CAZyme Information: RVD80456.1

Basic Information

• Species: Arthrobotrys flagrans
• Lineage: Ascomycota; Orbiliomycetes; ; Orbiliaceae; Arthrobotrys; Arthrobotrys flagrans
• CAZyme ID: RVD80456.1
• CAZy Family: AA3
• CAZyme Description: Rhamnogalacturonan endolyase [Source:UniProtKB/TrEMBL;Acc:A0A436ZNM5]

CAZyme Property

Protein Length	CGC	Molecular Weight	Isoelectric Point
596	SAEB01000012|CGC23	62887.22	8.5575

Genome Property

Genome Version/Assembly ID	Genes	Strain NCBI Taxon ID	Non Protein Coding Genes	Protein Coding Genes
FungiDB-61_AflagransCBSH-5679	9927	N/A	30	9897

• Gene Location: location=SAEB01000012:1184575-1186429(+)

Full Sequence      

MRISKPLVWAFCVRVTFAAFGITTSGNNFEVDTGAGLIYQVSKSTGDVVSLKYNGVEYQD
SSKYTHINSGLGTSTVSGSLVSGYTKITIQSSGLPVTQYIVSKSGDPTLYLATYITGEVD
PGELRWIARLKKSVLPTGVRHPVSDIVGGTAIEGSDVFLVSGQTRCKFYSSERFVEDNVH
GVTGSGVGVWMIIPPQAYETSSGGPFMRDINNQGGTVQELYWYMNSGHVRTEPWRMGLKG
PYAMTFTTGSTPSANIDTSFFSSLSINGYVAQSGRGRVSGTVSGIPSGFEGVVHWYNSDN
QYWVKSTGSFTSPYMKPGTYTMKLYKGELEVASSSVSVTAGGTTSKSIASTEASPSIVWR
IGQFDGQPFELKNGDKFLRMHPSDSRMSSWGGTYTVGSSSASAFPMAVFKSIGGSAIVKF
TLSSSQLVQMTLRIGTTLSFAGARPSVTINNWSGSIPAAPVKIDSRGVTRGAYRGYGEQY
TWTVPASAFVSGTNTLTIGVASGSSGTDYLSPNFIFDAVELQGPSGSSGGTTTTTTTTRT
TTAATTAATTPTTTGSSGGCTAAIYAQCGGLGFTGCTNCVSGTTCNYSNDWYSQCL

Enzyme Prediction     

EC	4.2.2.23:4

CAZyme Signature Domains

Family	Start	End	Evalue	family coverage
PL4	17	512	2.8e-208	0.9959919839679359

CDD Domains     

Cdd ID	Domain	E-Value	qStart	qEnd	sStart	sEnd	Domain Description
401282	RhgB_N	4.22e-134	20	268	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).
199905	RGL4_C	6.88e-57	359	522	1	161	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.
405384	CBM-like	2.42e-52	358	521	2	157	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.
199907	RGL4_N	1.84e-47	20	254	1	264	N-terminal catalytic 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; the middle and C-terminal domains are both 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	1.24e-17	274	345	1	74	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.

CAZyme Hits     

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End
EGX51477.1|CBM1|PL4_1	0.0	1	596	1	597
QRD05666.1|PL4_1	2.11e-209	18	522	19	526
QDS74173.1|PL4_1	3.93e-202	11	528	13	533
CCA68112.1|PL4_1	5.21e-199	17	521	20	522
QRW20454.1|PL4_1	1.24e-197	7	521	9	513

PDB Hits     

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End	Description
1NKG_A	1.12e-187	19	521	1	506	Rhamnogalacturonan lyase from Aspergillus aculeatus [Aspergillus aculeatus]
2XHN_A	9.05e-187	19	521	1	506	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	3.65e-186	19	521	1	506	Rhamnogalacturonan Lyase from Aspergillus aculeatus mutant H210A [Aspergillus aculeatus]
4BMF_A	4.44e-12	560	596	2	38	Chain A, ENDOGLUCANASE EG-1 [Trichoderma reesei]
6MVI_A	6.45e-09	559	595	256	292	Apo Cel45A from Neurospora crassa OR74A [Neurospora crassa OR74A],6MVJ_A Cellobiose complex Cel45A from Neurospora crassa OR74A [Neurospora crassa OR74A]

Swiss-Prot Hits     

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End	Description
sp|Q5AX45|RGLA_EMENI	5.60e-192	3	521	8	525	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|Q4W9T6|RGLA_ASPFU	1.34e-190	9	521	14	526	Probable rhamnogalacturonate lyase A OS=Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100) OX=330879 GN=rglA PE=3 SV=1
sp|B0YEH9|RGLA_ASPFC	1.34e-190	9	521	14	526	Probable rhamnogalacturonate lyase A OS=Neosartorya fumigata (strain CEA10 / CBS 144.89 / FGSC A1163) OX=451804 GN=rglA PE=3 SV=1
sp|Q00019|RGLA_ASPAC	2.97e-189	10	521	11	525	Rhamnogalacturonate lyase A OS=Aspergillus aculeatus OX=5053 GN=rglA PE=1 SV=1
sp|Q0CVU1|RGLA_ASPTN	1.18e-184	4	515	10	520	Probable rhamnogalacturonate lyase A OS=Aspergillus terreus (strain NIH 2624 / FGSC A1156) OX=341663 GN=rglA PE=3 SV=2

SignalP and Lipop Annotations

This protein is predicted as SP

Other	SP_Sec_SPI	CS Position
0.000425	0.999565	CS pos: 26-27. Pr: 0.3809

TMHMM  Annotations     

There is no transmembrane helices in RVD80456.1.