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Conserved domains on  [gi|498117271|ref|WP_010431427|]
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MULTISPECIES: ricin-type beta-trefoil lectin domain protein [Vibrio]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
beta-trefoil_Ricin-like super family cl49609
ricin B-type lectin domain, beta-trefoil fold; The ricin B-type lectin domain is a ...
 95-159 3.88e-05

ricin B-type lectin domain, beta-trefoil fold; The ricin B-type lectin domain is a carbohydrate-binding domain formed from presumed gene triplication. It shows a beta-trefoil fold characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. The ricin B-type lectin domain was originally found in Ricin, which is a legume lectin from the seeds of the castor bean plant, Ricinus communis. It is also found in many carbohydrate-recognition proteins like plant and bacterial AB-toxins, glycosidases, or proteases, which serve diverse functions such as inhibitory toxicity, enzymatic activity, and signal transduction. The ricin B-type lectin domain can be present in one or more copies and has been shown in some instances to bind simple sugars, such as galactose or lactose. The most characteristic, though not completely conserved, sequence feature is the presence of a Q-W pattern. Consequently, the ricin B-type lectin domain has also been referred as the (QxW)3 domain and the three homologous regions as the QxW repeats. A disulfide bond is also conserved in some QxW repeats.


The actual alignment was detected with superfamily member cd23456:

Pssm-ID: 483949 [Multi-domain]  Cd Length: 122  Bit Score: 41.19  E-value: 3.88e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 498117271  95 QIQSyAFEGLCM--QGLLAKGkSELALLECSDAKNQGFVYsENDQTIRLKADSSYCLAVTSETQEAG 159
Cdd:cd23456    4 QLKS-QASGLCLdvSGGATNG-ANVVVYDCNNSNSQKWYY-DATGRLHSKANPGKCLDAGGENSNGA 67
 
Name Accession Description Interval E-value
beta-trefoil_Ricin_SCDase cd23456
ricin B-type lectin domain, beta-trefoil fold, found in Shewanella algae sphingolipid ceramide ...
 95-159 3.88e-05

ricin B-type lectin domain, beta-trefoil fold, found in Shewanella algae sphingolipid ceramide N-deacylase (SCDase) and similar proteins; SCDase (EC 3.5.1.69) is an enzyme which hydrolyzes the N-acyl linkage between fatty acid and sphingosine in ceramide of various glycosphingolipids and sphingomyelin. Shewanella algae SCDase contains two ricin B-type lectin domains at its C-terminus. The ricin B-type lectin domain shows a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. Each subdomain may harbor a sugar-binding pocket.


Pssm-ID: 467334 [Multi-domain]  Cd Length: 122  Bit Score: 41.19  E-value: 3.88e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 498117271  95 QIQSyAFEGLCM--QGLLAKGkSELALLECSDAKNQGFVYsENDQTIRLKADSSYCLAVTSETQEAG 159
Cdd:cd23456    4 QLKS-QASGLCLdvSGGATNG-ANVVVYDCNNSNSQKWYY-DATGRLHSKANPGKCLDAGGENSNGA 67
 
Name Accession Description Interval E-value
beta-trefoil_Ricin_SCDase cd23456
ricin B-type lectin domain, beta-trefoil fold, found in Shewanella algae sphingolipid ceramide ...
 95-159 3.88e-05

ricin B-type lectin domain, beta-trefoil fold, found in Shewanella algae sphingolipid ceramide N-deacylase (SCDase) and similar proteins; SCDase (EC 3.5.1.69) is an enzyme which hydrolyzes the N-acyl linkage between fatty acid and sphingosine in ceramide of various glycosphingolipids and sphingomyelin. Shewanella algae SCDase contains two ricin B-type lectin domains at its C-terminus. The ricin B-type lectin domain shows a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. Each subdomain may harbor a sugar-binding pocket.


Pssm-ID: 467334 [Multi-domain]  Cd Length: 122  Bit Score: 41.19  E-value: 3.88e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 498117271  95 QIQSyAFEGLCM--QGLLAKGkSELALLECSDAKNQGFVYsENDQTIRLKADSSYCLAVTSETQEAG 159
Cdd:cd23456    4 QLKS-QASGLCLdvSGGATNG-ANVVVYDCNNSNSQKWYY-DATGRLHSKANPGKCLDAGGENSNGA 67
beta-trefoil_Ricin_hemolysin cd23423
ricin B-type lectin domain, beta-trefoil fold, found in bacterial hemolysin and similar ...
 95-149 7.78e-04

ricin B-type lectin domain, beta-trefoil fold, found in bacterial hemolysin and similar proteins; Bacterial hemolysins are exotoxins that attack blood cell membranes and cause cytolysis by forming heptameric pores in target host membranes. After binding to target membranes, the protein assembles into a heptameric pre-pore complex. Proteolytic cleavage triggers a conformation change that is required for membrane insertion and pore formation. Hemolysin may be called "cytolysin" or "cytolytic toxin", according to a specific action for certain cells. For example, this subfamily includes Vibrio vulnificus cytolysin that attack blood cell membranes and cause cell rupture, thereby liberating hemoglobins. Members of this subfamily contain a ricin B-type lectin domain with a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. Each subdomain may harbor a putative sugar-binding pocket.


Pssm-ID: 467301 [Multi-domain]  Cd Length: 119  Bit Score: 37.75  E-value: 7.78e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 498117271  95 QIQSYAFEGLCMQgllAKGKSELALLECSDA-KNQGFVYsENDQTIRLKADSSYCL 149
Cdd:cd23423    6 NLQSLSFNNRCLT---VDNNGRVTLESCDSGdRNQSWIL-DSEGRYRSRVAPDLCL 57
beta-trefoil_Ricin_GALNT7 cd23437
ricin B-type lectin domain, beta-trefoil fold, found in polypeptide ...
 46-157 8.98e-04

ricin B-type lectin domain, beta-trefoil fold, found in polypeptide N-acetylgalactosaminyltransferase 7 (GALNT7) and similar proteins; GALNT7 (EC 2.4.1.41), also called polypeptide GalNAc transferase 7, GalNAc-T7, pp-GaNTase 7, protein-UDP acetylgalactosaminyltransferase 7, or UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase 7, acts as glycopeptide transferase involved in O-linked oligosaccharide biosynthesis, which catalyzes the transfer of an N-acetyl-D-galactosamine residue to an already glycosylated peptide. In contrast to other proteins of the family, it does not act as a peptide transferase that transfers GalNAc onto serine or threonine residue on the protein receptor, but instead requires the prior addition of a GalNAc on a peptide before adding additional GalNAc moieties. Its appropriate peptide substrate remains unidentified. GALNT7 comprises a glycosyltransferase region and a ricin B-type lectin domain. The glycosyltransferase region contains two conserved domains, domain A (also called GT1 motif) and domain B (also called Gal/GalNAc-T motif). This model corresponds to ricin B-type lectin domain with a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. The ricin B-type lectin domain binds to GalNAc and contributes to the glycopeptide specificity.


Pssm-ID: 467315 [Multi-domain]  Cd Length: 124  Bit Score: 37.66  E-value: 8.98e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 498117271  46 NGYGFCIDTYGPGQSELMQTHTCkpkapegsprNYSGHDVRFEFNnETDQIQSYafeGLCMqgLLAKGKSELALLECSDA 125
Cdd:cd23437   11 LGTGLCLDTMGHQNGGPVGLYPC----------HGMGGNQLFRLN-EAGQLAVG---EQCL--TASGSGGKVKLRKCNLG 74

                         90       100       110
                 ....*....|....*....|....*....|..
gi 498117271 126 KNQGFVYSENDQTIRLKaDSSYCLAVTSETQE 157
Cdd:cd23437   75 ETGKWEYDEATGQIRHK-GTGKCLDLNEGTNK 105
beta-trefoil_Ricin_RIPs_II_rpt2 cd23444
second ricin B-type lectin domain, beta-trefoil fold, found in type II ribosome-inactivating ...
 101-150 1.99e-03

second ricin B-type lectin domain, beta-trefoil fold, found in type II ribosome-inactivating proteins (RIPs); Type II ribosome-inactivating proteins (RIPs) inhibit translation in eukaryotes by irreversibly inactivating the 28S rRNA and preventing the binding of elongation factor II to the ribosome. They consist of a catalytic A-chain which has rRNA N-glycosidase activity and a lectin B-chain containing two ricin B-type lectin domains with a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. The lectin chain facilitates the internalization of the catalytic chain on binding to the cell surface. The two chains are connected by a disulfide bridge. This model corresponds to the second ricin B-type lectin domain. Members of this family includes Ricinus communis ricin, bitter gourd (Momordica charantia) seed lectin (BGSL), snake gourd (Trichosanthes anguina) seed lectin (SGSL), Sambucus ebulus ebulin I, Sambucus nigra nigrin b (also known as agglutinin V or SNAV), SNAI (also known as agglutinin I), SNAI' and SNAIf, Abrus precatorius abrin (ABR) and agglutinin-I (AAG), and Viscum album beta-galactoside-specific lectins 1-4 (also known as mistletoe lectins or MLs).


Pssm-ID: 467322 [Multi-domain]  Cd Length: 122  Bit Score: 36.48  E-value: 1.99e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 498117271 101 FEGLCMQgllAKGKSELALLECSDAKN--QGFVYSenDQTIRLKADSSYCLA 150
Cdd:cd23444    9 LNDLCLQ---ANGGNNVWLEECVSNKKeqKWALYP--DGTIRPNQNRNLCLT 55
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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