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Conserved domains on  [gi|309243123|ref|NP_001184248|]
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C-type lectin domain family 2 member D isoform 5 [Homo sapiens]

Protein Classification

C-type lectin-like domain-containing protein( domain architecture ID 96)

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

PubMed:  16336259|10508765

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
CLECT super family cl02432
C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type ...
 38-82 5.17e-17

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.


The actual alignment was detected with superfamily member cd03593:

Pssm-ID: 470576  Cd Length: 116  Bit Score: 69.67  E-value: 5.17e-17
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 309243123  38 CPESWIGFQRKCFYFSDDTKNWTSSQRFCDSQDADLAQVESFQEL 82
Cdd:cd03593    1 CPKDWICYGNKCYYFSMEKKTWNESKEACSSKNSSLLKIDDEEEL 45
 
Name Accession Description Interval E-value
CLECT_NK_receptors_like cd03593
C-type lectin-like domain (CTLD) of the type found in natural killer cell receptors (NKRs); ...
 38-82 5.17e-17

C-type lectin-like domain (CTLD) of the type found in natural killer cell receptors (NKRs); CLECT_NK_receptors_like: C-type lectin-like domain (CTLD) of the type found in natural killer cell receptors (NKRs), including proteins similar to oxidized low density lipoprotein (OxLDL) receptor (LOX-1), CD94, CD69, NKG2-A and -D, osteoclast inhibitory lectin (OCIL), dendritic cell-associated C-type lectin-1 (dectin-1), human myeloid inhibitory C-type lectin-like receptor (MICL), mast cell-associated functional antigen (MAFA), killer cell lectin-like receptors: subfamily F, member 1 (KLRF1) and subfamily B, member 1 (KLRB1), and lys49 receptors. CTLD refers to a domain homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins. NKRs are variously associated with activation or inhibition of natural killer (NK) cells. Activating NKRs stimulate cytolysis by NK cells of virally infected or transformed cells; inhibitory NKRs block cytolysis upon recognition of markers of healthy self cells. Most Lys49 receptors are inhibitory; some are stimulatory. OCIL inhibits NK cell function via binding to the receptor NKRP1D. Murine OCIL in addition to inhibiting NK cell function inhibits osteoclast differentiation. MAFA clusters with the type I Fc epsilon receptor (FcepsilonRI) and inhibits the mast cells secretory response to FcepsilonRI stimulus. CD72 is a negative regulator of B cell receptor signaling. NKG2D is an activating receptor for stress-induced antigens; human NKG2D ligands include the stress induced MHC-I homologs, MICA, MICB, and ULBP family of glycoproteins Several NKRs have a carbohydrate-binding capacity which is not mediated through calcium ions (e.g. OCIL binds a range of high molecular weight sulfated glycosaminoglycans including dextran sulfate, fucoidan, and gamma-carrageenan sugars). Dectin-1 binds fungal beta-glucans and in involved in the innate immune responses to fungal pathogens. MAFA binds saccharides having terminal alpha-D mannose residues in a calcium-dependent manner. LOX-1 is the major receptor for OxLDL in endothelial cells and thought to play a role in the pathology of atherosclerosis. Some NKRs exist as homodimers (e.g.Lys49, NKG2D, CD69, LOX-1) and some as heterodimers (e.g. CD94/NKG2A). Dectin-1 can function as a monomer in vitro.


Pssm-ID: 153063  Cd Length: 116  Bit Score: 69.67  E-value: 5.17e-17
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 309243123  38 CPESWIGFQRKCFYFSDDTKNWTSSQRFCDSQDADLAQVESFQEL 82
Cdd:cd03593    1 CPKDWICYGNKCYYFSMEKKTWNESKEACSSKNSSLLKIDDEEEL 45
PHA02642 PHA02642
C-type lectin-like protein; Provisional
 28-82 1.06e-13

C-type lectin-like protein; Provisional


Pssm-ID: 165024 [Multi-domain]  Cd Length: 216  Bit Score: 63.60  E-value: 1.06e-13
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 309243123  28 QEPSVcLQAACPESWIGFQRKCFYFSDDTKNWTSSQRFCDSQDADLAQVESFQEL 82
Cdd:PHA02642  79 QEPTI-KYVTCPKGWIGFGYKCFYFSEDSKNWTFGNTFCTSLGATLVKVETEEEL 132
CLECT smart00034
C-type lectin (CTL) or carbohydrate-recognition domain (CRD); Many of these domains function ...
 38-82 5.06e-12

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: 57.22  E-value: 5.06e-12
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 309243123    38 CPESWIGFQRKCFYFSDDTKNWTSSQRFCDSQDADLAQVESFQEL 82
Cdd:smart00034   1 CPSGWISYGGKCYKFSTEKKTWEDAQAFCQSLGGHLASIHSEAEN 45
 
Name Accession Description Interval E-value
CLECT_NK_receptors_like cd03593
C-type lectin-like domain (CTLD) of the type found in natural killer cell receptors (NKRs); ...
 38-82 5.17e-17

C-type lectin-like domain (CTLD) of the type found in natural killer cell receptors (NKRs); CLECT_NK_receptors_like: C-type lectin-like domain (CTLD) of the type found in natural killer cell receptors (NKRs), including proteins similar to oxidized low density lipoprotein (OxLDL) receptor (LOX-1), CD94, CD69, NKG2-A and -D, osteoclast inhibitory lectin (OCIL), dendritic cell-associated C-type lectin-1 (dectin-1), human myeloid inhibitory C-type lectin-like receptor (MICL), mast cell-associated functional antigen (MAFA), killer cell lectin-like receptors: subfamily F, member 1 (KLRF1) and subfamily B, member 1 (KLRB1), and lys49 receptors. CTLD refers to a domain homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins. NKRs are variously associated with activation or inhibition of natural killer (NK) cells. Activating NKRs stimulate cytolysis by NK cells of virally infected or transformed cells; inhibitory NKRs block cytolysis upon recognition of markers of healthy self cells. Most Lys49 receptors are inhibitory; some are stimulatory. OCIL inhibits NK cell function via binding to the receptor NKRP1D. Murine OCIL in addition to inhibiting NK cell function inhibits osteoclast differentiation. MAFA clusters with the type I Fc epsilon receptor (FcepsilonRI) and inhibits the mast cells secretory response to FcepsilonRI stimulus. CD72 is a negative regulator of B cell receptor signaling. NKG2D is an activating receptor for stress-induced antigens; human NKG2D ligands include the stress induced MHC-I homologs, MICA, MICB, and ULBP family of glycoproteins Several NKRs have a carbohydrate-binding capacity which is not mediated through calcium ions (e.g. OCIL binds a range of high molecular weight sulfated glycosaminoglycans including dextran sulfate, fucoidan, and gamma-carrageenan sugars). Dectin-1 binds fungal beta-glucans and in involved in the innate immune responses to fungal pathogens. MAFA binds saccharides having terminal alpha-D mannose residues in a calcium-dependent manner. LOX-1 is the major receptor for OxLDL in endothelial cells and thought to play a role in the pathology of atherosclerosis. Some NKRs exist as homodimers (e.g.Lys49, NKG2D, CD69, LOX-1) and some as heterodimers (e.g. CD94/NKG2A). Dectin-1 can function as a monomer in vitro.


Pssm-ID: 153063  Cd Length: 116  Bit Score: 69.67  E-value: 5.17e-17
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 309243123  38 CPESWIGFQRKCFYFSDDTKNWTSSQRFCDSQDADLAQVESFQEL 82
Cdd:cd03593    1 CPKDWICYGNKCYYFSMEKKTWNESKEACSSKNSSLLKIDDEEEL 45
PHA02642 PHA02642
C-type lectin-like protein; Provisional
 28-82 1.06e-13

C-type lectin-like protein; Provisional


Pssm-ID: 165024 [Multi-domain]  Cd Length: 216  Bit Score: 63.60  E-value: 1.06e-13
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 309243123  28 QEPSVcLQAACPESWIGFQRKCFYFSDDTKNWTSSQRFCDSQDADLAQVESFQEL 82
Cdd:PHA02642  79 QEPTI-KYVTCPKGWIGFGYKCFYFSEDSKNWTFGNTFCTSLGATLVKVETEEEL 132
CLECT smart00034
C-type lectin (CTL) or carbohydrate-recognition domain (CRD); Many of these domains function ...
 38-82 5.06e-12

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: 57.22  E-value: 5.06e-12
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 309243123    38 CPESWIGFQRKCFYFSDDTKNWTSSQRFCDSQDADLAQVESFQEL 82
Cdd:smart00034   1 CPSGWISYGGKCYKFSTEKKTWEDAQAFCQSLGGHLASIHSEAEN 45
CLECT_DC-SIGN_like cd03590
C-type lectin-like domain (CTLD) of the type found in human dendritic cell (DC)-specific ...
 38-74 4.72e-10

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: 52.31  E-value: 4.72e-10
                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 309243123  38 CPESWIGFQRKCFYFSDDTKNWTSSQRFCDSQDADLA 74
Cdd:cd03590    1 CPTNWKSFQSSCYFFSTEKKSWEESRQFCEDMGAHLV 37
PHA02867 PHA02867
C-type lectin protein; Provisional
 38-77 1.34e-08

C-type lectin protein; Provisional


Pssm-ID: 165201  Cd Length: 167  Bit Score: 49.30  E-value: 1.34e-08
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 309243123  38 CPESWIGFQRKCFYFSDDTKNWTSSQRFCDSQDADLAQVE 77
Cdd:PHA02867  49 CPDEWIGYNSKCYYFTINETNWNDSKKLCDVMDSSLIRFD 88
CLECT cd00037
C-type lectin (CTL)/C-type lectin-like (CTLD) domain; CLECT: C-type lectin (CTL)/C-type ...
 48-82 1.91e-06

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: 42.61  E-value: 1.91e-06
                         10        20        30
                 ....*....|....*....|....*....|....*
gi 309243123  48 KCFYFSDDTKNWTSSQRFCDSQDADLAQVESFQEL 82
Cdd:cd00037    1 SCYKFSTEKLTWEEAQEYCRSLGGHLASIHSEEEN 35
PHA03097 PHA03097
C-type lectin-like protein; Provisional
 38-82 1.47e-04

C-type lectin-like protein; Provisional


Pssm-ID: 222982 [Multi-domain]  Cd Length: 157  Bit Score: 38.31  E-value: 1.47e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 309243123  38 CPESWIGFQRKCFYFSDDTKNWTSSQRFCDSQDADLAQVESFQEL 82
Cdd:PHA03097  46 CRSGWVGYNNKCYTFSENITNKHLAIERCADMDGILTLIDDQKEV 90
CLECT_1 cd03602
C-type lectin (CTL)/C-type lectin-like (CTLD) domain subgroup 1; a subgroup of protein domains ...
 50-85 1.78e-03

C-type lectin (CTL)/C-type lectin-like (CTLD) domain subgroup 1; a subgroup of protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins; CLECT_1: C-type lectin (CTL)/C-type lectin-like (CTLD) domain subgroup 1; a subgroup of protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins. 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. CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose. CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers from which ligand-binding sites project in different orientations. In some CTLDs a loop extends to the adjoining domain to form a loop-swapped dimer.


Pssm-ID: 153072  Cd Length: 108  Bit Score: 34.66  E-value: 1.78e-03
                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 309243123  50 FYFSDDTKNWTSSQRFCDSQDADLAQVESFQELVSY 85
Cdd:cd03602    3 FYLVNESKTWSEAQQYCRENYTDLATVQNQEDNALL 38
CLECT_CSPGs cd03588
C-type lectin-like domain (CTLD) of the type found in chondroitin sulfate proteoglycan core ...
 38-81 8.83e-03

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: 32.93  E-value: 8.83e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 309243123  38 CPESWIGFQRKCFYFSDDTKNWTSSQRFCDSQDADLAQVESFQE 81
Cdd:cd03588    1 CEEGWDKFQGHCYRHFPDRETWEDAERRCREQQGHLSSIVTPEE 44
 
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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