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Conserved domains on  [gi|8131967|gb|AAF73156|]
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ING1-like tumor suppressor protein [Homo sapiens]

Protein Classification

PHD finger domain-containing protein( domain architecture ID 366290)

PHD (plant homeodomain) finger domain-containing protein

Gene Ontology:  GO:0008270|GO:0005515
PubMed:  16297627|21514168

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
PHD_SF super family cl22851
PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) ...
1-36 1.57e-11

PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) finger typically characterized as Cys4HisCys3, and a non-canonical extended PHD finger, characterized as Cys2HisCys5HisCys2His. Variations include the RAG2 PHD finger characterized by Cys3His2Cys2His and the PHD finger 5 found in nuclear receptor-binding SET domain-containing proteins characterized by Cys4HisCys2His. The PHD finger is also termed LAP (leukemia-associated protein) motif or TTC (trithorax consensus) domain. Single or multiple copies of PHD fingers have been found in a variety of eukaryotic proteins involved in the control of gene transcription and chromatin dynamics. PHD fingers can recognize the unmodified and modified histone H3 tail, and some have been found to interact with non-histone proteins. They also function as epigenome readers controlling gene expression through molecular recruitment of multi-protein complexes of chromatin regulators and transcription factors. The PHD finger domain SF is structurally similar to the RING and FYVE_like superfamilies.


The actual alignment was detected with superfamily member cd15682:

Pssm-ID: 473978 [Multi-domain]  Cd Length: 49  Bit Score: 51.93  E-value: 1.57e-11
                       10        20        30
               ....*....|....*....|....*....|....*..
gi 8131967   1 MIRCDNE-CPIEWFRFSCVSLNHKPKRKWYCSRCRGK 36
Cdd:cd15682 13 MIGCDNDeCPIEWFHFSCVGLNHKPKGKWYCPKCRGE 49
 
Name Accession Description Interval E-value
PHD_ING1 cd15682
PHD finger found in inhibitor of growth protein 1 (ING1); ING1 is an epigenetic regulator and ...
1-36 1.57e-11

PHD finger found in inhibitor of growth protein 1 (ING1); ING1 is an epigenetic regulator and a type II tumor suppressor that impacts cell growth, aging, apoptosis, and DNA repair, by affecting chromatin conformation and gene expression. It acts as a reader of the active chromatin mark, the trimethylation of histone H3 lysine 4 (H3K4me3). It binds and directs Growth arrest and DNA damage inducible protein 45 a (Gadd45a) to target sites, thus linking the histone code with DNA demethylation. It interacts with the proliferating cell nuclear antigen (PCNA) via the PCNA-interacting protein (PIP) domain in a UV-inducible manner. It also interacts with a PCNA-interacting protein, p15 (PAF). Moreover, ING1 associates with members of the 14-3-3 family, which is necessary for the cytoplasmic relocalization. Endogenous ING1 protein specifically interacts with the pro-apoptotic BCL2 family member BAX and colocalizes with BAX in a UV-inducible manner. It stabilizes the p53 tumor suppressor by inhibiting polyubiquitination of multi-monoubiquitinated forms via interaction with and colocalization of the herpesvirus-associated ubiquitin-specific protease (HAUSP)-deubiquitinase with p53. It is also involved in trichostatin A-induced apoptosis and caspase 3 signaling in p53-deficient glioblastoma cells. In addition, tyrosine kinase Src can bind phosphorylate ING1 and further regulates its activity. ING1 contains an N-terminal ING domain and a C-terminal plant homeodomain (PHD) finger.


Pssm-ID: 277152 [Multi-domain]  Cd Length: 49  Bit Score: 51.93  E-value: 1.57e-11
                       10        20        30
               ....*....|....*....|....*....|....*..
gi 8131967   1 MIRCDNE-CPIEWFRFSCVSLNHKPKRKWYCSRCRGK 36
Cdd:cd15682 13 MIGCDNDeCPIEWFHFSCVGLNHKPKGKWYCPKCRGE 49
TNG2 COG5034
Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics];
1-34 3.41e-10

Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics];


Pssm-ID: 227367 [Multi-domain]  Cd Length: 271  Bit Score: 51.86  E-value: 3.41e-10
                        10        20        30
                ....*....|....*....|....*....|....*
gi 8131967    1 MIRCDNE-CPIEWFRFSCVSLNHKPKRKWYCSRCR 34
Cdd:COG5034 234 MVACDNAnCKREWFHLECVGLKEPPKGKWYCPECK 268
 
Name Accession Description Interval E-value
PHD_ING1 cd15682
PHD finger found in inhibitor of growth protein 1 (ING1); ING1 is an epigenetic regulator and ...
1-36 1.57e-11

PHD finger found in inhibitor of growth protein 1 (ING1); ING1 is an epigenetic regulator and a type II tumor suppressor that impacts cell growth, aging, apoptosis, and DNA repair, by affecting chromatin conformation and gene expression. It acts as a reader of the active chromatin mark, the trimethylation of histone H3 lysine 4 (H3K4me3). It binds and directs Growth arrest and DNA damage inducible protein 45 a (Gadd45a) to target sites, thus linking the histone code with DNA demethylation. It interacts with the proliferating cell nuclear antigen (PCNA) via the PCNA-interacting protein (PIP) domain in a UV-inducible manner. It also interacts with a PCNA-interacting protein, p15 (PAF). Moreover, ING1 associates with members of the 14-3-3 family, which is necessary for the cytoplasmic relocalization. Endogenous ING1 protein specifically interacts with the pro-apoptotic BCL2 family member BAX and colocalizes with BAX in a UV-inducible manner. It stabilizes the p53 tumor suppressor by inhibiting polyubiquitination of multi-monoubiquitinated forms via interaction with and colocalization of the herpesvirus-associated ubiquitin-specific protease (HAUSP)-deubiquitinase with p53. It is also involved in trichostatin A-induced apoptosis and caspase 3 signaling in p53-deficient glioblastoma cells. In addition, tyrosine kinase Src can bind phosphorylate ING1 and further regulates its activity. ING1 contains an N-terminal ING domain and a C-terminal plant homeodomain (PHD) finger.


Pssm-ID: 277152 [Multi-domain]  Cd Length: 49  Bit Score: 51.93  E-value: 1.57e-11
                       10        20        30
               ....*....|....*....|....*....|....*..
gi 8131967   1 MIRCDNE-CPIEWFRFSCVSLNHKPKRKWYCSRCRGK 36
Cdd:cd15682 13 MIGCDNDeCPIEWFHFSCVGLNHKPKGKWYCPKCRGE 49
PHD_ING1_2 cd15584
PHD finger found in inhibitor of growth protein 1 (ING1) and 2 (ING2); ING1 is an epigenetic ...
1-33 3.55e-11

PHD finger found in inhibitor of growth protein 1 (ING1) and 2 (ING2); ING1 is an epigenetic regulator and a type II tumor suppressor that impacts cell growth, aging, apoptosis, and DNA repair, by affecting chromatin conformation and gene expression. It acts as a reader of the active chromatin mark, the trimethylation of histone H3 lysine 4 (H3K4me3). It binds and directs Growth arrest and DNA damage inducible protein 45 a (Gadd45a) to target sites, thus linking the histone code with DNA demethylation. It interacts with the proliferating cell nuclear antigen (PCNA) via the PCNA-interacting protein (PIP) domain in a UV-inducible manner. It also interacts with a PCNA-interacting protein, p15 (PAF). Moreover, ING1 associates with members of the 14-3-3 family, which is necessary for cytoplasmic relocalization. Endogenous ING1 protein specifically interacts with the pro-apoptotic BCL2 family member BAX and colocalizes with BAX in a UV-inducible manner. It stabilizes the p53 tumor suppressor by inhibiting polyubiquitination of multi-monoubiquitinated forms via interaction with and colocalization of the herpesvirus-associated ubiquitin-specific protease (HAUSP)-deubiquitinase with p53. It is also involved in trichostatin A-induced apoptosis and caspase 3 signaling in p53-deficient glioblastoma cells. In addition, tyrosine kinase Src can bind and phosphorylate ING1 and further regulates its activity. ING2, also termed inhibitor of growth 1-like protein (ING1Lp), or p32, or p33ING2, belongs to the inhibitor of growth (ING) family of type II tumor suppressors. It is a core component of a multi-factor chromatin-modifying complex containing the transcriptional co-repressor SIN3A and histone deacetylase 1 (HDAC1). It has been implicated in the control of cell cycle, in genome stability, and in muscle differentiation. ING2 independently interacts with H3K4me3 (Histone H3 trimethylated on lysine 4) and PtdIns(5)P, and modulates crosstalk between lysine methylation and lysine acetylation on histone proteins through association with chromatin in the presence of DNA damage. It collaborates with SnoN to mediate transforming growth factor (TGF)-beta-induced Smad-dependent transcription and cellular responses. It is upregulated in colon cancer and increases invasion by enhanced MMP13 expression. It also acts as a cofactor of p300 for p53 acetylation and plays a positive regulatory role during p53-mediated replicative senescence. Both ING1 and ING2 contain an N-terminal ING domain and a C-terminal plant homeodomain (PHD) finger.


Pssm-ID: 277059 [Multi-domain]  Cd Length: 45  Bit Score: 50.91  E-value: 3.55e-11
                       10        20        30
               ....*....|....*....|....*....|....
gi 8131967   1 MIRCDN-ECPIEWFRFSCVSLNHKPKRKWYCSRC 33
Cdd:cd15584 12 MIGCDNdECPIEWFHFSCVGLTHKPKGKWYCPKC 45
PHD_ING2 cd15683
PHD finger found in inhibitor of growth protein 2 (ING2); ING2, also termed inhibitor of ...
1-35 9.74e-11

PHD finger found in inhibitor of growth protein 2 (ING2); ING2, also termed inhibitor of growth 1-like protein (ING1Lp), or p32, or p33ING2, is one member of the inhibitor of growth (ING) family of type II tumor suppressors. It is a core component of a multi-factor chromatin-modifying complex containing the transcriptional co-repressor SIN3A and histone deacetylase 1 (HDAC1). It has been implicated in the control of cell cycle, in genome stability, and in muscle differentiation. ING2 independently interacts with H3K4me3 (Histone H3 trimethylated on lysine 4) and PtdIns(5)P, and modulates crosstalk between lysine methylation and lysine acetylation on histone proteins through association with chromatin in the presence of DNA damage. It collaborates with SnoN to mediate transforming growth factor (TGF)-beta-induced Smad-dependent transcription and cellular responses. It is upregulated in colon cancer and increases invasion by enhanced MMP13 expression. It also acts as a cofactor of p300 for p53 acetylation and plays a positive regulatory role during p53-mediated replicative senescence. ING2 contains an N-terminal ING domain and a C-terminal plant homeodomain (PHD) finger.


Pssm-ID: 277153 [Multi-domain]  Cd Length: 49  Bit Score: 50.02  E-value: 9.74e-11
                       10        20        30
               ....*....|....*....|....*....|....*.
gi 8131967   1 MIRCDNE-CPIEWFRFSCVSLNHKPKRKWYCSRCRG 35
Cdd:cd15683 13 MIGCDNEqCPIEWFHFSCVGLTYKPKGKWYCPKCRG 48
TNG2 COG5034
Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics];
1-34 3.41e-10

Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics];


Pssm-ID: 227367 [Multi-domain]  Cd Length: 271  Bit Score: 51.86  E-value: 3.41e-10
                        10        20        30
                ....*....|....*....|....*....|....*
gi 8131967    1 MIRCDNE-CPIEWFRFSCVSLNHKPKRKWYCSRCR 34
Cdd:COG5034 234 MVACDNAnCKREWFHLECVGLKEPPKGKWYCPECK 268
PHD_ING4_5 cd15586
PHD finger found in inhibitor of growth protein 4 (ING4) and 5 (ING5); ING4, also termed ...
1-33 7.53e-10

PHD finger found in inhibitor of growth protein 4 (ING4) and 5 (ING5); ING4, also termed p29ING4, and ING5, also termed p28ING5, belong to the inhibitor of growth (ING) family of type II tumor suppressors. ING4 acts as an E3 ubiquitin ligase to induce ubiquitination of the p65 subunit of NF-kappaB and inhibit the transactivation of NF-kappaB target genes. It also induces apoptosis through a p53 dependent pathway, including increasing p53 acetylation, inhibiting Mdm2-mediated degradation of p53 and enhancing the expression of p53 responsive genes both at the transcriptional and post-translational levels. Moreover, ING4 can inhibit the translation of proto-oncogene MYC by interacting with AUF1. It also regulates other transcription factors, such as hypoxia-inducible factor (HIF). ING5 is a Tip60 cofactor that acetylates p53 at K120 and subsequently activates the expression of p53-dependent apoptotic genes in response to DNA damage. Aberrant ING5 expression may contribute to pathogenesis, growth, and invasion of gastric carcinomas and colorectal cancer. ING5 can physically interact with p300 and p53 in vivo, and its overexpression induces apoptosis in colorectal cancer cells. It also associates with cyclin A1 (INCA1) and functions as a growth suppressor with suppressed expression in Acute Myeloid Leukemia (AML). Moreover, ING5 translocation from the nucleus to the cytoplasm might be a critical event for carcinogenesis and tumor progression in human head and neck squamous cell carcinoma. Both ING4 and ING5 contain an N-terminal ING histone-binding domain and a C-terminal plant homeodomain (PHD) finger. They associate with histone acetyltransferase (HAT) complexes containing MOZ (monocytic leukemia zinc finger protein)/MORF (MOZ-related factor) and HBO1, and further direct the MOZ/MORF and HBO1 complexes to chromatin.


Pssm-ID: 277061 [Multi-domain]  Cd Length: 45  Bit Score: 47.57  E-value: 7.53e-10
                       10        20        30
               ....*....|....*....|....*....|....
gi 8131967   1 MIRCDN-ECPIEWFRFSCVSLNHKPKRKWYCSRC 33
Cdd:cd15586 12 MIGCDNpDCPIEWFHFACVGLTTKPKGKWFCPRC 45
PHD_ING cd15505
PHD finger found in the inhibitor of growth (ING) protein family; The ING family includes a ...
1-33 2.89e-09

PHD finger found in the inhibitor of growth (ING) protein family; The ING family includes a group of tumor suppressors, ING1-5, which act as readers and writers of the histone epigenetic code, affecting DNA damage response, chromatin remodeling, cellular senescence, differentiation, cell cycle regulation and apoptosis. They may have a general role in mediating the cellular response to genotoxic stress through binding to and regulating the activities of histone acetyltransferase (HAT) and histone deacetylase (HDAC) chromatin remodeling complexes. All ING proteins contain an N-terminal ING domain and a C-terminal plant homeodomain (PHD) finger.


Pssm-ID: 276980 [Multi-domain]  Cd Length: 45  Bit Score: 46.14  E-value: 2.89e-09
                       10        20        30
               ....*....|....*....|....*....|....
gi 8131967   1 MIRCDN-ECPIEWFRFSCVSLNHKPKRKWYCSRC 33
Cdd:cd15505 12 MVACDNpNCPIEWFHFECVGLTAKPKGKWYCPEC 45
PHD_ING5 cd15685
PHD finger found in inhibitor of growth protein 5 (ING5); ING5, also termed p28ING5, is one ...
1-33 1.17e-08

PHD finger found in inhibitor of growth protein 5 (ING5); ING5, also termed p28ING5, is one member of the inhibitor of growth (ING) family of type II tumor suppressors. It acts as a Tip60 cofactor that acetylates p53 at K120 and subsequently activates the expression of p53-dependent apoptotic genes in response to DNA damage. Aberrant ING5 expression may contribute to pathogenesis, growth, and invasion of gastric carcinomas and colorectal cancer. ING5 can physically interact with p300 and p53 in vivo, and its overexpression induces apoptosis in colorectal cancer cells. It also associates with cyclin A1 (INCA1) and functions as a growth suppressor with suppressed expression in Acute Myeloid Leukemia (AML). Moreover, ING5 translocation from the nucleus to the cytoplasm might be a critical event for carcinogenesis and tumor progression in human head and neck squamous cell carcinoma. In addition, ING5 associates with histone acetyltransferase (HAT) complexes containing MOZ (monocytic leukemia zinc finger protein)/MORF (MOZ-related factor) and HBO1, and further directs the MOZ/MORF and HBO1 complexes to chromatin. ING5 contains an N-terminal ING histone-binding domain and a C-terminal plant homeodomain (PHD) finger.


Pssm-ID: 277155 [Multi-domain]  Cd Length: 49  Bit Score: 44.66  E-value: 1.17e-08
                       10        20        30
               ....*....|....*....|....*....|....
gi 8131967   1 MIRCDN-ECPIEWFRFSCVSLNHKPKRKWYCSRC 33
Cdd:cd15685 13 MIGCDNpDCPIEWFHFACVDLTTKPKGKWFCPRC 46
PHD_Yng1p_like cd15587
PHD finger found in yeast orthologs of ING tumor suppressor family; The yeast orthologs of the ...
1-33 1.98e-08

PHD finger found in yeast orthologs of ING tumor suppressor family; The yeast orthologs of the plant homeodomain (PHD) finger-containing ING tumor suppressor family consists of chromatin modification-related protein YNG1 (Yng1p), YNG2 (Yng2p), and transcriptional regulatory protein PHO23 (Pho23p). Yng1p, also termed ING1 homolog 1, is one of the components of the NuA3 histone acetyltransferase (HAT) complex. Its PHD finger binding to H3 Trimethylated at K4 (H3K4me3) promotes NuA3 H3 HAT activity at K14 of H3 on chromatin. Yng2p, also termed ESA1-associated factor 4, or ING1 homolog 2, is a subunit of the NuA4 HAT complex. It plays a critical role in intra-S-phase DNA damage response. Pho23p is part of the Rpd3/Sin3 histone deacetylase (HDAC) complex. It is required for the normal function of Rpd3 in the silencing of rDNA, telomeric, and mating-type loci. Yng1p and Pho23p inhibit p53-dependent transcription. In contrast, Yng2p has the opposite effect. All family members contain an N-terminal ING histone-binding domain and a C-terminal PHD finger.


Pssm-ID: 277062 [Multi-domain]  Cd Length: 47  Bit Score: 43.94  E-value: 1.98e-08
                       10        20        30
               ....*....|....*....|....*....|....
gi 8131967   1 MIRCDN-ECPIEWFRFSCVSLNHKPKRKWYCSRC 33
Cdd:cd15587 12 MVACDNpDCKIEWFHFECVGLTETPKGKWYCSDC 45
PHD_ING3 cd15585
PHD finger found in inhibitor of growth protein 3 (ING3) and similar proteins; ING3, also ...
1-33 2.05e-08

PHD finger found in inhibitor of growth protein 3 (ING3) and similar proteins; ING3, also termed p47ING3, is one member of the inhibitor of growth (ING) family of type II tumor suppressors. It is ubiquitously expressed and has been implicated in transcription modulation, cell cycle control, and the induction of apoptosis. It is an important subunit of human NuA4 histone acetyltransferase complex, which regulates the acetylation of histones H2A and H4. Moreover, ING3 promotes ultraviolet (UV)-induced apoptosis through the Fas/caspase-8-dependent pathway in melanoma cells. It physically interacts with subunits of E3 ligase Skp1-Cullin-F-boxprotein complex (SCF complex) and is degraded by the SCF (F-box protein S-phase kinase-associated protein 2, Skp2)-mediated ubiquitin-proteasome system. It also acts as a suppression factor during tumorigenesis and progression of hepatocellular carcinoma (HCC). ING3 contains an N-terminal ING domain and a C-terminal plant homeodomain (PHD) finger.


Pssm-ID: 277060 [Multi-domain]  Cd Length: 45  Bit Score: 43.98  E-value: 2.05e-08
                       10        20        30
               ....*....|....*....|....*....|....
gi 8131967   1 MIRCDNE-CPIEWFRFSCVSLNHKPKRKWYCSRC 33
Cdd:cd15585 12 MVGCDNDdCPIEWFHYGCVGLTEAPKGKWYCPQC 45
PHD_ING4 cd15684
PHD finger found in inhibitor of growth protein 4 (ING4); ING4, also termed p29ING4, is one ...
1-33 4.58e-07

PHD finger found in inhibitor of growth protein 4 (ING4); ING4, also termed p29ING4, is one member of the inhibitor of growth (ING) family of type II tumor suppressors. It acts as an E3 ubiquitin ligase to induce ubiquitination of the p65 subunit of NF-kappaB and inhibit the transactivation of NF-kappaB target genes. It also induces apoptosis through a p53 dependent pathway, including increasing p53 acetylation, inhibiting Mdm2-mediated degradation of p53 and enhancing the expression of p53 responsive genes both at the transcriptional and post-translational levels. Moreover, ING4 can inhibit the translation of proto-oncogene MYC by interacting with AUF1. It also regulates other transcription factors, such as hypoxia-inducible factor (HIF). In addition, ING4 associates with histone acetyltransferase (HAT) complexes containing MOZ (monocytic leukemia zinc finger protein)/MORF (MOZ-related factor) and HBO1, and further directs the MOZ/MORF and HBO1 complexes to chromatin. ING4 contains an N-terminal ING histone-binding domain and a C-terminal plant homeodomain (PHD) finger.


Pssm-ID: 277154 [Multi-domain]  Cd Length: 48  Bit Score: 40.44  E-value: 4.58e-07
                       10        20        30
               ....*....|....*....|....*....|....
gi 8131967   1 MIRCDN-ECPIEWFRFSCVSLNHKPKRKWYCSRC 33
Cdd:cd15684 13 MIGCDNpDCSIEWFHFACVGLTTKPRGKWFCPRC 46
 
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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