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Conserved domains on  [gi|18408968|ref|NP_564924|]
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Ubiquitin-like superfamily protein [Arabidopsis thaliana]

Protein Classification

sumo domain-containing protein( domain architecture ID 10109906)

sumo (small ubiquitin-related modifier) domain-containing protein is involved in post-translational protein modification called sumoylation which covalently attaches to and detaches from other proteins in cells to modify their function.

Gene Ontology:  GO:0016925
PubMed:  15189146

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Ubl_SUMO_like cd01763
ubiquitin-like (Ubl) domain found in small ubiquitin-related modifier (SUMO) and similar ...
 142-211 2.41e-17

ubiquitin-like (Ubl) domain found in small ubiquitin-related modifier (SUMO) and similar proteins; SUMO (also known as "Smt3" and "sentrin" in other organisms) resembles ubiquitin (Ub) in structure, ligation to other proteins, and the mechanism of ligation. Ubiquitin is a protein modifier in eukaryotes that is involved in various cellular processes, including transcriptional regulation, cell cycle control, and DNA repair. Ubiquitination is comprised of a cascade of E1, E2 and E3 enzymes that results in a covalent bond between the C-terminus of Ub and the epsilon-amino group of a substrate lysine. SUMOs, like Ub, are covalently conjugated to lysine residues in a wide variety of target proteins in eukaryotic cells and regulate numerous cellular processes, such as transcription, epigenetic gene control, genomic instability, and protein degradation. The mammalian SUMOs have four paralogs, SUMO1 through SUMO4, which all regulate different cellular functions by conjugating to different proteins. SUMO2-4 are more closely related to each other than to SUMO1.


:

Pssm-ID: 340462 [Multi-domain]  Cd Length: 72  Bit Score: 73.00  E-value: 2.41e-17
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 18408968 142 KIVITIQDKDGQKTL--RVFADEKFERVIKLYTDKAKLDPQNLVFIFDGDKIDPSTTPSELGMEDHDMIEVH 211
Cdd:cd01763   1 KITIKVRGQDGGKKVrfKVKKTTKLKKLFDAYAEKKGLDPDSLRFTFDGERISPNDTPESLGLEDGDIIDVV 72
 
Name Accession Description Interval E-value
Ubl_SUMO_like cd01763
ubiquitin-like (Ubl) domain found in small ubiquitin-related modifier (SUMO) and similar ...
 142-211 2.41e-17

ubiquitin-like (Ubl) domain found in small ubiquitin-related modifier (SUMO) and similar proteins; SUMO (also known as "Smt3" and "sentrin" in other organisms) resembles ubiquitin (Ub) in structure, ligation to other proteins, and the mechanism of ligation. Ubiquitin is a protein modifier in eukaryotes that is involved in various cellular processes, including transcriptional regulation, cell cycle control, and DNA repair. Ubiquitination is comprised of a cascade of E1, E2 and E3 enzymes that results in a covalent bond between the C-terminus of Ub and the epsilon-amino group of a substrate lysine. SUMOs, like Ub, are covalently conjugated to lysine residues in a wide variety of target proteins in eukaryotic cells and regulate numerous cellular processes, such as transcription, epigenetic gene control, genomic instability, and protein degradation. The mammalian SUMOs have four paralogs, SUMO1 through SUMO4, which all regulate different cellular functions by conjugating to different proteins. SUMO2-4 are more closely related to each other than to SUMO1.


Pssm-ID: 340462 [Multi-domain]  Cd Length: 72  Bit Score: 73.00  E-value: 2.41e-17
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 18408968 142 KIVITIQDKDGQKTL--RVFADEKFERVIKLYTDKAKLDPQNLVFIFDGDKIDPSTTPSELGMEDHDMIEVH 211
Cdd:cd01763   1 KITIKVRGQDGGKKVrfKVKKTTKLKKLFDAYAEKKGLDPDSLRFTFDGERISPNDTPESLGLEDGDIIDVV 72
Rad60-SLD pfam11976
Ubiquitin-2 like Rad60 SUMO-like; The small ubiquitin-related modifier SUMO-1 is a Ub/Ubl ...
 143-210 1.86e-10

Ubiquitin-2 like Rad60 SUMO-like; The small ubiquitin-related modifier SUMO-1 is a Ub/Ubl family member, and although SUMO-1 shares structural similarity to Ub, SUMO's cellular functions remain distinct insomuch as SUMO modification alters protein function through changes in activity, cellular localization, or by protecting substrates from ubiquitination. Rad60 family members contain functionally enigmatic, integral SUMO-like domains (SLDs). Despite their divergence from SUMO, each Rad60 SLD interacts with a subset of SUMO pathway enzymes: SLD2 specifically binds the SUMO E2 conjugating enzyme (Ubc9)), whereas SLD1 binds the SUMO E1 (Fub2, also called Uba2) activating and E3 (Pli1, also called Siz1 and Siz2) specificity enzymes. Structural analysis of PDB:2uyz reveals a mechanistic basis for the near-synonymous roles of Rad60 and SUMO in survival of genotoxic stress and suggest unprecedented DNA-damage-response functions for SLDs in regulating SUMOylation. The Rad60 branch of this family is also known as RENi (Rad60-Esc2-Nip45), and biologically it should be two distinct families SUMO and RENi (Rad60-Esc2-Nip45).


Pssm-ID: 403255 [Multi-domain]  Cd Length: 72  Bit Score: 54.87  E-value: 1.86e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18408968   143 IVITIQDKDGQK-TLRVFADEKFERVIKLYTDKAKLDP-QNLVFIFDGDKIDPSTTPSELGMEDHDMIEV 210
Cdd:pfam11976   1 IKIILKGKDGKEvFIKVKPTTTVSKLINAYRKKRGIPPsQQVRLIFDGERLDPNSTVEDLDIEDGDTIDV 70
SMT3 COG5227
Ubiquitin-like protein (sentrin) [Posttranslational modification, protein turnover, chaperones] ...
 109-214 1.66e-07

Ubiquitin-like protein (sentrin) [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 227552  Cd Length: 103  Bit Score: 48.00  E-value: 1.66e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18408968 109 EVEESAKREVEESRNPSSEtaaqlpseptndraKIVITIQDKDGQKTL-RVFADEKFERVIKLYTDKAKLDPQNLVFIFD 187
Cdd:COG5227   5 DSGSEFKTNENPLVKPITK--------------HINLKVVDQDGTELFfKIKKTTTFKKLMDAFSRRQGKNMSSLRFLFD 70

                        90       100
                ....*....|....*....|....*..
gi 18408968 188 GDKIDPSTTPSELGMEDHDMIEVHTKK 214
Cdd:COG5227  71 GKRIDLDQTPGDLDMEDNDEIEAVTEQ 97
 
Name Accession Description Interval E-value
Ubl_SUMO_like cd01763
ubiquitin-like (Ubl) domain found in small ubiquitin-related modifier (SUMO) and similar ...
 142-211 2.41e-17

ubiquitin-like (Ubl) domain found in small ubiquitin-related modifier (SUMO) and similar proteins; SUMO (also known as "Smt3" and "sentrin" in other organisms) resembles ubiquitin (Ub) in structure, ligation to other proteins, and the mechanism of ligation. Ubiquitin is a protein modifier in eukaryotes that is involved in various cellular processes, including transcriptional regulation, cell cycle control, and DNA repair. Ubiquitination is comprised of a cascade of E1, E2 and E3 enzymes that results in a covalent bond between the C-terminus of Ub and the epsilon-amino group of a substrate lysine. SUMOs, like Ub, are covalently conjugated to lysine residues in a wide variety of target proteins in eukaryotic cells and regulate numerous cellular processes, such as transcription, epigenetic gene control, genomic instability, and protein degradation. The mammalian SUMOs have four paralogs, SUMO1 through SUMO4, which all regulate different cellular functions by conjugating to different proteins. SUMO2-4 are more closely related to each other than to SUMO1.


Pssm-ID: 340462 [Multi-domain]  Cd Length: 72  Bit Score: 73.00  E-value: 2.41e-17
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 18408968 142 KIVITIQDKDGQKTL--RVFADEKFERVIKLYTDKAKLDPQNLVFIFDGDKIDPSTTPSELGMEDHDMIEVH 211
Cdd:cd01763   1 KITIKVRGQDGGKKVrfKVKKTTKLKKLFDAYAEKKGLDPDSLRFTFDGERISPNDTPESLGLEDGDIIDVV 72
Rad60-SLD pfam11976
Ubiquitin-2 like Rad60 SUMO-like; The small ubiquitin-related modifier SUMO-1 is a Ub/Ubl ...
 143-210 1.86e-10

Ubiquitin-2 like Rad60 SUMO-like; The small ubiquitin-related modifier SUMO-1 is a Ub/Ubl family member, and although SUMO-1 shares structural similarity to Ub, SUMO's cellular functions remain distinct insomuch as SUMO modification alters protein function through changes in activity, cellular localization, or by protecting substrates from ubiquitination. Rad60 family members contain functionally enigmatic, integral SUMO-like domains (SLDs). Despite their divergence from SUMO, each Rad60 SLD interacts with a subset of SUMO pathway enzymes: SLD2 specifically binds the SUMO E2 conjugating enzyme (Ubc9)), whereas SLD1 binds the SUMO E1 (Fub2, also called Uba2) activating and E3 (Pli1, also called Siz1 and Siz2) specificity enzymes. Structural analysis of PDB:2uyz reveals a mechanistic basis for the near-synonymous roles of Rad60 and SUMO in survival of genotoxic stress and suggest unprecedented DNA-damage-response functions for SLDs in regulating SUMOylation. The Rad60 branch of this family is also known as RENi (Rad60-Esc2-Nip45), and biologically it should be two distinct families SUMO and RENi (Rad60-Esc2-Nip45).


Pssm-ID: 403255 [Multi-domain]  Cd Length: 72  Bit Score: 54.87  E-value: 1.86e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18408968   143 IVITIQDKDGQK-TLRVFADEKFERVIKLYTDKAKLDP-QNLVFIFDGDKIDPSTTPSELGMEDHDMIEV 210
Cdd:pfam11976   1 IKIILKGKDGKEvFIKVKPTTTVSKLINAYRKKRGIPPsQQVRLIFDGERLDPNSTVEDLDIEDGDTIDV 70
Ubl_SLD2_Esc2_like cd17080
SUMO-like domain 2 (SLD2), structurally similar to a beta-grasp ubiquitin-like fold, found in ...
 142-211 5.48e-09

SUMO-like domain 2 (SLD2), structurally similar to a beta-grasp ubiquitin-like fold, found in Saccharomyces cerevisiae establishes silent chromatin protein 2 (Esc2p) and similar proteins; Protein Esc2p belongs to the eukaryotic-specific Rad60-Esc2-Nip45 (RENi) protein family, whose members may act as factors in transcriptional regulation, chromatin silencing and genomic stability, and typically contain an N-terminal polar/charged low-complexity segment and two C-terminal consecutive unique small ubiquitin-related modifier (SUMO)-like domains (SLD1 and SLD2) with beta-grasp fold. Yeast Esc2p was identified as a factor promoting gene silencing. It is also required for genome integrity during DNA replication and sister chromatid cohesion in Saccharomyces cerevisiae. Esc2p promotes Mus81p complex-activity via its SUMO-like and DNA binding domains. It also acts as a novel structure-specific DNA-binding factor implicated in the local regulation of the Srs2p helicase through promoting recombination at sites of stalled replication. In addition, Esc2p specifically promotes the accumulation of SUMOylated Mms21-specific substrates and functions with Mms21p to suppress gross chromosomal rearrangements (GCRs). This family also includes DNA repair protein Rad60p from Schizosaccharomyces pombe. It is a SUMO mimetic and SUMO-targeted ubiquitin ligase (STUbL)-interacting protein that is required for the repair of DNA double strand breaks, recovery from S phase replication arrest, and plays an essential role in cell viability. Like other RENi family members, Rad60p has two SLD domains.


Pssm-ID: 340600  Cd Length: 74  Bit Score: 51.07  E-value: 5.48e-09
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 18408968 142 KIVITIQDKDGQK-TLRVFADEKFERVIKLYTDKAKL--DPQNLVFIFDGDKIDPSTTPSELGMEDHDMIEVH 211
Cdd:cd17080   2 LIKLKLRGKDNKRlSLKVKPSTTLSDLVEAYKIKKKLslAAAKVKLEFDGEPLDLSETVEDLDLEDEDMLEVV 74
Ubl_Smt3_like cd16116
ubiquitin-like (Ubl) domain found in Saccharomyces cerevisiae ubiquitin-like protein Smt3p and ...
 163-211 1.15e-08

ubiquitin-like (Ubl) domain found in Saccharomyces cerevisiae ubiquitin-like protein Smt3p and similar proteins; Smt3 (Suppressor of Mif Two 3) was originally isolated as a high-copy suppressor of a mutation in MIF2, the gene of a centromere binding protein in S. cerevisiae. Smt3p is the yeast homolog of small ubiquitin-related modifier (SUMO) proteins that are involved in post-translational protein modification called SUMOylation, covalently attaching to and detaching from other proteins in cells to modify their function. SUMO resembles ubiquitin (Ub) in its structure, its ability to be ligated to other proteins, as well as in the mechanism of ligation. Ubiquitin is a protein modifier in eukaryotes that is involved in various cellular processes including transcriptional regulation, cell cycle control, and DNA repair. Ubiquitination is comprised of a cascade of E1, E2 and E3 enzymes that results in a covalent bond between the C-terminus of Ub and the epsilon-amino group of a substrate lysine. Smt3p plays essential roles in cell-cycle regulation and chromosome segregation in budding yeast. It interacts with different modification enzymes, and regulates their functions through linking covalently to its targets.


Pssm-ID: 340533 [Multi-domain]  Cd Length: 74  Bit Score: 50.30  E-value: 1.15e-08
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*....
gi 18408968 163 KFERVIKLYTDKAKLDPQNLVFIFDGDKIDPSTTPSELGMEDHDMIEVH 211
Cdd:cd16116  24 PLRKLMEAYCKRQGKSMDSVRFLFDGERIREDQTPEDLGMEDGDEIDAM 72
Ubl_SLD2_NFATC2ip cd17079
SUMO-like domain 2 (SLD2), structurally similar to a beta-grasp ubiquitin-like fold, found in ...
 142-210 1.26e-08

SUMO-like domain 2 (SLD2), structurally similar to a beta-grasp ubiquitin-like fold, found in nuclear factor of activated T-cells 2 interacting protein (NFATC2ip) and similar proteins; NFATC2ip, also termed nuclear factor of activated T cells (NFAT), cytoplasmic, calcineurin dependent 2 interacting protein, or 45 kDa NF-AT-interacting protein, or 45 kDa NFAT-interacting protein (Nip45), or nuclear factor of activated T-cells, or cytoplasmic 2-interacting protein, belongs to the eukaryotic-specific Rad60-Esc2-Nip45 (RENi) protein family. The family members may act as factors in transcriptional regulation, chromatin silencing and genomic stability, and typically contain an N-terminal polar/charged low-complexity segment and two C-terminal consecutive unique small ubiquitin-related modifier (SUMO)-like domains (SLD1 and SLD2) with beta-grasp fold. NFATC2ip was firstly identified as a co-regulator with NFAT and the T helper 2 (Th2)-specific transcription factor, c-Maf, to induce IL-4 production. NFATC2ip has also been involved in cellular differentiation and coordination of the immune response in humans and mice. NFATC2ip SLD2 domain binds to E2 SUMOylation enzyme, Ubc9, in an almost identical manner to that of SUMO and thereby inhibits elongation of poly-SUMO chains.


Pssm-ID: 340599  Cd Length: 73  Bit Score: 50.14  E-value: 1.26e-08
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 18408968 142 KIVITIQ--DKDGQKTLRVFADEKFERVIKLYTDKAKLDPQNLVFIFDGDKIDPSTTPSELGMEDHDMIEV 210
Cdd:cd17079   2 EICLRVQgkEKHSQLEVSVSKTAPLKSLMSQYEEAMGLSGRKLSFFFDGTKLSGKETPADLGMESGDVIEV 72
SMT3 COG5227
Ubiquitin-like protein (sentrin) [Posttranslational modification, protein turnover, chaperones] ...
 109-214 1.66e-07

Ubiquitin-like protein (sentrin) [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 227552  Cd Length: 103  Bit Score: 48.00  E-value: 1.66e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18408968 109 EVEESAKREVEESRNPSSEtaaqlpseptndraKIVITIQDKDGQKTL-RVFADEKFERVIKLYTDKAKLDPQNLVFIFD 187
Cdd:COG5227   5 DSGSEFKTNENPLVKPITK--------------HINLKVVDQDGTELFfKIKKTTTFKKLMDAFSRRQGKNMSSLRFLFD 70

                        90       100
                ....*....|....*....|....*..
gi 18408968 188 GDKIDPSTTPSELGMEDHDMIEVHTKK 214
Cdd:COG5227  71 GKRIDLDQTPGDLDMEDNDEIEAVTEQ 97
Ubl_SUMO2_3_4 cd16115
ubiquitin-like (Ubl) domain found in small ubiquitin-related modifier SUMO-2, SUMO-3, SUMO-4, ...
 164-210 4.94e-07

ubiquitin-like (Ubl) domain found in small ubiquitin-related modifier SUMO-2, SUMO-3, SUMO-4, and similar proteins; SUMO (also known as "Smt3" and "sentrin" in other organisms) resembles ubiquitin (Ub) in structure, ligation to other proteins and the mechanism of ligation. Ubiquitin is a protein modifier in eukaryotes that is involved in various cellular processes including transcriptional regulation, cell cycle control, and DNA repair. Ubiquitination is comprised of a cascade of E1, E2 and E3 enzymes that results in a covalent bond between the C-terminus of Ub and the epsilon-amino group of a substrate lysine. SUMOs, like Ub, are covalently conjugated to lysine residues in a wide variety of target proteins in eukaryotic cells and regulate numerous cellular processes, such as transcription, epigenetic gene control, genomic instability, and protein degradation. The mammalian SUMOs have four paralogs, SUMO1 through SUMO4. SUMO2 and SUMO3 are more closely related to each other than they are to SUMO1. SUMO2/3 are capable of forming chains on substrate proteins through internal lysine residues. The basic biology of SUMO4 remains unclear. A M55V polymorphism in SUMO4 has been associated with susceptibility to type I diabetes in some genetic studies.


Pssm-ID: 340532 [Multi-domain]  Cd Length: 72  Bit Score: 45.82  E-value: 4.94e-07
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*..
gi 18408968 164 FERVIKLYTDKAKLDPQNLVFIFDGDKIDPSTTPSELGMEDHDMIEV 210
Cdd:cd16115  24 LSKLMKAYCDRQGLSMRQIRFRFDGQPINETDTPAQLEMEDEDTIDV 70
Ubl_SUMO1 cd16114
ubiquitin-like (Ubl) domain found in small ubiquitin-related modifier 1 (SUMO-1) and similar ...
 157-215 2.93e-06

ubiquitin-like (Ubl) domain found in small ubiquitin-related modifier 1 (SUMO-1) and similar proteins; SUMO (also known as "Smt3" and "sentrin" in other organisms) resembles ubiquitin (Ub) in structure, ligation to other proteins and the mechanism of ligation. Ubiquitin is a protein modifier in eukaryotes that is involved in various cellular processes including transcriptional regulation, cell cycle control, and DNA repair. Ubiquitination is comprised of a cascade of E1, E2 and E3 enzymes that results in a covalent bond between the C-terminus of Ub and the epsilon-amino group of a substrate lysine. SUMOs, like Ub, are covalently conjugated to lysine residues in a wide variety of target proteins in eukaryotic cells and regulate numerous cellular processes, such as transcription, epigenetic gene control, genomic instability, and protein degradation. Four SUMO paralogs exist in mammals, SUMO1 through SUMO4. SUMO2-SUMO4 are more closely related to each other than they are to SUMO1. SUMO1 is a binding partner of the RAD51/52 nucleoprotein filament proteins, which mediate DNA strand exchange. SUMO1 conjugation to cellular proteins has been implicated in multiple important cellular processes, such as nuclear transport, cell cycle control, oncogenesis, inflammation, and the response to virus infection.


Pssm-ID: 340531 [Multi-domain]  Cd Length: 76  Bit Score: 43.60  E-value: 2.93e-06
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 18408968 157 RVFADEKFERVIKLYTDKAKLDPQNLVFIFDGDKIDPSTTPSELGMEDHDMIEVHTKKT 215
Cdd:cd16114  17 KVKMTTHLKKLKESYCQRQGVPMNSLRFLFEGQRINDNHTPKELGMEEEDVIEVYQEQT 75
 
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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