Conserved Site

Low-density lipoprotein (LDL) receptor class A, conserved site (IPR023415)

Short name: LDLR_class-A_CS

Description

Low-density lipoprotein (LDL) receptors are the major cholesterol-carrying lipoproteins of plasma. Seven successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein [PMID: 6091915]. Similar domains have been found (see references in [PMID: 7603991]) in other extracellular and membrane proteins which are listed below:

  • Vertebrate very low density lipoprotein (VLDL) receptor, which binds and transports VLDL. Its extracellular domain is composed of 8 LDLRA domains, 3 EGF-like domains and 6 LDL-receptor class B domains (LDLRB).
  • Vertebrate low-density lipoprotein receptor-related protein 1 (LRP1) (reviewed in [PMID: 7979249]), which may act as a receptor for the endocytosis of extracellular ligands. LRP1 contains 31 LDLRA domains and 22 EGF-like domains.
  • Vertebrate low-density lipoprotein receptor-related protein 2 (LRP2) (also known as gp330 or megalin). LRP2 contains 36 LDLRA domains and 17 EGF-like domains.
  • A LRP-homologue from Caenorhabditis elegans, which contains 35 LDLRA domains and 17 EGF-like domains.
  • Drosophila putative vitellogenin receptor, with 13 copies of LDLRA domains and 17 EGF-like repeats.
  • Complement factor I, which is responsible for cleaving the alpha-chains of C4b and C3b. It consists of a FIMAC domain (Factor I/MAC proteins C6/C7), a scavenger receptor-like domain, 2 copies of LDLRA and a C-terminal serine protease domain.
  • Complement components C6, C7, C8 and C9. They contain each one LDLRA domain.
  • Perlecan, a large multidomain basement membrane heparan sulphate proteoglycan composed of 4 LDLRA domains, 3 LamB domains, 12 laminin EGF- like domains, 14-21 IG-like domains, 3 LamG domains, and 4 EGF-like domains. A similar but shorter proteoglycan (UNC52) is found in Caenorhabditis elegans which has 3 repeats of LDLRA.
  • Invertebrate giant extracellular hemoglobin linker chains, which allow heme-containing chains to construct giant hemoglobin (1 LDLRA domain).
  • G-protein coupled receptor Grl101 of the snail Lymnaea stagnalis, which might directly transduce signals carried by large extracellular proteins.
  • Vertebrate enterokinase (EC 3.4.21.9), a type II membrane protein of the intestinal brush border, which activates trypsinogen. It consists at least of a catalytic light chain and a multidomain heavy chain which has 2 LDLRA, a MAM domain (see PDOC00604), a SRCR domain (see PDOC00348) and a CUB domain (see PDOC00908).
  • Human autosomal dominant polycystic kidney disease protein 1 (PKD1), which is involved in adhesive protein-protein and protein-carbohydrate interactions. The potential calcium-binding site of its single LDLRA domain is missing.
  • Vertebrate integral membrane protein DGCR2/IDD, a potential adhesion receptor with 1 LDLRA domain, a C-type lectin and a VWFC domain (see PDOC00928).
  • Drosophila serine protease nudel (EC 3.4.21.-), which is involved in the induction of dorsoventral polarity of the embryo. It has 11 LDLRA domains, 3 of which miss the first disulphide bond (C1-C3).
  • Avian subgroup A rous sarcoma virus receptor (1 copy of LDLRA).
  • Bovine Sco-spondin, which is secreted by the subcommissural organ in embryos and is involved in the modulation of neuronal aggregation. It contains at least 2 EGF-like domains and 3 LDLRA domains.

The LDL-receptor class A domain contains 6 disulphide-bound cysteines [PMID: 7548065] and a highly conserved cluster of negatively charged amino acids, of which many are clustered on one face of the module [PMID: 7603991]. A schematic representation of this domain is shown here:

     +---------------------+        +--------------------------------+
     |                     |        |                                |
    -CxxxxxxxxxxxxCxxxxxxxxCxxxxxxxxCxxxxxxxxxxCxxxxxxxxxxxxxxxxxxxxxC-
                  |        *******************************************
                  |                            |
                  +----------------------------+

'C': conserved cysteine involved in a disulphide bond.
'x': any residue.
'*': position of the pattern.

In LDL-receptors the class A domains form the binding site for LDL [PMID: 6091915] and calcium. The acidic residues between the fourth and sixth cysteines are important for high-affinity binding of positively charged sequences in LDLR's ligands [PMID: 3283935]. The repeat has been shown [PMID: 7603991] to consist of a beta-hairpin structure followed by a series of beta-turns. The binding of calcium seems to induce no significant conformational change.

Contributing signatures

Signatures from InterPro member databases are used to construct an entry.
PROSITE patterns