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Conserved domains on  [gi|1958763761|ref|XP_038961694|]
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ranBP-type and C3HC4-type zinc finger-containing protein 1 isoform X5 [Rattus norvegicus]

Protein Classification

Ubl_HOIL1 and ZnF_RBZ domain-containing protein( domain architecture ID 10110434)

Ubl_HOIL1 and ZnF_RBZ domain-containing protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Ubl_HOIL1 cd01799
ubiquitin-like (Ubl) domain found in heme-oxidized IRP2 ubiquitin ligase 1 (HOIL-1) and ...
 53-133 5.09e-37

ubiquitin-like (Ubl) domain found in heme-oxidized IRP2 ubiquitin ligase 1 (HOIL-1) and similar proteins; HOIL-1, also termed RBCK1, or HOIL-1L, or RanBP-type and C3HC4-type zinc finger-containing protein 1, HBV-associated factor 4, or Hepatitis B virus X-associated protein 4, or RING finger protein 54 (RNF54), or ubiquitin-conjugating enzyme 7-interacting protein 3, or UbcM4-interacting protein 28 (UIP28), together with E3 ubiquitin-protein ligase RNF31 (also known as HOIP) and SHANK-associated RH domain interacting protein (SHARPIN), forms the E3-ligase complex (also known as linear-ubiquitin-chain assembly complex LUBAC) that regulates NF-kappaB activity and apoptosis through conjugation of linear polyubiquitin chains to NF-kappaB essential modulator (also known as NEMO or IKBKG). HOIL-1 plays a crucial role in TNF-alpha-mediated NF-kappaB activation. It also functions as an ubiquitin-protein ligase E3 that interacts with not only PKCbeta but also PKCzeta. It can recognize heme-oxidized IRP2 (iron regulatory protein2) and is thought to affect the turnover of oxidatively damaged proteins. HOIL-1 contains an N-terminal ubiqutin-like (UBL) domain and an Npl4 zinc-finger (NZF) domain, which regulate the interaction with the LUBAC subunit RNF31 and ubiquitin, respectively. The NZF domain belongs to RanBP2-type zinc finger (zf-RanBP2) domain superfamily. In addition, HOIL-1 has a RBR domain that was previously known as RING-BetweenRING-RING domain or TRIAD [two RING fingers and a DRIL (double RING finger linked)] domain. Based on current understanding of the structural biology of RBR ligases, the nomenclature of RBR has been corrected as RING-BRcat (benign-catalytic)-Rcat (required-for-catalysis) recently. The RBR (RING1-BRcat-Rcat) domain use an auto-inhibitory mechanism to modulate ubiquitination activity, as well as a hybrid mechanism that combines aspects from both RING and HECT E3 ligase function to facilitate the ubiquitination reaction.


:

Pssm-ID: 340497  Cd Length: 81  Bit Score: 125.79  E-value: 5.09e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958763761  53 QDIRLCVSVEDAYMHTVTIWLTVRPDMTVASLKDMVFLDYGFPPSLQQWVVGQRLARDQETLHSHGIRRNGDSAYLYLLS 132
Cdd:cd01799     1 TEISIKVYVEDKSSSSGPITLKVRPHTTIASLKRQIFLEYGFPPSVQRWIIGKRLATDDETLLSYGIKDSGDPAFLYLVS 80


                  .
gi 1958763761 133 A 133
Cdd:cd01799    81 A 81
ZnF_RBZ smart00547
Zinc finger domain; Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. ...
 195-215 2.79e-06

Zinc finger domain; Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. In RanBPs, this domain binds RanGDP.


:

Pssm-ID: 197784 [Multi-domain]  Cd Length: 25  Bit Score: 43.08  E-value: 2.79e-06
                           10        20
                   ....*....|....*....|.
gi 1958763761  195 WQCPGCTFINKPTRPGCEMCC 215
Cdd:smart00547   3 WECPACTFLNFASRSKCFACG 23
 
Name Accession Description Interval E-value
Ubl_HOIL1 cd01799
ubiquitin-like (Ubl) domain found in heme-oxidized IRP2 ubiquitin ligase 1 (HOIL-1) and ...
 53-133 5.09e-37

ubiquitin-like (Ubl) domain found in heme-oxidized IRP2 ubiquitin ligase 1 (HOIL-1) and similar proteins; HOIL-1, also termed RBCK1, or HOIL-1L, or RanBP-type and C3HC4-type zinc finger-containing protein 1, HBV-associated factor 4, or Hepatitis B virus X-associated protein 4, or RING finger protein 54 (RNF54), or ubiquitin-conjugating enzyme 7-interacting protein 3, or UbcM4-interacting protein 28 (UIP28), together with E3 ubiquitin-protein ligase RNF31 (also known as HOIP) and SHANK-associated RH domain interacting protein (SHARPIN), forms the E3-ligase complex (also known as linear-ubiquitin-chain assembly complex LUBAC) that regulates NF-kappaB activity and apoptosis through conjugation of linear polyubiquitin chains to NF-kappaB essential modulator (also known as NEMO or IKBKG). HOIL-1 plays a crucial role in TNF-alpha-mediated NF-kappaB activation. It also functions as an ubiquitin-protein ligase E3 that interacts with not only PKCbeta but also PKCzeta. It can recognize heme-oxidized IRP2 (iron regulatory protein2) and is thought to affect the turnover of oxidatively damaged proteins. HOIL-1 contains an N-terminal ubiqutin-like (UBL) domain and an Npl4 zinc-finger (NZF) domain, which regulate the interaction with the LUBAC subunit RNF31 and ubiquitin, respectively. The NZF domain belongs to RanBP2-type zinc finger (zf-RanBP2) domain superfamily. In addition, HOIL-1 has a RBR domain that was previously known as RING-BetweenRING-RING domain or TRIAD [two RING fingers and a DRIL (double RING finger linked)] domain. Based on current understanding of the structural biology of RBR ligases, the nomenclature of RBR has been corrected as RING-BRcat (benign-catalytic)-Rcat (required-for-catalysis) recently. The RBR (RING1-BRcat-Rcat) domain use an auto-inhibitory mechanism to modulate ubiquitination activity, as well as a hybrid mechanism that combines aspects from both RING and HECT E3 ligase function to facilitate the ubiquitination reaction.


Pssm-ID: 340497  Cd Length: 81  Bit Score: 125.79  E-value: 5.09e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958763761  53 QDIRLCVSVEDAYMHTVTIWLTVRPDMTVASLKDMVFLDYGFPPSLQQWVVGQRLARDQETLHSHGIRRNGDSAYLYLLS 132
Cdd:cd01799     1 TEISIKVYVEDKSSSSGPITLKVRPHTTIASLKRQIFLEYGFPPSVQRWIIGKRLATDDETLLSYGIKDSGDPAFLYLVS 80


                  .
gi 1958763761 133 A 133
Cdd:cd01799    81 A 81
ZnF_RBZ smart00547
Zinc finger domain; Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. ...
 195-215 2.79e-06

Zinc finger domain; Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. In RanBPs, this domain binds RanGDP.


Pssm-ID: 197784 [Multi-domain]  Cd Length: 25  Bit Score: 43.08  E-value: 2.79e-06
                           10        20
                   ....*....|....*....|.
gi 1958763761  195 WQCPGCTFINKPTRPGCEMCC 215
Cdd:smart00547   3 WECPACTFLNFASRSKCFACG 23
zf-RanBP pfam00641
Zn-finger in Ran binding protein and others;
195-214 2.00e-04

Zn-finger in Ran binding protein and others;


Pssm-ID: 395516 [Multi-domain]  Cd Length: 30  Bit Score: 37.72  E-value: 2.00e-04
                          10        20
                  ....*....|....*....|
gi 1958763761 195 WQCPGCTFINKPTRPGCEMC 214
Cdd:pfam00641   5 WDCSKCLVQNFATSTKCVAC 24
ubiquitin pfam00240
Ubiquitin family; This family contains a number of ubiquitin-like proteins: SUMO (smt3 homolog) ...
 70-130 7.50e-03

Ubiquitin family; This family contains a number of ubiquitin-like proteins: SUMO (smt3 homolog), Nedd8, Elongin B, Rub1, and Parkin. A number of them are thought to carry a distinctive five-residue motif termed the proteasome-interacting motif (PIM), which may have a biologically significant role in protein delivery to proteasomes and recruitment of proteasomes to transcription sites.


Pssm-ID: 459726 [Multi-domain]  Cd Length: 72  Bit Score: 34.45  E-value: 7.50e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1958763761  70 TIWLTVRPDMTVASLKDMVFLDYGFPPSLQQWVVGQRLARDQETLHSHGIrRNGDSAYLYL 130
Cdd:pfam00240  10 KITLEVDPTDTVLELKEKIAEKEGVPPEQQRLIYSGKVLEDDQTLGEYGI-EDGSTIHLVL 69
 
Name Accession Description Interval E-value
Ubl_HOIL1 cd01799
ubiquitin-like (Ubl) domain found in heme-oxidized IRP2 ubiquitin ligase 1 (HOIL-1) and ...
 53-133 5.09e-37

ubiquitin-like (Ubl) domain found in heme-oxidized IRP2 ubiquitin ligase 1 (HOIL-1) and similar proteins; HOIL-1, also termed RBCK1, or HOIL-1L, or RanBP-type and C3HC4-type zinc finger-containing protein 1, HBV-associated factor 4, or Hepatitis B virus X-associated protein 4, or RING finger protein 54 (RNF54), or ubiquitin-conjugating enzyme 7-interacting protein 3, or UbcM4-interacting protein 28 (UIP28), together with E3 ubiquitin-protein ligase RNF31 (also known as HOIP) and SHANK-associated RH domain interacting protein (SHARPIN), forms the E3-ligase complex (also known as linear-ubiquitin-chain assembly complex LUBAC) that regulates NF-kappaB activity and apoptosis through conjugation of linear polyubiquitin chains to NF-kappaB essential modulator (also known as NEMO or IKBKG). HOIL-1 plays a crucial role in TNF-alpha-mediated NF-kappaB activation. It also functions as an ubiquitin-protein ligase E3 that interacts with not only PKCbeta but also PKCzeta. It can recognize heme-oxidized IRP2 (iron regulatory protein2) and is thought to affect the turnover of oxidatively damaged proteins. HOIL-1 contains an N-terminal ubiqutin-like (UBL) domain and an Npl4 zinc-finger (NZF) domain, which regulate the interaction with the LUBAC subunit RNF31 and ubiquitin, respectively. The NZF domain belongs to RanBP2-type zinc finger (zf-RanBP2) domain superfamily. In addition, HOIL-1 has a RBR domain that was previously known as RING-BetweenRING-RING domain or TRIAD [two RING fingers and a DRIL (double RING finger linked)] domain. Based on current understanding of the structural biology of RBR ligases, the nomenclature of RBR has been corrected as RING-BRcat (benign-catalytic)-Rcat (required-for-catalysis) recently. The RBR (RING1-BRcat-Rcat) domain use an auto-inhibitory mechanism to modulate ubiquitination activity, as well as a hybrid mechanism that combines aspects from both RING and HECT E3 ligase function to facilitate the ubiquitination reaction.


Pssm-ID: 340497  Cd Length: 81  Bit Score: 125.79  E-value: 5.09e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958763761  53 QDIRLCVSVEDAYMHTVTIWLTVRPDMTVASLKDMVFLDYGFPPSLQQWVVGQRLARDQETLHSHGIRRNGDSAYLYLLS 132
Cdd:cd01799     1 TEISIKVYVEDKSSSSGPITLKVRPHTTIASLKRQIFLEYGFPPSVQRWIIGKRLATDDETLLSYGIKDSGDPAFLYLVS 80


                  .
gi 1958763761 133 A 133
Cdd:cd01799    81 A 81
Ubl_ubiquitin_like cd17039
ubiquitin-like (Ubl) domain found in ubiquitin and ubiquitin-like Ubl proteins; Ubiquitin-like ...
 65-129 5.84e-11

ubiquitin-like (Ubl) domain found in ubiquitin and ubiquitin-like Ubl proteins; Ubiquitin-like (Ubl) proteins have a similar ubiquitin (Ub) beta-grasp fold and attach to other proteins in a Ubl manner but with biochemically distinct roles. Ub and Ubl proteins conjugate and deconjugate via ligases and peptidases to covalently modify target polypeptides. Some Ubl domains have adaptor roles in Ub-signaling by mediating protein-protein interaction. Prokaryotic sulfur carrier proteins are Ub-related proteins that can be activated in an ATP-dependent manner. Polyubiquitination signals for a diverse set of cellular events via different isopeptide linkages formed between the C terminus of one ubiquitin (Ub) and the epsilon-amine of K6, K11, K27, K29, K33, K48, or K63 of a second Ub. One of these seven lysine residues (K27, Ub numbering) is conserved in this Ubl_ubiquitin_like family. K27-linked Ub chains are versatile and can be recognized by several downstream receptor proteins. K27 has roles beyond chain linkage, such as in Ubl NEDD8 (which contains many of the same lysines (K6, K11, K27, K33, K48) as Ub) where K27 has a role (other than conjugation) in the mechanism of protein neddylation.


Pssm-ID: 340559 [Multi-domain]  Cd Length: 68  Bit Score: 56.84  E-value: 5.84e-11
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1958763761  65 YMHTVTIWLTVRPDMTVASLKDMVFLDYGFPPSLQQWVVGQRLARDQETLHSHGIrRNGDSAYLY 129
Cdd:cd17039     5 TLDGKTYTVEVDPDDTVADLKEKIEEKTGIPVEQQRLIYNGKELKDDKTLSDYGI-KDGSTIHLV 68
Ubl2_FAT10 cd17053
ubiquitin-like (Ubl) domain 2 found in leukocyte antigen F (HLA-F) adjacent transcript 10 ...
 70-128 1.68e-07

ubiquitin-like (Ubl) domain 2 found in leukocyte antigen F (HLA-F) adjacent transcript 10 (FAT10) and similar proteins; FAT10, also termed ubiquitin D (UBD), or diubiquitin, is a cytokine-inducible ubiquitin-like (Ubl) modifer that is highly expressed in the thymus, and targets substrates covalently for 26S proteasomal degradation. It is also associated with cancer development, antigen processing and antimicrobial defense, chromosomal stability and cell cycle regulation. FAT10 is presented on immune cells and under the inflammatory conditions, is synergistically induced by interferon gamma (IFNgamma) and tumor necrosis factor (TNFalpha) in the non-immune (liver parenchymal) cells. FAT10 contains two Ubl domains. The family corresponds to the second Ubl domain of FAT10. Some family members contain only one Ubl domain.


Pssm-ID: 340573  Cd Length: 71  Bit Score: 47.34  E-value: 1.68e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1958763761  70 TIWLTVRPDMTVASLKDMVFLDYGFPPSlQQWVV--GQRLARDQETLHSHGIrRNGDSAYL 128
Cdd:cd17053    12 VHTLQVSRSTTVAQVKAMIEDQSGVPPN-EQILVynGKRLEDGDKTLGEYGI-KTGDTLYL 70
ZnF_RBZ smart00547
Zinc finger domain; Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. ...
 195-215 2.79e-06

Zinc finger domain; Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. In RanBPs, this domain binds RanGDP.


Pssm-ID: 197784 [Multi-domain]  Cd Length: 25  Bit Score: 43.08  E-value: 2.79e-06
                           10        20
                   ....*....|....*....|.
gi 1958763761  195 WQCPGCTFINKPTRPGCEMCC 215
Cdd:smart00547   3 WECPACTFLNFASRSKCFACG 23
zf-RanBP pfam00641
Zn-finger in Ran binding protein and others;
195-214 2.00e-04

Zn-finger in Ran binding protein and others;


Pssm-ID: 395516 [Multi-domain]  Cd Length: 30  Bit Score: 37.72  E-value: 2.00e-04
                          10        20
                  ....*....|....*....|
gi 1958763761 195 WQCPGCTFINKPTRPGCEMC 214
Cdd:pfam00641   5 WDCSKCLVQNFATSTKCVAC 24
Ubl_Ddi1_like cd01796
ubiquitin-like (Ubl) domain found in the eukaryotic Ddi1 family; The eukaryotic Ddi1 family, ...
 73-124 2.95e-04

ubiquitin-like (Ubl) domain found in the eukaryotic Ddi1 family; The eukaryotic Ddi1 family, including yeast aspartyl protease DNA-damage inducible 1 (Ddi1) and Ddi1-like proteins from vertebrates and other eukaryotes, has been characterized by containing an N-terminal ubiquitin-like (Ubl) domain and a conserved retroviral aspartyl-protease-like domain (RVP) that is important in cell-cycle control. Yeast Ddi1 and many family members also contain a C-terminal ubiquitin-association (UBA) domain, however, Ddi1-like proteins from all vertebrates lack the UBA domain. Ddi1, also termed v-SNARE-master 1 (Vsm1), is an ubiquitin receptor involved in the cell cycle and late secretory pathway in Saccharomyces cerevisiae. It functions as an UBA-Ubl shuttle protein that is required for the proteasome to enable ubiquitin-dependent degradation of its ligands. For instance, Ddi1 plays an essential role in the final stages of proteasomal degradation of Ho endonuclease and of its cognate FBP, Ufo1. Moreover, Ddi1 and its associated protein Rad23p play a cooperative role as negative regulators in yeast PHO pathway. This family also includes mammalian regulatory solute carrier protein family 1 member 1 (RSC1A1), also termed transporter regulator RS1 (RS1), which mediates transcriptional and post-transcriptional regulation of Na(+)-D-glucose cotransporter SGLT1. Ddi1-like proteins play a significant role in cell cycle control, growth control, and trafficking in yeast and may play a crucial role in embryogenesis in higher eukaryotes.


Pssm-ID: 340494 [Multi-domain]  Cd Length: 73  Bit Score: 38.31  E-value: 2.95e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1958763761  73 LTVRPDMTVASLKDMVFLDYGFPPSLQQ-WVVGQRLARDQETLHSHGIrRNGD 124
Cdd:cd01796    16 LEVSPDMTLEDLKALCEAETGIPAAEQVlLHNGQPLTDDKKTLEALGL-KDGD 67
ubiquitin pfam00240
Ubiquitin family; This family contains a number of ubiquitin-like proteins: SUMO (smt3 homolog) ...
 70-130 7.50e-03

Ubiquitin family; This family contains a number of ubiquitin-like proteins: SUMO (smt3 homolog), Nedd8, Elongin B, Rub1, and Parkin. A number of them are thought to carry a distinctive five-residue motif termed the proteasome-interacting motif (PIM), which may have a biologically significant role in protein delivery to proteasomes and recruitment of proteasomes to transcription sites.


Pssm-ID: 459726 [Multi-domain]  Cd Length: 72  Bit Score: 34.45  E-value: 7.50e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1958763761  70 TIWLTVRPDMTVASLKDMVFLDYGFPPSLQQWVVGQRLARDQETLHSHGIrRNGDSAYLYL 130
Cdd:pfam00240  10 KITLEVDPTDTVLELKEKIAEKEGVPPEQQRLIYSGKVLEDDQTLGEYGI-EDGSTIHLVL 69
Ubl_Dsk2p_like cd16106
ubiquitin-like (Ubl) domain found in Saccharomyces cerevisiae proteasome interacting protein ...
 73-119 7.68e-03

ubiquitin-like (Ubl) domain found in Saccharomyces cerevisiae proteasome interacting protein Dsk2p and similar proteins; The family contains several fungal multiubiquitin receptors, including Saccharomyces cerevisiae Dsk2p and Schizosaccharomyces pombe Dph1p, both of which have been characterized as shuttle proteins transporting ubiquitinated substrates destined for degradation from the E3 ligase to the 26S proteasome. They interact with the proteasome through their N-terminal ubiquitin-like domain (Ubl) and with ubiquitin (Ub) through their C-terminal Ub-associated domain (UBA). S. cerevisiae Dsk2p is a nuclear-enriched protein that may involve in the ubiquitin-proteasome proteolytic pathway through interacting with K48-linked polyubiquitin and the proteasome. Moreover, it has been implicated in spindle pole duplication through assisting in Cdc31 assembly into the new spindle pole body (SPB). S. pombe Dph1p is an ubiquitin (Ub0 receptor working in concert with the class V myosin, Myo52, to target the degradation of the S. pombe CLIP-170 homolog, Tip1. It also can protect Ub chains against disassembly by deubiquitinating enzymes.


Pssm-ID: 340523 [Multi-domain]  Cd Length: 73  Bit Score: 34.54  E-value: 7.68e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1958763761  73 LTVRPDMTVASLKDMVFLDYGFPPSLQQWVVGQRLARDQETLHSHGI 119
Cdd:cd16106    15 VEVEPDATVLELKELIAEKSDIPAEQQRLIYKGKILKDEETLSSYKI 61
 
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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