally homologous to carbohydrate binding modules (CBMs), and it carries two sulfate ions and a hexa-coordinated calcium ion.
199905	RGL4_C	1.13e-17	255	358	1	123	C-terminal domain of rhamnogalacturonan lyase, a family 4 polysaccharide lyase. The rhamnogalacturonan lyase of the polysaccharide lyase family 4 (RGL4) is involved in the degradation of RG (rhamnogalacturonan) type-I, an important pectic plant cell wall polysaccharide, by cleaving the alpha-1,4 glycoside bond between L-rhamnose and D-galacturonic acids in the backbone of RG type-I through a beta-elimination reaction. RGL4 consists of three domains, an N-terminal catalytic domain, a middle domain with a FNIII type fold and a C-terminal domain with a jelly roll fold. Both the middle and the C-terminal domain are putative carbohydrate binding modules. There are two types of RG lyases, which both cleave the alpha-1,4 bonds of the RG-I main chain (RG chain) through the beta-elimination reaction, but belong to two structurally unrelated polysaccharide lyase (PL) families, 4 and 11.
405387	fn3_3	1.72e-12	172	240	3	73	Polysaccharide lyase family 4, domain II. FnIII-like is domain II of rhamnogalacturonan lyase (RG-lyase). The full-length protein specifically recognizes and cleaves alpha-1,4 glycosidic bonds between l-rhamnose and d-galacturonic acids in the backbone of rhamnogalacturonan-I, a major component of the plant cell wall polysaccharide, pectin. This domain displays an immunoglobulin-like or more specifically Fibronectin-III type fold and shows highest structural similarity to the C-terminal beta-sandwich subdomain of the pro-hormone/propeptide processing enzyme carboxypeptidase gp180 from duck. It serves to assist in producing the deep pocket, with domain III, into which the substrate fits.
199904	RGL4_M	4.81e-12	166	243	1	90	Middle domain of rhamnogalacturonan lyase, a family 4 polysaccharide lyase. The rhamnogalacturonan lyase of the polysaccharide lyase family 4 (RGL4) is involved in the degradation of RG (rhamnogalacturonan) type-I, an important pectic plant cell wall polysaccharide, by cleaving the alpha-1,4 glycoside bond between L-rhamnose and D-galacturonic acids in the backbone of RG type-I through a beta-elimination reaction. RGL4 consists of three domains, an N-terminal catalytic domain, a middle domain with a FNIII type fold and a C-terminal domain with a jelly roll fold. Both the middle domain represented by this model and the C-terminal domain are putative carbohydrate binding modules. There are two types of RG lyases, which both cleave the alpha-1,4 bonds of the RG-I main chain (RG chain) through the beta-elimination reaction, but belong to two structurally unrelated polysaccharide lyase (PL) families, 4 and 11.

CAZyme Hits     

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End
CCA68112.1|PL4_1	8.76e-111	2	358	7	481
QRW20454.1|PL4_1	1.73e-96	12	358	16	472
QRV98672.1|PL4_1	1.68e-94	12	358	16	472
QRW13230.1|PL4_1	2.27e-91	98	352	184	454
QRW22552.1|PL4_1	3.34e-83	11	358	12	480

PDB Hits     

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End	Description
1NKG_A	5.26e-59	104	360	194	467	Rhamnogalacturonan lyase from Aspergillus aculeatus [Aspergillus aculeatus]
2XHN_A	5.26e-59	104	360	194	467	Rhamnogalacturonan lyase from Aspergillus aculeatus K150A active site mutant [Aspergillus aculeatus],2XHN_B Rhamnogalacturonan lyase from Aspergillus aculeatus K150A active site mutant [Aspergillus aculeatus],3NJV_A Rhamnogalacturonan lyase from Aspergillus aculeatus K150A substrate complex [Aspergillus aculeatus]
3NJX_A	1.52e-57	104	360	194	467	Rhamnogalacturonan Lyase from Aspergillus aculeatus mutant H210A [Aspergillus aculeatus]

Swiss-Prot Hits     

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End	Description
sp|Q0CVU1|RGLA_ASPTN	1.02e-60	14	360	18	487	Probable rhamnogalacturonate lyase A OS=Aspergillus terreus (strain NIH 2624 / FGSC A1156) OX=341663 GN=rglA PE=3 SV=2
sp|Q5AX45|RGLA_EMENI	3.61e-60	98	360	207	486	Rhamnogalacturonate lyase A OS=Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139) OX=227321 GN=rglA PE=2 SV=1
sp|A1C995|RGLA_ASPCL	1.42e-59	3	360	7	487	Probable rhamnogalacturonate lyase A OS=Aspergillus clavatus (strain ATCC 1007 / CBS 513.65 / DSM 816 / NCTC 3887 / NRRL 1 / QM 1276 / 107) OX=344612 GN=rglA PE=3 SV=1
sp|Q00019|RGLA_ASPAC	3.99e-58	104	360	213	486	Rhamnogalacturonate lyase A OS=Aspergillus aculeatus OX=5053 GN=rglA PE=1 SV=1
sp|Q8NJK5|RGLA_ASPNG	4.63e-57	104	360	213	486	Rhamnogalacturonate lyase A (Fragment) OS=Aspergillus niger OX=5061 GN=rglA PE=3 SV=1

SignalP and Lipop Annotations

This protein is predicted as SP

Other	SP_Sec_SPI	CS Position
0.000213	0.999751	CS pos: 16-17. Pr: 0.9808

TMHMM  Annotations     

There is no transmembrane helices in CC1G_02937-t26_1-p1.