Affinage

GEM

GTP-binding protein GEM · UniProt P55040

Round 2 corrected
Length
296 aa
Mass
33.9 kDa
Annotated
2026-04-28
130 papers in source corpus 4 papers cited in narrative 4 extracted findings

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

GEM is a mitogen-induced, immediate-early RGK-family GTPase that localizes to the cytosolic face of the plasma membrane, is phosphorylated on tyrosine, and participates in receptor-mediated signal transduction in T cells and fibroblasts (PMID:7912851). Its G domain binds GDP and GTP with unusually low (micromolar) affinity owing to a distinctive DXWEX motif in switch II that distorts the phosphate-binding site, and its intrinsic GTPase activity is modulated by N- and C-terminal extensions, as revealed by a 2.1 Å crystal structure (PMID:17107948). Ca²⁺/calmodulin binds the C-terminal extension with ~1 nM affinity and inhibits GTP loading, directly coupling calcium signaling to GEM nucleotide cycling (PMID:8810259). GEM also functions as a negative regulator of the Rho–Rho kinase cytoskeletal pathway, inducing cell elongation that is indirectly antagonized by the microtubule-binding activity of tau (PMID:15087445).

Mechanistic history

Synthesis pass · year-by-year structured walk · 4 steps
  1. 1994 High

    Identification of GEM as a mitogen-induced GTPase established the existence of a Ras-related protein linking mitogenic receptor signaling to cell proliferation control.

    Evidence Molecular cloning from stimulated human T cells, subcellular fractionation, tyrosine phosphorylation assay, and overexpression-induced growth arrest in 3T3 fibroblasts

    PMID:7912851

    Open questions at the time
    • Downstream effectors of GEM signaling were not identified
    • The kinase responsible for GEM tyrosine phosphorylation is unknown
    • Whether GEM acts in the GTP- or GDP-bound state for its anti-proliferative effect was not resolved
  2. 1996 High

    Demonstration that Ca²⁺/calmodulin binds the C-terminal extension and inhibits GTP loading revealed a direct regulatory link between calcium signaling and GEM nucleotide cycling.

    Evidence Fluorescence titration with dansyl-CaM, W269G point mutant ablating binding, [³²P]CaM overlay, and GTP-binding inhibition assays with recombinant GST-GEM

    PMID:8810259

    Open questions at the time
    • Physiological consequences of CaM-mediated GTP-loading inhibition in cells were not tested
    • Whether CaM binding affects GEM localization or effector interactions is unknown
  3. 2004 Medium

    Showing that GEM overexpression induces cell elongation through inhibition of the Rho–Rho kinase pathway provided the first defined cytoskeletal effector axis for this GTPase, and revealed an indirect antagonism by tau through microtubule binding.

    Evidence Transcriptomic profiling of tau-KO mouse brain, overexpression in CHO cells, co-expression rescue with tau and MAPs, direct binding assay (negative)

    PMID:15087445

    Open questions at the time
    • The direct molecular target through which GEM inhibits Rho–Rho kinase signaling was not identified
    • Reliance on overexpression in a single cell type limits generalizability
    • Whether endogenous GEM levels are sufficient to modulate cytoskeletal organization in neurons or T cells is untested
  4. 2006 High

    The 2.1 Å crystal structure of the GEM G domain explained the biochemical basis for its unusually low nucleotide affinity and showed how the N- and C-terminal extensions regulate GTPase activity, providing a structural framework for understanding RGK-family divergence from classical Ras.

    Evidence X-ray crystallography of truncated GEM·Mg·GDP complex, nucleotide-binding and GTPase activity assays with truncation mutants

    PMID:17107948

    Open questions at the time
    • No structure of full-length GEM or GEM bound to an effector or calmodulin is available
    • Whether the GTP-bound conformation differs sufficiently to act as a classical switch remains unresolved
    • The structural basis of membrane association is not captured in the truncated construct

Open questions

Synthesis pass · forward-looking unresolved questions
  • The direct effector(s) mediating GEM's anti-proliferative and cytoskeletal functions, and the in vivo physiological roles of GEM in immune cells and neurons, remain undefined.
  • No GEM effector protein has been identified by direct binding
  • Loss-of-function studies (knockout, knockdown) in physiologically relevant cell types are lacking
  • Regulation of GEM by upstream kinases is uncharacterized

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0003924 GTPase activity 2
Localization
GO:0005886 plasma membrane 1
Pathway
R-HSA-162582 Signal Transduction 2
Partners

Evidence

Reading pass · 4 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
1994 GEM was identified as a mitogen-induced immediate-early gene encoding a 35 kDa GTP-binding protein (Ras-family, RGK subfamily) expressed in human peripheral blood T cells following mitogenic stimulation. GEM protein was found to be phosphorylated on tyrosine residues, localized to the cytosolic face of the plasma membrane, and deregulated expression prevented proliferation of normal and transformed 3T3 cells, indicating a role in receptor-mediated signal transduction. Molecular cloning, subcellular fractionation, tyrosine phosphorylation assay, GTP-binding assay, proliferation assay (overexpression in 3T3 cells) Science High 7912851
1996 Calmodulin (CaM) binds to the C-terminal extension of GEM/Kir in a strict Ca2+-dependent manner with ~1 nM affinity, and this binding inhibits GTP binding to GEM. A single point mutation W269G in the CaM-binding domain abolished the interaction. Full-length GEM and Rad proteins were confirmed to bind CaM by a [32P]CaM overlay technique. This establishes a direct link between Ca2+/CaM signaling and the RGK GTPase. Fluorescence spectrometry (dansyl-CaM titration), site-directed mutagenesis (W269G), [32P]CaM overlay assay, GTP-binding inhibition assay with GST-fusion proteins The Journal of Biological Chemistry High 8810259
2006 Crystal structure of a truncated human GEM protein (G domain plus first part of C-terminal extension) complexed with Mg·GDP was solved at 2.1 Å resolution. The G-domain fold is similar to other Ras GTPases, but the DXWEX motif in switch II (characteristic of RGK proteins) distorts switch I and the phosphate-binding site. The C-terminal extension adopts an α-helical conformation extending along the α5 helix and interacting with the interswitch. GEM's affinities for GDP and GTP are in the micromolar range (much lower than H-Ras), and GTPase activity is higher than H-Ras and regulated by both N- and C-terminal extensions. X-ray crystallography (2.1 Å), biochemical nucleotide-binding assays, GTPase activity assays with truncation mutants The Journal of Biological Chemistry High 17107948
2004 GEM GTPase expression was upregulated in tau-deficient mouse brains. Overexpression of GEM GTPase in CHO cells (which lack tau) induced marked cell elongation, acting as a negative regulator of the Rho–Rho kinase pathway for cytoskeletal organization. Co-expression of tau antagonized this elongation effect, an activity attributed to tau's microtubule-binding domain (homologous domains of MAP2 and MAP4 showed similar antagonism). Tau did not bind directly to GEM GTPase, indicating the antagonism is indirect, mediated through microtubule binding. Transcriptomic profiling (tau-KO mouse brain, ~11,000 mRNAs), transient overexpression in CHO cells, co-expression rescue experiments, direct binding assay (negative result), domain mapping The Journal of Biological Chemistry Medium 15087445

Source papers

Stage 0 corpus · 130 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2002 Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Proceedings of the National Academy of Sciences of the United States of America 1479 12477932
2015 The BioPlex Network: A Systematic Exploration of the Human Interactome. Cell 1118 26186194
2017 Architecture of the human interactome defines protein communities and disease networks. Nature 1085 28514442
2015 A human interactome in three quantitative dimensions organized by stoichiometries and abundances. Cell 1015 26496610
2014 A proteome-scale map of the human interactome network. Cell 977 25416956
2020 A reference map of the human binary protein interactome. Nature 849 32296183
1998 Geminin, an inhibitor of DNA replication, is degraded during mitosis. Cell 765 9635433
2003 Complete sequencing and characterization of 21,243 full-length human cDNAs. Nature genetics 754 14702039
2001 KIR: diverse, rapidly evolving receptors of innate and adaptive immunity. Annual review of immunology 742 11861603
2021 Dual proteome-scale networks reveal cell-specific remodeling of the human interactome. Cell 705 33961781
2011 Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Briefings in bioinformatics 656 21873635
2000 Inhibition of eukaryotic DNA replication by geminin binding to Cdt1. Science (New York, N.Y.) 604 11125146
2000 Plasticity in the organization and sequences of human KIR/ILT gene families. Proceedings of the National Academy of Sciences of the United States of America 505 10781084
1994 Oligo-capping: a simple method to replace the cap structure of eukaryotic mRNAs with oligoribonucleotides. Gene 492 8125298
2004 The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). Genome research 438 15489334
2022 OpenCell: Endogenous tagging for the cartography of human cellular organization. Science (New York, N.Y.) 432 35271311
2010 Systematic analysis of human protein complexes identifies chromosome segregation proteins. Science (New York, N.Y.) 421 20360068
2004 Self-assembling protein microarrays. Science (New York, N.Y.) 409 15232106
2015 Panorama of ancient metazoan macromolecular complexes. Nature 407 26344197
1996 Normalization and subtraction: two approaches to facilitate gene discovery. Genome research 401 8889548
2006 Two E3 ubiquitin ligases, SCF-Skp2 and DDB1-Cul4, target human Cdt1 for proteolysis. The EMBO journal 328 16482215
2008 The Yin and Yang of HLA and KIR in human disease. Seminars in immunology 292 18635379
2003 Radiation-mediated proteolysis of CDT1 by CUL4-ROC1 and CSN complexes constitutes a new checkpoint. Nature cell biology 256 14578910
2004 Autonomous regulation of the anaphase-promoting complex couples mitosis to S-phase entry. Nature 248 15558010
2003 The DNA sequence and analysis of human chromosome 6. Nature 242 14574404
2006 KIR and disease: a model system or system of models? Immunological reviews 230 17100885
2006 Inwardly rectifying potassium channels (Kir) in central nervous system glia: a special role for Kir4.1 in glial functions. Journal of cellular and molecular medicine 229 16563220
2010 The extensive polymorphism of KIR genes. Immunology 226 20028428
2007 hORFeome v3.1: a resource of human open reading frames representing over 10,000 human genes. Genomics 222 17207965
2004 Loss of Geminin induces rereplication in the presence of functional p53. The Journal of cell biology 218 15159417
2016 A High-Density Map for Navigating the Human Polycomb Complexome. Cell reports 216 27705803
2022 KIR+CD8+ T cells suppress pathogenic T cells and are active in autoimmune diseases and COVID-19. Science (New York, N.Y.) 211 35258337
2011 Toward an understanding of the protein interaction network of the human liver. Molecular systems biology 207 21988832
2004 Rereplication by depletion of geminin is seen regardless of p53 status and activates a G2/M checkpoint. Molecular and cellular biology 204 15282313
2001 Substrate recognition by the Cdc20 and Cdh1 components of the anaphase-promoting complex. Genes & development 203 11562349
2004 Direct interaction of geminin and Six3 in eye development. Nature 202 14973488
2007 Global diversity and evidence for coevolution of KIR and HLA. Nature genetics 190 17694058
1998 Geminin, a neuralizing molecule that demarcates the future neural plate at the onset of gastrulation. Development (Cambridge, England) 190 9671596
1994 Gem: an induced, immediate early protein belonging to the Ras family. Science (New York, N.Y.) 179 7912851
2005 Understanding how combinations of HLA and KIR genes influence disease. The Journal of experimental medicine 178 15809348
2012 NK cell MHC class I specific receptors (KIR): from biology to clinical intervention. Current opinion in immunology 159 22264929
2002 Distinctive KIR and HLA diversity in a panel of north Indian Hindus. Immunogenetics 133 11904677
2011 Maternal KIR and fetal HLA-C: a fine balance. Journal of leukocyte biology 131 21873457
1994 Perlecan: a gem of a proteoglycan. Matrix biology : journal of the International Society for Matrix Biology 122 7921536
2009 Natural killer cells and cancer: regulation by the killer cell Ig-like receptors (KIR). Cancer biology & therapy 118 19923897
2015 Innovative genomic collaboration using the GENESIS (GEM.app) platform. Human mutation 96 26173844
2006 The impact of variation at the KIR gene cluster on human disease. Current topics in microbiology and immunology 96 16329188
2015 Human KIR repertoires: shaped by genetic diversity and evolution. Immunological reviews 94 26284478
2011 KIR/HLA interactions and pathogen immunity. Journal of biomedicine & biotechnology 79 21629750
2005 The KIR gene family: life in the fast lane of evolution. European journal of immunology 78 15580655
2005 Hanging in the balance. KIR and their role in disease. Molecular interventions 78 16123537
2008 KIR locus polymorphisms: genotyping and disease association analysis. Methods in molecular biology (Clifton, N.J.) 72 18370147
2013 Influence of KIR gene copy number on natural killer cell education. Blood 69 23637128
2014 TLR/NCR/KIR: Which One to Use and When? Frontiers in immunology 65 24678311
2008 Role of KIRs and KIR ligands in hematopoietic transplantation. Current opinion in immunology 64 18675345
2013 Recombinant structures expand and contract inter and intragenic diversification at the KIR locus. BMC genomics 62 23394822
2004 Expression and coexpression of CO2-sensitive Kir channels in brainstem neurons of rats. The Journal of membrane biology 62 15042349
2009 Activating and inhibitory killer immunoglobulin-like receptors (KIR) in haploidentical haemopoietic stem cell transplantation to cure high-risk leukaemias. Clinical and experimental immunology 60 19664139
2017 The role of KIR and HLA interactions in pregnancy complications. Immunogenetics 59 28695287
2006 Killer Ig-like receptor (KIR) genotype and HLA ligand combinations in ulcerative colitis susceptibility. Genes and immunity 55 16929347
2006 KIR gene in ethnic and Mestizo populations from Mexico. Human immunology 54 16698429
2017 Neuroblastoma Patients' KIR and KIR-Ligand Genotypes Influence Clinical Outcome for Dinutuximab-based Immunotherapy: A Report from the Children's Oncology Group. Clinical cancer research : an official journal of the American Association for Cancer Research 51 28972044
2013 Genotype List String: a grammar for describing HLA and KIR genotyping results in a text string. Tissue antigens 50 23849068
1996 Calmodulin binds to and inhibits GTP binding of the ras-like GTPase Kir/Gem. The Journal of biological chemistry 50 8810259
2020 Role of Astrocytic Inwardly Rectifying Potassium (Kir) 4.1 Channels in Epileptogenesis. Frontiers in neurology 49 33424762
2017 Revealing complete complex KIR haplotypes phased by long-read sequencing technology. Genes and immunity 48 28569259
2005 Shaping the human NK cell repertoire: an epigenetic glance at KIR gene regulation. Molecular immunology 47 15607801
2001 The KIR and CD94/NKG2 families of molecules in the rhesus monkey. Immunological reviews 44 11782245
2023 Efficient and accurate KIR and HLA genotyping with massively parallel sequencing data. Genome research 39 37169596
2012 Modulation of the natural killer cell KIR repertoire by cytomegalovirus infection. European journal of immunology 35 23161492
2015 2DL1, 2DL2 and 2DL3 all contribute to KIR phenotype variability on human NK cells. Genes and immunity 34 25950617
2016 How important is NK alloreactivity and KIR in allogeneic transplantation? Best practice & research. Clinical haematology 33 27890259
2014 Phosphoinositide regulation of inward rectifier potassium (Kir) channels. Frontiers in physiology 33 24409153
2014 KIR diversity in Māori and Polynesians: populations in which HLA-B is not a significant KIR ligand. Immunogenetics 33 25139336
2013 Altered Kir and gap junction channels in temporal lobe epilepsy. Neurochemistry international 33 23357483
2006 Biochemical and structural characterization of the gem GTPase. The Journal of biological chemistry 33 17107948
2005 KIR matching in hematopoietic stem cell transplantation. Current opinion in immunology 32 16085405
2012 Activating killer-cell immunoglobulin-like receptors (KIR) and their cognate HLA ligands are significantly increased in autism. Brain, behavior, and immunity 31 22884899
2004 Gem GTPase and tau: morphological changes induced by gem GTPase in cho cells are antagonized by tau. The Journal of biological chemistry 31 15087445
2020 novoPathFinder: a webserver of designing novel-pathway with integrating GEM-model. Nucleic acids research 29 32313937
2018 HLA and KIR Associations of Cervical Neoplasia. The Journal of infectious diseases 28 30099516
2013 Role of HLA, KIR, MICA, and cytokines genes in leprosy. BioMed research international 28 23936864
2010 Distribution of killer cell immunoglobulin-like receptors (KIR) and their HLA-C ligands in two Iranian populations. Immunogenetics 28 19936734
2011 Diversity of the KIR gene cluster in an urban Brazilian population. Immunogenetics 27 21850526
2006 Identification of distal KIR promoters and transcripts. Genes and immunity 27 17159886
2016 Can we make a better match or mismatch with KIR genotyping? Hematology. American Society of Hematology. Education Program 26 27913469
2013 Inward-rectifying potassium (Kir) channels regulate pacemaker activity in spinal nociceptive circuits during early life. The Journal of neuroscience : the official journal of the Society for Neuroscience 26 23426663
2020 Killer cell immunoglobulin-like receptors (KIR) and human leukocyte antigen-C (HLA-C) allorecognition patterns in women with endometriosis. Scientific reports 25 32184413
2020 The Genetic Mechanisms Driving Diversification of the KIR Gene Cluster in Primates. Frontiers in immunology 25 33013938
2003 Expression of KIR and C-type lectin receptors in Behcet's disease. Rheumatology (Oxford, England) 25 14679294
2018 Extensive Alternative Splicing of KIR Transcripts. Frontiers in immunology 24 30564240
2011 Killer cell Ig-like receptor (KIR) 3DL1 down-regulation enhances inhibition of type 1 diabetes by autoantigen-specific regulatory T cells. Proceedings of the National Academy of Sciences of the United States of America 24 21245333
2022 Immunity at maternal-fetal interface: KIR/HLA (Allo)recognition. Immunological reviews 23 35610960
2017 Venom-derived peptides inhibiting Kir channels: Past, present, and future. Neuropharmacology 23 28716449
2015 MHC and KIR Polymorphisms in Rhesus Macaque SIV Infection. Frontiers in immunology 23 26557119
2007 Complexity in cattle KIR genes: transcription and genome analysis. Immunogenetics 23 17450354
2007 A green GEM: intriguing analogies with animal geminin. Trends in cell biology 23 17997094
2021 Association of KIR gene polymorphisms with COVID-19 disease. Clinical immunology (Orlando, Fla.) 22 34929414
2020 Estimation of German KIR Allele Group Haplotype Frequencies. Frontiers in immunology 22 32226430
2020 Significance of KIR like natural killer cell receptors in autoimmune disorders. Clinical immunology (Orlando, Fla.) 22 32376502
2015 Identification of the Conformational transition pathway in PIP2 Opening Kir Channels. Scientific reports 22 26063437
2011 The extreme plasticity of killer cell Ig-like receptor (KIR) haplotypes differentiates rhesus macaques from humans. European journal of immunology 22 21710469
2019 Sequential regiospecific gem-diprenylation of tetrahydroxyxanthone by prenyltransferases from Hypericum sp. The New phytologist 21 30485455
2017 Cancer treatment and the KIR-HLA system: an overview. Clinical and experimental medicine 21 28188495
2011 Molecular determinant-based typing of KIR alleles and KIR ligands. Clinical immunology (Orlando, Fla.) 21 21239231
2024 Full-resolution HLA and KIR gene annotations for human genome assemblies. Genome research 20 38839374
2022 A molecular switch controls the impact of cholesterol on a Kir channel. Proceedings of the National Academy of Sciences of the United States of America 20 35333652
2021 Regulatory KIR+ RA+ T cells accumulate with age and are highly activated during viral respiratory disease. Aging cell 20 34043881
2021 ERAP, KIR, and HLA-C Profile in Recurrent Implantation Failure. Frontiers in immunology 20 34745129
2010 Natural killer-cell KIR repertoire reconstitution after haploidentical SCT. Bone marrow transplantation 20 20173785
2010 The tortoise and the hare: slowly evolving T-cell responses take hastily evolving KIR. Immunology 20 20722764
2006 Inhibitory and activatory KIR gene frequencies in the Polish population. International journal of immunogenetics 20 16712646
2020 The Role of HLA and KIR Immunogenetics in BK Virus Infection after Kidney Transplantation. Viruses 19 33317205
2018 Human and Rhesus Macaque KIR Haplotypes Defined by Their Transcriptomes. Journal of immunology (Baltimore, Md. : 1950) 19 29358278
2015 Characterization of KIR intermediate promoters reveals four promoter types associated with distinct expression patterns of KIR subtypes. Genes and immunity 19 26656451
2013 Identification of a KIR antisense lncRNA expressed by progenitor cells. Genes and immunity 19 23863987
2010 Killer cell immunoglobulin-like receptor (KIR) genes in systemic sclerosis. Clinical and experimental immunology 19 20082621
2010 Differential RNA expression of KIR alleles. Immunogenetics 19 20454893
2005 Methodology and recruitment of probands and their families for the Genes in Myopia (GEM) Study. Ophthalmic epidemiology 19 16283990
2022 High-resolution human KIR genotyping. Immunogenetics 18 35050404
2022 Ion currents through Kir potassium channels are gated by anionic lipids. Nature communications 18 35079013
2020 The combinatorial diversity of KIR and HLA class I allotypes in Peninsular Malaysia. Immunology 18 33283280
2018 Report from the Killer-cell Immunoglobulin-like Receptors (KIR) component of the 17th International HLA and Immunogenetics Workshop. Human immunology 18 30321631
2014 The role of KIR2DS1 in multiple sclerosis--KIR in Portuguese MS patients. Journal of neuroimmunology 18 24529855
2013 Genetic profile of KIR and HLA in southern Chinese Han population. Human immunology 18 24055695
2008 KIR and HLA gene combinations in Vogt-Koyanagi-Harada disease. Human immunology 18 18571006
2004 Role of a KIR/HLA-C allorecognition system in pregnancy. Journal of reproductive immunology 18 15288178
2020 Ascorbic Acid Promotes KIR Demethylation during Early NK Cell Differentiation. Journal of immunology (Baltimore, Md. : 1950) 17 32759296
2018 Nomenclature for the KIR of non-human species. Immunogenetics 17 29869002
2010 Lipids driving protein structure? Evolutionary adaptations in Kir channels. Channels (Austin, Tex.) 17 21150302