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Conserved domains on  [gi|212645223|ref|NP_492871|]
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C-type lectin domain-containing protein [Caenorhabditis elegans]

Protein Classification

C-type lectin domain-containing protein( domain architecture ID 10636995)

C-type lectin (CTL)/C-type lectin-like (CTLD) domain-containing protein may bind carbohydrate in a calcium-dependent manner

CATH:  3.10.100.10
Gene Ontology:  GO:0030246|GO:0120153
PubMed:  16336259|10508765
SCOP:  4002453

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
CLECT smart00034
C-type lectin (CTL) or carbohydrate-recognition domain (CRD); Many of these domains function ...
 43-172 2.17e-14

C-type lectin (CTL) or carbohydrate-recognition domain (CRD); Many of these domains function as calcium-dependent carbohydrate binding modules.


:

Pssm-ID: 214480 [Multi-domain]  Cd Length: 124  Bit Score: 67.62  E-value: 2.17e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212645223    43 CDSGWKRFNRpsgaWCIRIYRGTHSQADAENRCRQNvGATLSGVQNQVEINFITKSALDLISeaSGSIWIGGRRtqacrn 122
Cdd:smart00034   1 CPSGWISYGG----KCYKFSTEKKTWEDAQAFCQSL-GGHLASIHSEAENDFVASLLKNSGS--SDYYWIGLSD------ 67

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|
gi 212645223   123 salstsCGSLNSFQWTDGSTTGTaGLVWNTNQPDNkdsRSQQCLVLLASR 172
Cdd:smart00034  68 ------PDSNGSWQWSDGSGPVS-YSNWAPGEPNN---SSGDCVVLSTSG 107
 
Name Accession Description Interval E-value
CLECT smart00034
C-type lectin (CTL) or carbohydrate-recognition domain (CRD); Many of these domains function ...
 43-172 2.17e-14

C-type lectin (CTL) or carbohydrate-recognition domain (CRD); Many of these domains function as calcium-dependent carbohydrate binding modules.


Pssm-ID: 214480 [Multi-domain]  Cd Length: 124  Bit Score: 67.62  E-value: 2.17e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212645223    43 CDSGWKRFNRpsgaWCIRIYRGTHSQADAENRCRQNvGATLSGVQNQVEINFITKSALDLISeaSGSIWIGGRRtqacrn 122
Cdd:smart00034   1 CPSGWISYGG----KCYKFSTEKKTWEDAQAFCQSL-GGHLASIHSEAENDFVASLLKNSGS--SDYYWIGLSD------ 67

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|
gi 212645223   123 salstsCGSLNSFQWTDGSTTGTaGLVWNTNQPDNkdsRSQQCLVLLASR 172
Cdd:smart00034  68 ------PDSNGSWQWSDGSGPVS-YSNWAPGEPNN---SSGDCVVLSTSG 107
CLECT cd00037
C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type ...
 57-178 1.05e-11

C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins. This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs. Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice. Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis; P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration. CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose. Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors. C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces. Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model. In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer. A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome. Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model.


Pssm-ID: 153057 [Multi-domain]  Cd Length: 116  Bit Score: 60.33  E-value: 1.05e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212645223  57 WCIRIYRGTHSQADAENRCRQNvGATLSGVQNQVEINFITKSALDLISEasgSIWIGGRRTQacrnsalstscgSLNSFQ 136
Cdd:cd00037    1 SCYKFSTEKLTWEEAQEYCRSL-GGHLASIHSEEENDFLASLLKKSSSS---DVWIGLNDLS------------SEGTWK 64

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 212645223 137 WTDGSTTGTaGLVWNTNQPDNkdSRSQQCLVLLASRASSIQD 178
Cdd:cd00037   65 WSDGSPLVD-YTNWAPGEPNP--GGSEDCVVLSSSSDGKWND 103
 
Name Accession Description Interval E-value
CLECT smart00034
C-type lectin (CTL) or carbohydrate-recognition domain (CRD); Many of these domains function ...
 43-172 2.17e-14

C-type lectin (CTL) or carbohydrate-recognition domain (CRD); Many of these domains function as calcium-dependent carbohydrate binding modules.


Pssm-ID: 214480 [Multi-domain]  Cd Length: 124  Bit Score: 67.62  E-value: 2.17e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212645223    43 CDSGWKRFNRpsgaWCIRIYRGTHSQADAENRCRQNvGATLSGVQNQVEINFITKSALDLISeaSGSIWIGGRRtqacrn 122
Cdd:smart00034   1 CPSGWISYGG----KCYKFSTEKKTWEDAQAFCQSL-GGHLASIHSEAENDFVASLLKNSGS--SDYYWIGLSD------ 67

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|
gi 212645223   123 salstsCGSLNSFQWTDGSTTGTaGLVWNTNQPDNkdsRSQQCLVLLASR 172
Cdd:smart00034  68 ------PDSNGSWQWSDGSGPVS-YSNWAPGEPNN---SSGDCVVLSTSG 107
CLECT cd00037
C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type ...
 57-178 1.05e-11

C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins. This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs. Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice. Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis; P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration. CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose. Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors. C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces. Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model. In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer. A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome. Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model.


Pssm-ID: 153057 [Multi-domain]  Cd Length: 116  Bit Score: 60.33  E-value: 1.05e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212645223  57 WCIRIYRGTHSQADAENRCRQNvGATLSGVQNQVEINFITKSALDLISEasgSIWIGGRRTQacrnsalstscgSLNSFQ 136
Cdd:cd00037    1 SCYKFSTEKLTWEEAQEYCRSL-GGHLASIHSEEENDFLASLLKKSSSS---DVWIGLNDLS------------SEGTWK 64

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 212645223 137 WTDGSTTGTaGLVWNTNQPDNkdSRSQQCLVLLASRASSIQD 178
Cdd:cd00037   65 WSDGSPLVD-YTNWAPGEPNP--GGSEDCVVLSSSSDGKWND 103
CLECT_DC-SIGN_like cd03590
C-type lectin-like domain (CTLD) of the type found in human dendritic cell (DC)-specific ...
 43-192 2.78e-07

C-type lectin-like domain (CTLD) of the type found in human dendritic cell (DC)-specific intercellular adhesion molecule 3-grabbing non-integrin (DC-SIGN) and the related receptor, DC-SIGN receptor (DC-SIGNR); CLECT_DC-SIGN_like: C-type lectin-like domain (CTLD) of the type found in human dendritic cell (DC)-specific intercellular adhesion molecule 3-grabbing non-integrin (DC-SIGN) and the related receptor, DC-SIGN receptor (DC-SIGNR). This group also contains proteins similar to hepatic asialoglycoprotein receptor (ASGP-R) and langerin in human. These proteins are type II membrane proteins with a CTLD ectodomain. CTLD refers to a domain homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins. DC-SIGN is thought to mediate the initial contact between dendritic cells and resting T cells, and may also mediate the rolling of DCs on epithelium. DC-SIGN and DC-SIGNR bind to oligosaccharides present on human tissues, as well as, on pathogens including parasites, bacteria, and viruses. DC-SIGN and DC-SIGNR bind to HIV enhancing viral infection of T cells. DC-SIGN and DC-SIGNR are homotetrameric, and contain four CTLDs stabilized by a coiled coil of alpha helices. The hepatic ASGP-R is an endocytic recycling receptor which binds and internalizes desialylated glycoproteins having a terminal galactose or N-acetylgalactosamine residues on their N-linked carbohydrate chains, via the clathrin-coated pit mediated endocytic pathway, and delivers them to lysosomes for degradation. It has been proposed that glycoproteins bearing terminal Sia (sialic acid) alpha2, 6GalNAc and Sia alpha2, 6Gal are endogenous ligands for ASGP-R and that ASGP-R participates in regulating the relative concentration of serum glycoproteins bearing alpha 2,6-linked Sia. The human ASGP-R is a hetero-oligomer composed of two subunits, both of which are found within this group. Langerin is expressed in a subset of dendritic leukocytes, the Langerhans cells (LC). Langerin induces the formation of Birbeck Granules (BGs) and associates with these BGs following internalization. Langerin binds, in a calcium-dependent manner, to glyco-conjugates containing mannose and related sugars mediating their uptake and degradation. Langerin molecules oligomerize as trimers with three CTLDs held together by a coiled-coil of alpha helices.


Pssm-ID: 153060 [Multi-domain]  Cd Length: 126  Bit Score: 48.07  E-value: 2.78e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212645223  43 CDSGWKRFnrpsGAWCIRIYRGTHSQADAENRCRQnVGATLSGVQNQVEINFITKsaldlISEASGSIWIGgrrtqacrn 122
Cdd:cd03590    1 CPTNWKSF----QSSCYFFSTEKKSWEESRQFCED-MGAHLVIINSQEEQEFISK-----ILSGNRSYWIG--------- 61

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212645223 123 saLSTScGSLNSFQWTDGSTTGTAGLVWNTNQPDNKDSRSQQClvllasrASSIQDKWTWYanrmdDVQC 192
Cdd:cd03590   62 --LSDE-ETEGEWKWVDGTPLNSSKTFWHPGEPNNWGGGGEDC-------AELVYDSGGWN-----DVPC 116
CLECT_CSPGs cd03588
C-type lectin-like domain (CTLD) of the type found in chondroitin sulfate proteoglycan core ...
 43-169 7.89e-06

C-type lectin-like domain (CTLD) of the type found in chondroitin sulfate proteoglycan core proteins; CLECT_CSPGs: C-type lectin-like domain (CTLD) of the type found in chondroitin sulfate proteoglycan core proteins (CSPGs) in human and chicken aggrecan, frog brevican, and zebra fish dermacan. CTLD refers to a domain homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins. In cartilage, aggrecan forms cartilage link protein stabilized aggregates with hyaluronan (HA). These aggregates contribute to the tissue's load bearing properties. Aggregates having other CSPGs substituting for aggrecan may contribute to the structural integrity of many different tissues. Xenopus brevican is expressed in the notochord and the brain during early embryogenesis. Zebra fish dermacan is expressed in dermal bones and may play a role in dermal bone development. CSPGs do contain LINK domain(s) which bind HA. These LINK domains are considered by one classification system to be a variety of CTLD, but are omitted from this hierarchical classification based on insignificant sequence similarity.


Pssm-ID: 153058  Cd Length: 124  Bit Score: 44.11  E-value: 7.89e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212645223  43 CDSGWKRFNrpsgAWCIRIYRGTHSQADAENRCRQNvGATLSGVQNQVEINFITKSALDLIseasgsiWIG-GRRTQAcr 121
Cdd:cd03588    1 CEEGWDKFQ----GHCYRHFPDRETWEDAERRCREQ-QGHLSSIVTPEEQEFVNNNAQDYQ-------WIGlNDRTIE-- 66

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 212645223 122 nsalstscgslNSFQWTDGSTTGTAGlvWNTNQPDNKDSRSQQCLVLL 169
Cdd:cd03588   67 -----------GDFRWSDGHPLQFEN--WRPNQPDNFFATGEDCVVMI 101
CLECT_thrombomodulin_like cd03600
C-type lectin-like domain (CTLD) of the type found in human thrombomodulin(TM), Endosialin, ...
 58-181 4.92e-04

C-type lectin-like domain (CTLD) of the type found in human thrombomodulin(TM), Endosialin, C14orf27, and C1qR; CLECT_thrombomodulin_like: C-type lectin-like domain (CTLD) of the type found in human thrombomodulin(TM), Endosialin, C14orf27, and C1qR. CTLD refers to a domain homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins. In these thrombomodulin-like proteins the residues involved in coordinating Ca2+ in the classical MBP-A CTLD are not conserved. TM exerts anti-fibrinolytic and anti-inflammatory activity. TM also regulates blood coagulation in the anticoagulant protein C pathway. In this pathway, the procoagulant properties of thrombin (T) are lost when it binds TM. TM also plays a key role in tumor biology. It is expressed on endothelial cells and on several type of tumor cell including squamous cell carcinoma. Loss of TM expression correlates with advanced stage and poor prognosis. Loss of function of TM function may be associated with arterial or venous thrombosis and with late fetal loss. Soluble molecules of TM retaining the CTLD are detected in human plasma and urine where higher levels indicate injury and/or enhanced turnover of the endothelium. C1qR is expressed on endothelial cells and stem cells. It is also expressed on monocots and neutrophils, where it is subject to ectodomain shedding. Soluble forms of C1qR retaining the CTLD is detected in human plasma. C1qR modulates the phagocytosis of apoptotic cells in vivo. C1qR-deficient mice are defective in clearance of apoptotic cells in vivo. The cytoplasmic tail of C1qR, C-terminal to the CTLD of CD93, contains a PDZ binding domain which interacts with the PDZ domain-containing adaptor protein, GIPC. The juxtamembrane region of this tail interacts with the ezrin/radixin/moesin family. Endosialin functions in the growth and progression of abdominal tumors and is expressed in the stroma of several tumors.


Pssm-ID: 153070  Cd Length: 141  Bit Score: 39.34  E-value: 4.92e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212645223  58 CIRIYRGTHSQADAENRCRQNvGATLSGVQNQVE---INFITKSALDLISEASGSIWIGGRRtqacRNSALSTSCGSLNS 134
Cdd:cd03600    6 CYTLHPQKLTFLEAQRSCIEL-GGNLATVRSGEEadvVSLLLAAGPGRHGRGSLRLWIGLQR----EPRQCSDPSLPLRG 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 212645223 135 FQWTDGStTGTAGLVWntNQPDNKDSRSQQCLVLLASRASSIQDKWT 181
Cdd:cd03600   81 FSWVTGD-QDTDFSNW--LQEPAGTCTSPRCVALSAAGSTPDNLKWK 124
 
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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