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Conserved domains on  [gi|6323802|ref|NP_013873|]
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FG-nucleoporin NUP53 [Saccharomyces cerevisiae S288C]

Protein Classification

Nup35/Nup53 family RNA-binding protein( domain architecture ID 10190776)

Nup35/Nup53 family RNA-binding protein similar to Saccharomyces cerevisiae nucleoporin NUP53 and nucleoporin ASM4

Gene Ontology:  GO:0003676
PubMed:  22278943|18515081

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RRM_Nup53p_fungi cd12721
RNA recognition motif (RRM) found in yeast nucleoporin Nup53p and similar proteins; This ...
 250-347 2.79e-34

RNA recognition motif (RRM) found in yeast nucleoporin Nup53p and similar proteins; This subgroup corresponds to the RRM of Saccharomyces cerevisiae Nup53p, the ortholog of vertebrate nucleoporin Nup53. A unique property of yeast Nup53p is that it contains an additional Kap121p-binding domain and interacts specifically with the karyopherin Kap121p, which is involved in the assembly of Nup53p into NPCs. Like vertebrate Nup35, yeast Nup53p contains an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a C-terminal amphipathic alpha-helix and several FG repeats. The RRM domain lacks the conserved residues that typically bind RNA in canonical RRM domains.


:

Pssm-ID: 410120 [Multi-domain]  Cd Length: 86  Bit Score: 123.67  E-value: 2.79e-34
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323802  250 DHAIIIFGYPETIANSIILHFANFGEILEDFRVIKDFKKLnsknmskspsltaQKYPIYTGDGWVKLTYKSELSKSRALQ 329
Cdd:cd12721   1 GTAVIVFGFPETITSQVIEHFSGFGEILEDFSVPRSGKAL-------------QKYPIPTGSNWLKLTYAEPSSALRALR 67

                        90
                ....*....|....*....
gi 6323802  330 ENGIIMNGT-LIGCVSYSP 347
Cdd:cd12721  68 ENGEILNGQcMIGCIWYDD 86
 
Name Accession Description Interval E-value
RRM_Nup53p_fungi cd12721
RNA recognition motif (RRM) found in yeast nucleoporin Nup53p and similar proteins; This ...
 250-347 2.79e-34

RNA recognition motif (RRM) found in yeast nucleoporin Nup53p and similar proteins; This subgroup corresponds to the RRM of Saccharomyces cerevisiae Nup53p, the ortholog of vertebrate nucleoporin Nup53. A unique property of yeast Nup53p is that it contains an additional Kap121p-binding domain and interacts specifically with the karyopherin Kap121p, which is involved in the assembly of Nup53p into NPCs. Like vertebrate Nup35, yeast Nup53p contains an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a C-terminal amphipathic alpha-helix and several FG repeats. The RRM domain lacks the conserved residues that typically bind RNA in canonical RRM domains.


Pssm-ID: 410120 [Multi-domain]  Cd Length: 86  Bit Score: 123.67  E-value: 2.79e-34
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323802  250 DHAIIIFGYPETIANSIILHFANFGEILEDFRVIKDFKKLnsknmskspsltaQKYPIYTGDGWVKLTYKSELSKSRALQ 329
Cdd:cd12721   1 GTAVIVFGFPETITSQVIEHFSGFGEILEDFSVPRSGKAL-------------QKYPIPTGSNWLKLTYAEPSSALRALR 67

                        90
                ....*....|....*....
gi 6323802  330 ENGIIMNGT-LIGCVSYSP 347
Cdd:cd12721  68 ENGEILNGQcMIGCIWYDD 86
Nup35_RRM pfam05172
Nup53/35/40-type RNA recognition motif; Members of this family belong to the nucleor pore ...
 250-355 3.43e-30

Nup53/35/40-type RNA recognition motif; Members of this family belong to the nucleor pore complex, NPC, the only gateway between the nucleus and the cytoplasm. The NPC consists of several subcomplexes each one of which is made up of multiple copies of several individual Nup, Nic or Sec protein subunits. In yeast, this Nup or nucleoporin subunit is numbered Nup53, Nup40 in Schizo. pombe and in vertebrates as Nup35. This subunit forms part of the inner ring within the membrane and interacts directly with Nup-Ndc1, considered to be an anchor for the NPC in the pore membrane. This region of the Nup is the RNA-recognition region.


Pssm-ID: 398713 [Multi-domain]  Cd Length: 81  Bit Score: 112.10  E-value: 3.43e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323802    250 DHAIIIFGYPETIANSIILHFANFGEILEDFrvikdfkklnsknmskspsltaqkyPIYTGDGWVKLTYKSELSKSRALQ 329
Cdd:pfam05172   1 DTWVTVFGFPPSITNIVLLHFSRFGEIVSHV-------------------------PGPTNGNWMHLTYSSRSSAQKALS 55

                          90       100
                  ....*....|....*....|....*.
gi 6323802    330 ENGIIMNGTLIGCVSYSPAALKQLAS 355
Cdd:pfam05172  56 ENGTIINGSVIVGVSYCPATDKQVIN 81
 
Name Accession Description Interval E-value
RRM_Nup53p_fungi cd12721
RNA recognition motif (RRM) found in yeast nucleoporin Nup53p and similar proteins; This ...
 250-347 2.79e-34

RNA recognition motif (RRM) found in yeast nucleoporin Nup53p and similar proteins; This subgroup corresponds to the RRM of Saccharomyces cerevisiae Nup53p, the ortholog of vertebrate nucleoporin Nup53. A unique property of yeast Nup53p is that it contains an additional Kap121p-binding domain and interacts specifically with the karyopherin Kap121p, which is involved in the assembly of Nup53p into NPCs. Like vertebrate Nup35, yeast Nup53p contains an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a C-terminal amphipathic alpha-helix and several FG repeats. The RRM domain lacks the conserved residues that typically bind RNA in canonical RRM domains.


Pssm-ID: 410120 [Multi-domain]  Cd Length: 86  Bit Score: 123.67  E-value: 2.79e-34
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323802  250 DHAIIIFGYPETIANSIILHFANFGEILEDFRVIKDFKKLnsknmskspsltaQKYPIYTGDGWVKLTYKSELSKSRALQ 329
Cdd:cd12721   1 GTAVIVFGFPETITSQVIEHFSGFGEILEDFSVPRSGKAL-------------QKYPIPTGSNWLKLTYAEPSSALRALR 67

                        90
                ....*....|....*....
gi 6323802  330 ENGIIMNGT-LIGCVSYSP 347
Cdd:cd12721  68 ENGEILNGQcMIGCIWYDD 86
Nup35_RRM pfam05172
Nup53/35/40-type RNA recognition motif; Members of this family belong to the nucleor pore ...
 250-355 3.43e-30

Nup53/35/40-type RNA recognition motif; Members of this family belong to the nucleor pore complex, NPC, the only gateway between the nucleus and the cytoplasm. The NPC consists of several subcomplexes each one of which is made up of multiple copies of several individual Nup, Nic or Sec protein subunits. In yeast, this Nup or nucleoporin subunit is numbered Nup53, Nup40 in Schizo. pombe and in vertebrates as Nup35. This subunit forms part of the inner ring within the membrane and interacts directly with Nup-Ndc1, considered to be an anchor for the NPC in the pore membrane. This region of the Nup is the RNA-recognition region.


Pssm-ID: 398713 [Multi-domain]  Cd Length: 81  Bit Score: 112.10  E-value: 3.43e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323802    250 DHAIIIFGYPETIANSIILHFANFGEILEDFrvikdfkklnsknmskspsltaqkyPIYTGDGWVKLTYKSELSKSRALQ 329
Cdd:pfam05172   1 DTWVTVFGFPPSITNIVLLHFSRFGEIVSHV-------------------------PGPTNGNWMHLTYSSRSSAQKALS 55

                          90       100
                  ....*....|....*....|....*.
gi 6323802    330 ENGIIMNGTLIGCVSYSPAALKQLAS 355
Cdd:pfam05172  56 ENGTIINGSVIVGVSYCPATDKQVIN 81
RRM_Nup53_like cd12441
RNA recognition motif (RRM) found in nucleoporin Nup53 and similar proteins; This subfamily ...
 250-340 2.35e-10

RNA recognition motif (RRM) found in nucleoporin Nup53 and similar proteins; This subfamily corresponds to the RRM domain of nucleoporin Nup53, also termed mitotic phosphoprotein 44 (MP-44), or nuclear pore complex protein Nup53, required for normal cell growth and nuclear morphology in vertebrate. It tightly associates with the nuclear envelope membrane and the nuclear lamina where it interacts with lamin B. It may also interact with a group of nucleoporins including Nup93, Nup155, and Nup205 and play a role in the association of the mitotic checkpoint protein Mad1 with the nuclear pore complex (NPC). The family also includes Saccharomyces cerevisiae Nup53p, an ortholog of vertebrate nucleoporin Nup53. A unique property of yeast Nup53p is that it contains an additional Kap121p-binding domain and interacts specifically with the karyopherin Kap121p, which is involved in the assembly of Nup53p into NPCs. Both, vertebrate Nup35 and yeast Nup53p, contain an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a C-terminal amphipathic alpha-helix and several FG repeats. This family corresponds to the RRM domain which lacks the conserved residues that typically bind RNA in canonical RRM domains.


Pssm-ID: 409875 [Multi-domain]  Cd Length: 73  Bit Score: 56.47  E-value: 2.35e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6323802  250 DHAIIIFGYPETIANSIILHFANFGEILEdfrvikdfkklnsknmskspsltaQKYPiyTGDGWVKLTYKSELSKSRALQ 329
Cdd:cd12441   1 DTWVTVFGFPPSNASLVLREFSKCGDIVE------------------------HEYP--PGGNWIHIRYENRLQAERALS 54

                        90
                ....*....|.
gi 6323802  330 ENGIIMNGTLI 340
Cdd:cd12441  55 KNGRVLNGNVM 65
 
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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