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Conserved domains on  [gi|17556288|ref|NP_499551|]
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Nuclear pore complex protein npp-16 [Caenorhabditis elegans]

Protein Classification

Nup50 family Ran-binding domain-containing protein( domain architecture ID 10192182)

Nup50 family Ran-binding domain (RanBD)-containing protein similar to RanBD domain region of Homo sapiens nuclear pore complex protein Nup50, a component of the nuclear pore complex that has a direct role in nuclear protein import

CATH:  2.30.29.30
Gene Ontology:  GO:0046907
SCOP:  4002438

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RanBD_NUP50 cd13170
Nucleoporin 50 Ran-binding domain; NUP50 acts as a cofactor for the importin-alpha: ...
 387-496 1.56e-24

Nucleoporin 50 Ran-binding domain; NUP50 acts as a cofactor for the importin-alpha:importin-beta heterodimer, which allows for transportation of many nuclear-targeted proteins through nuclear pore complexes. It is thought to function primarily at the terminal stages of nuclear protein import to coordinate import complex disassembly and importin recycling. NUP50 is composed of a N-terminal NUP50 domain which binds the C-terminus of importin-beta, a central domain which binds importin-beta, and a C-terminal RanBD which binds importin-beta through Ran-GTP. NUP50:importin-alpha then binds cargo and can stimulate nuclear import. The N-terminal domain of NUP50 is also able to displace nuclear localization signals from importin-alpha. NUP50 interacts with cyclin-dependent kinase inhibitor 1B which binds to cyclin E-CDK2 or cyclin D-CDK4 complexes and prevents its activation, thereby controling the cell cycle progression at G1. Fungal Nup2 transiently associates with nuclear pore complexes (NPCs) and when artificially tethered to DNA, can prevent the spread of transcriptional activation or repression between flanking genes, a function termed boundary activity (BA). Nup2 and the Ran guanylyl-nucleotide exchange factor, Prp20, interact at specific chromatin regions and enable the NPC to play an active role in chromatin organization. Nup60p, the nup responsible for anchoring Nup2 and the Mlp proteins to the NPC is required for Nup2-dependent BA. Nup2 contains an N-terminal Nup50 family domain and a C-terminal RanBD. Ran is a Ras-like nuclear small GTPase, which regulates receptor-mediated transport between the nucleus and the cytoplasm. RanGTP hydrolysis is stimulated by RanGAP together with the Ran-binding domain containing acessory proteins RanBP1 and RanBP2. These accessory proteins stabilize the active GTP-bound form of Ran. RabBD shares structural similarity to the PH domain, but lacks detectable sequence similarity.


:

Pssm-ID: 269991  Cd Length: 111  Bit Score: 98.06  E-value: 1.56e-24
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17556288 387 ENQEPDAVLSSKVSVFKFT-GKEYTKLGVGMLHIKDND--GKFSVLIRAATaTGTVWLNSLCNKAMKATVvdAKGDRIRL 463
Cdd:cd13170   2 GEEEEDTVFEVRAKLFKKKdDGEWKDKGVGTLRLKKHKttGKARILVRADT-LGKILLNFLLYKGMPYSV--AGKNNVFV 78

                        90       100       110
                ....*....|....*....|....*....|...
gi 17556288 464 TCPSSSTEMATMMIRFGTADGAKKFTDKILEVA 496
Cdd:cd13170  79 GCVPNPGKPVTYLLRVKTAEDADELAKALEEEK 111
PRK04537 super family cl35267
ATP-dependent RNA helicase RhlB; Provisional
 79-235 1.85e-03

ATP-dependent RNA helicase RhlB; Provisional


The actual alignment was detected with superfamily member PRK04537:

Pssm-ID: 235307 [Multi-domain]  Cd Length: 572  Bit Score: 40.70  E-value: 1.85e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17556288   79 RTENSSESSGETVAPRKIAKAVRKNGTPKNPLNSTVFAASSPAATVASVPKFGdiSVITKETPAPLAKTAEPlvapaaPA 158
Cdd:PRK04537 436 RSGPGGGSRSGSVGGGGRRDGAGADGKPRPRRKPRVEGEADAAAAGAETPVVA--AAAAQAPGVVAADGERA------PR 507

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 17556288  159 TARKRaiRGGGPLGGAESVVFKSGeDGQAATSSVKIPATTIKfpeptkdfwtkksdapaAPSNSGSLFAFLGKDGDK 235
Cdd:PRK04537 508 KRRRR--RNGRPVEGAEPVSTPVP-APAAPRKPTQVVATPVR-----------------AAAKSSGSPSLLGRIGRR 564
 
Name Accession Description Interval E-value
RanBD_NUP50 cd13170
Nucleoporin 50 Ran-binding domain; NUP50 acts as a cofactor for the importin-alpha: ...
 387-496 1.56e-24

Nucleoporin 50 Ran-binding domain; NUP50 acts as a cofactor for the importin-alpha:importin-beta heterodimer, which allows for transportation of many nuclear-targeted proteins through nuclear pore complexes. It is thought to function primarily at the terminal stages of nuclear protein import to coordinate import complex disassembly and importin recycling. NUP50 is composed of a N-terminal NUP50 domain which binds the C-terminus of importin-beta, a central domain which binds importin-beta, and a C-terminal RanBD which binds importin-beta through Ran-GTP. NUP50:importin-alpha then binds cargo and can stimulate nuclear import. The N-terminal domain of NUP50 is also able to displace nuclear localization signals from importin-alpha. NUP50 interacts with cyclin-dependent kinase inhibitor 1B which binds to cyclin E-CDK2 or cyclin D-CDK4 complexes and prevents its activation, thereby controling the cell cycle progression at G1. Fungal Nup2 transiently associates with nuclear pore complexes (NPCs) and when artificially tethered to DNA, can prevent the spread of transcriptional activation or repression between flanking genes, a function termed boundary activity (BA). Nup2 and the Ran guanylyl-nucleotide exchange factor, Prp20, interact at specific chromatin regions and enable the NPC to play an active role in chromatin organization. Nup60p, the nup responsible for anchoring Nup2 and the Mlp proteins to the NPC is required for Nup2-dependent BA. Nup2 contains an N-terminal Nup50 family domain and a C-terminal RanBD. Ran is a Ras-like nuclear small GTPase, which regulates receptor-mediated transport between the nucleus and the cytoplasm. RanGTP hydrolysis is stimulated by RanGAP together with the Ran-binding domain containing acessory proteins RanBP1 and RanBP2. These accessory proteins stabilize the active GTP-bound form of Ran. RabBD shares structural similarity to the PH domain, but lacks detectable sequence similarity.


Pssm-ID: 269991  Cd Length: 111  Bit Score: 98.06  E-value: 1.56e-24
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17556288 387 ENQEPDAVLSSKVSVFKFT-GKEYTKLGVGMLHIKDND--GKFSVLIRAATaTGTVWLNSLCNKAMKATVvdAKGDRIRL 463
Cdd:cd13170   2 GEEEEDTVFEVRAKLFKKKdDGEWKDKGVGTLRLKKHKttGKARILVRADT-LGKILLNFLLYKGMPYSV--AGKNNVFV 78

                        90       100       110
                ....*....|....*....|....*....|...
gi 17556288 464 TCPSSSTEMATMMIRFGTADGAKKFTDKILEVA 496
Cdd:cd13170  79 GCVPNPGKPVTYLLRVKTAEDADELAKALEEEK 111
PRK04537 PRK04537
ATP-dependent RNA helicase RhlB; Provisional
 79-235 1.85e-03

ATP-dependent RNA helicase RhlB; Provisional


Pssm-ID: 235307 [Multi-domain]  Cd Length: 572  Bit Score: 40.70  E-value: 1.85e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17556288   79 RTENSSESSGETVAPRKIAKAVRKNGTPKNPLNSTVFAASSPAATVASVPKFGdiSVITKETPAPLAKTAEPlvapaaPA 158
Cdd:PRK04537 436 RSGPGGGSRSGSVGGGGRRDGAGADGKPRPRRKPRVEGEADAAAAGAETPVVA--AAAAQAPGVVAADGERA------PR 507

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 17556288  159 TARKRaiRGGGPLGGAESVVFKSGeDGQAATSSVKIPATTIKfpeptkdfwtkksdapaAPSNSGSLFAFLGKDGDK 235
Cdd:PRK04537 508 KRRRR--RNGRPVEGAEPVSTPVP-APAAPRKPTQVVATPVR-----------------AAAKSSGSPSLLGRIGRR 564
 
Name Accession Description Interval E-value
RanBD_NUP50 cd13170
Nucleoporin 50 Ran-binding domain; NUP50 acts as a cofactor for the importin-alpha: ...
 387-496 1.56e-24

Nucleoporin 50 Ran-binding domain; NUP50 acts as a cofactor for the importin-alpha:importin-beta heterodimer, which allows for transportation of many nuclear-targeted proteins through nuclear pore complexes. It is thought to function primarily at the terminal stages of nuclear protein import to coordinate import complex disassembly and importin recycling. NUP50 is composed of a N-terminal NUP50 domain which binds the C-terminus of importin-beta, a central domain which binds importin-beta, and a C-terminal RanBD which binds importin-beta through Ran-GTP. NUP50:importin-alpha then binds cargo and can stimulate nuclear import. The N-terminal domain of NUP50 is also able to displace nuclear localization signals from importin-alpha. NUP50 interacts with cyclin-dependent kinase inhibitor 1B which binds to cyclin E-CDK2 or cyclin D-CDK4 complexes and prevents its activation, thereby controling the cell cycle progression at G1. Fungal Nup2 transiently associates with nuclear pore complexes (NPCs) and when artificially tethered to DNA, can prevent the spread of transcriptional activation or repression between flanking genes, a function termed boundary activity (BA). Nup2 and the Ran guanylyl-nucleotide exchange factor, Prp20, interact at specific chromatin regions and enable the NPC to play an active role in chromatin organization. Nup60p, the nup responsible for anchoring Nup2 and the Mlp proteins to the NPC is required for Nup2-dependent BA. Nup2 contains an N-terminal Nup50 family domain and a C-terminal RanBD. Ran is a Ras-like nuclear small GTPase, which regulates receptor-mediated transport between the nucleus and the cytoplasm. RanGTP hydrolysis is stimulated by RanGAP together with the Ran-binding domain containing acessory proteins RanBP1 and RanBP2. These accessory proteins stabilize the active GTP-bound form of Ran. RabBD shares structural similarity to the PH domain, but lacks detectable sequence similarity.


Pssm-ID: 269991  Cd Length: 111  Bit Score: 98.06  E-value: 1.56e-24
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17556288 387 ENQEPDAVLSSKVSVFKFT-GKEYTKLGVGMLHIKDND--GKFSVLIRAATaTGTVWLNSLCNKAMKATVvdAKGDRIRL 463
Cdd:cd13170   2 GEEEEDTVFEVRAKLFKKKdDGEWKDKGVGTLRLKKHKttGKARILVRADT-LGKILLNFLLYKGMPYSV--AGKNNVFV 78

                        90       100       110
                ....*....|....*....|....*....|...
gi 17556288 464 TCPSSSTEMATMMIRFGTADGAKKFTDKILEVA 496
Cdd:cd13170  79 GCVPNPGKPVTYLLRVKTAEDADELAKALEEEK 111
RanBD_family cd00835
Ran-binding domain; The RanBD is present in RanBP1, RanBP2, RanBP3, Nuc2, and Nuc50. Most of ...
 387-494 3.09e-07

Ran-binding domain; The RanBD is present in RanBP1, RanBP2, RanBP3, Nuc2, and Nuc50. Most of these proteins have a single RanBD, with the exception of RanBP2 which has 4 RanBDs. Ran is a Ras-like nuclear small GTPase, which regulates receptor-mediated transport between the nucleus and the cytoplasm. RanGTP hydrolysis is stimulated by RanGAP together with the Ran-binding domain containing acessory proteins RanBP1 and RanBP2. These accessory proteins stabilize the active GTP-bound form of Ran. The Ran-binding domain is found in multiple copies in Nuclear pore complex proteins. RabBD shares structural similarity to the PH domain, but lacks detectable sequence similarity. The RanBD proteins of the nuclear pore complex (NPC): nucleoporin 1 (NUP1), NUP2, NUP61, and Nuclear Pore complex Protein 9 (npp-9) are present in the parent, but specific models were not made due to lineage. To date there been no reports of inositol phosphate or phosphoinositide binding by Ran-binding proteins.


Pssm-ID: 269907 [Multi-domain]  Cd Length: 118  Bit Score: 49.13  E-value: 3.09e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17556288 387 ENQEpdAVLSSKVSVFKF--TGKEYTKLGVGMLHIKDN--DGKFSVLIRAATaTGTVWLNSLCNKAMKATVVDAKGDRIR 462
Cdd:cd00835   4 ENEE--VLFEKRAKLFRFdkETKEWKERGVGDLKILKNkdTGKYRIVMRRDQ-VLKLCCNHYILPDMKLTKMGNNDRAWV 80

                        90       100       110
                ....*....|....*....|....*....|....*.
gi 17556288 463 LTCPSSSTEMA----TMMIRFGTADGAKKFTDKILE 494
Cdd:cd00835  81 WTAMDDSEDGEgkpeTFAVRFKTAEDAEEFKKAFEE 116
PRK04537 PRK04537
ATP-dependent RNA helicase RhlB; Provisional
 79-235 1.85e-03

ATP-dependent RNA helicase RhlB; Provisional


Pssm-ID: 235307 [Multi-domain]  Cd Length: 572  Bit Score: 40.70  E-value: 1.85e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17556288   79 RTENSSESSGETVAPRKIAKAVRKNGTPKNPLNSTVFAASSPAATVASVPKFGdiSVITKETPAPLAKTAEPlvapaaPA 158
Cdd:PRK04537 436 RSGPGGGSRSGSVGGGGRRDGAGADGKPRPRRKPRVEGEADAAAAGAETPVVA--AAAAQAPGVVAADGERA------PR 507

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 17556288  159 TARKRaiRGGGPLGGAESVVFKSGeDGQAATSSVKIPATTIKfpeptkdfwtkksdapaAPSNSGSLFAFLGKDGDK 235
Cdd:PRK04537 508 KRRRR--RNGRPVEGAEPVSTPVP-APAAPRKPTQVVATPVR-----------------AAAKSSGSPSLLGRIGRR 564
 
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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