GRAM domain containing 1B, also known as GRAMD1B, Aster-B and KIAA1201, is a cholesterol transport protein that is encoded by the GRAMD1B gene.[1] [2] It contains a transmembrane region and two domains of known function; the GRAM domain and a VASt domain. It is anchored to the endoplasmic reticulum.[3] This highly conserved gene is found in a variety of vertebrates and invertebrates. Homologs (Lam/Ltc proteins) are found in yeast.[3]
GRAMD1B, also known as KIAA1201, is located in the human genome at 11q24.1.[4] It is located on the + strand and is flanked by a variety of other genes. It spans 269,347 bases.
The most verified isoform, isoform 1, contains 21 exons. There are four validated isoform variants of human GRAMD1B. These consist of truncated 5’ and 3’ regions, resulting in the loss of an exon. One prominent analysis of the mouse gene predicts one form of Gramd1b that is 699 amino acids long.[5]
| Isoform | mRNA length (bp) | Exons | Protein length (aa) | Status | |
|---|---|---|---|---|---|
| 1 | 7927 | 21 | 745 | Validated | |
| 2 | 7906 | 20 | 738 | Validated | |
| 3 | 7636 | 20 | 698 | Validated | |
| 4 | 7561 | 20 | 694 | Validated |
GRAMD1B is an integral membrane protein that contains several domains, motifs and signals.
There are two confirmed cytoplasmic domains within GRAMD1B. The protein gets its name from the GRAM domain, located approximately 100 amino acids from the start codon. The GRAM domain is commonly found in myotubularin family phosphatases and predominantly involved in membrane coupled processes.[6] GRAMD1B also contains the VASt (VAD1 Analog of StAR-related lipid transfer) domain. The VASt domain is predominantly associated with lipid binding domains, such as GRAM. It is most likely to function in binding large hydrophobic ligands and may be specific for sterol.[7] A C-terminal domain in GRAMD1B sits within the lumen of the ER, is predicted to have alpha-helical secondary structure,[8] and is modified by tryptophan C-mannosyaltion.[9]
There are two negative charge clusters, located from amino acids 232-267 and 348-377.[10] The first cluster is not highly conserved, nor is it located in a motif or domain. The second cluster is located directly before the VASt domain and is conserved.
There are three repeat sequence regions, all fairly conserved in orthologs.
| Repeat # | Sets of Repeats | Length (aa) | Location | Similarity Score | |
|---|---|---|---|---|---|
| 1 | 3 | 18 | Within first 100 amino acids | 83.44 | |
| 2 | 2 | 21 | GRAM domain | 77.22 | |
| 3 | 2 | 22 | VASt domain | 67.94 |
| Region | Amino Acids | Isoelectric point[11] | Molecular Weight (kdal)[12] | |
|---|---|---|---|---|
| Human GRAMD1B | 745 | pH of 6.02 | 86.5 | |
| GRAM domain | 94 | pH of 8.27 | 11.3 | |
| VASt domain | 144 | pH of 9.41 | 17.3 | |
| Transmembrane region | 21 | pH of 5.18 | 2.3 |
The protein contains four dileucine motifs, three located within or close to the GRAM domain.[13] A predicted leucine zipper pattern extends through a majority the transmembrane region though it is not a nuclear protein. A SUMOylation site is located directly after the VASt domain.[14] The proteins secondary structure consists of alpha-helices, beta-strands and coils.[15] Beta-strands are mainly located within the two domains, while the alpha-helixes are concentrated near the transmembrane region. Three disulfide bonds are predicted throughout the protein.[16]
GRAMD1B is anchored to in the endoplasmic reticulum by a transmembrane domain.[3] [5]
GRAMD1B is expressed in a variety of tissues. It is most highly expressed in the gonadal tissue, adrenal gland, brain and placenta.[5] [3] [17] It has raised expression rates in adrenal tumors, lung tumors. Developmentally, it is most highly expressed during infancy. The EST profile is supported with experimental data from multiple sources[18]
The ortholog space for GRAMD1B spans a large portion of evolutionary time. GRAMD1B can be found in mammals, bird, fish and invertebrates. Homologous proteins (Lam/Ltc) are found in yeast.[3]
| Genus species | Common Name | Accession Number | Date of Divergence (MYA)[19] | Identity[20] | |
|---|---|---|---|---|---|
| Homo sapiens | Human | NP_001273492.1 | 0 | 100.00% | |
| Aotus nancymaae | Nancy Ma's Night Monkey | XP_012325676.1 | 3.2 | 99.00% | |
| Papio anubis | Olive Baboon | XP_017804515.1 | 29.44 | 97.00% | |
| Castor canadensis | Beaver | XP_020037170.1 | 90 | 98.00% | |
| Octodon degus | Dengu | XP_004636450.1 | 90 | 97.00% | |
| Pantholops hodgsonii | Tibetan Antelope | XP_005958036.1 | 96 | 99.00% | |
| Bos mutus | Domestic Yak | XP_005896826.1 | 96 | 98.00% | |
| Tursiops truncatus | Dolphin | XP_019797543 | 96 | 83.00% | |
| Elephantulus edwardii | Cape Elephant Shrew | XP_006895663.1 | 105 | 98.00% | |
| Gallus gallus | Chicken | XP_015153638.1 | 312 | 93.00% | |
| Calypte anna | Anna's Humming Bird | XP_008490701.1 | 312 | 91.00% | |
| Pygoscelis adeliae | Adelie Penguin | XP_009331694.1 | 312 | 91.00% | |
| Coturnix japonica | Japanese Quail | XP_015739426.1 | 312 | 90.00% | |
| Anolis carolinensis | Carolina Anole | XP_008111963.1 | 312 | 87.00% | |
| Danio rerio | Zebra Fish | XP_009303888.1 | 435 | 73.00% | |
| Callorhinchus milii | Australian Ghost Shark | XP_007894251.1 | 473 | 77.00% | |
| Branchiostoma belcheri | Lancelet | XP_019624725.1 | 684 | 40.00% | |
| Octopus bimaculoides | California Two-Spot Octopus | XP_014769036.1 | 797 | 40.00% | |
| Lingula anatina | Brachiopod | XP_013415578 | 797 | 38.00% | |
| Zootermopsis nevadensis | Termite | KDR17240.1 | 797 | 37.00% | |
| Trachymyrmex cornetzi | Ant | XP_018362289.1 | 797 | 34.00% |
There are four paralogs of GRAMD1B. The most closely related is GRAMD1A while the most distant ortholog is GRAMD2A/GRAMD2.
| Paralog | Sequence Length | Sequence Identity | Date of Divergence (MYA) | |
|---|---|---|---|---|
| GRAMD1A | 724 aa | 46.60% | 421.0 | |
| GRAMD1C | 662 aa | 37.90% | 934.7 | |
| GRAMD2B/GRAMD3 | 491 aa | 18.50% | 1625.6 | |
| GRAMD2A | 353 aa | 16.70% | 1724.2 |
GRAMD2 diverged earliest in history while the most recent split is GRAMD1A. The GRAMD1B gene’s rate of divergence significantly faster than Fibrinogen but is not as high as Cytochrome C.
When the plasma membrane contains high levels of cholesterol, GRAMD1b as well as GRAMD1a and GRAMD1c move to sites of contact between the plasma membrane and the endoplasmic reticulum.[5] GRAMD1 proteins then facilitate the transport of cholesterol into the endoplasmic reticulum.[3] [5] In the case of GRAMD1b, the plasma membrane source of cholesterol is high-density lipoprotein (HDL).[3] [5] The VASt domain is responsible for binding cholesterol while the GRAM domain determines the location of the protein through sensing of cholesterol and binding partially negatively charged lipids in the plasma membrane, especially phosphatidylserine.[5] [21]
GRAMD1b is also implicated in transporting carotenoids within the cell.[22]
Several different proteins have been experimentally confirmed or predicted to interact with GRAMD1B.[23] [24]
| Protein | Interaction identified via | Function | Location | |
|---|---|---|---|---|
| COPA | Experimental | Binds dilysine motifs. Required for budding from the Golgi and retrograde Golgi to ER transport | systolic | |
| SPICE1 | Data Mining | Spindle and centriole associated. Regulates centriole duplication, proper bipolar spindle formation and chromosome congregation in mitosis | nuclear | |
| GTPBP8 | Data Mining | GTP binding protein | unconfirmed | |
| Ywhae | Co-sedimentation | Adapter protein associated with regulating nuclear transport to the cytoplasm | nuclear |
Mutations and other genetic studies link GRAMD1B to neurodevelopmental disorders, such as intellectual disability and schizophrenia.[3] Loss of GRAMD1b results in reduced cholesterol storage in the adrenal gland and serum corticosterone levels in mice.[3] Reduction of GRAMD1B and GRAMD1C suppresses the onset of a form of non-alcoholic fatty liver disease, non-alcoholic steatohepatitis (NASH) in mice.[3]
A study tagging SNPs from chronic lymphocytic leukemia found GRAMD1B to be the second strongest risk allele region.[25] This association is supported through a number of studies[26] [27] The aberrant tri-methylation of histone H3 lysine 27 induces inflammation and has been shown to increase GRAMD1B levels in colon tumors.[28]