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Conserved domains on  [gi|1049480185|ref|NP_001316845|]
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RNA-binding protein PNO1 isoform 2 [Homo sapiens]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
KH-I_PNO1_rpt1 cd22391
first type I K homology (KH) RNA-binding domain found in partner of NOB1 (PNO1) and similar ...
 73-152 4.93e-57

first type I K homology (KH) RNA-binding domain found in partner of NOB1 (PNO1) and similar proteins; PNO1 is an RNA-binding protein that acts as a ribosome assembly factor and plays an important role in ribosome biogenesis. It positively regulates dimethylation of two adjacent adenosines in the loop of a conserved hairpin near the 3'-end of 18S rRNA. PNO1 contains two K-homology (KH) RNA-binding domains. The model corresponds to the first one. The KH1 domain is a divergent KH domain that lacks the RNA-binding GXXG motif.


:

Pssm-ID: 411819  Cd Length: 80  Bit Score: 175.03  E-value: 4.93e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1049480185  73 EETRKIPVPANRYTPLKENWMKIFTPIVEHLGLQIRFNLKSRNVEIRTCKETKDVSALTKAADFVKAFILGFQVEDALAL 152
Cdd:cd22391     1 PEFRKVPVPPHRYTPLKENWMKIYTPIVEHLKLQIRMNLKTRKVELRTSKETEDIGALQKAADFVKAFMLGFEVEDALAL 80
KH-I super family cl00098
K homology (KH) RNA-binding domain, type I; KH binds single-stranded RNA or DNA. It is found ...
 154-208 2.44e-38

K homology (KH) RNA-binding domain, type I; KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include an N-terminal extension and type I KH domains (e.g. hnRNP K) contain a C-terminal extension. Some KH-I superfamily members contain a divergent KH domain that lacks the RNA-binding GXXG motif. Some others have a mutated GXXG motif which may or may not have nucleic acid binding ability.


The actual alignment was detected with superfamily member cd22392:

Pssm-ID: 469614  Cd Length: 96  Bit Score: 128.09  E-value: 2.44e-38
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1049480185 154 RLDDLFLESFEITDVKPLKGDHLSRAIGRIAGKGGKTKFTIENVTRTRIVLADVK 208
Cdd:cd22392     1 RLDDLYIESFEVKDVKTLKGDHLSRAIGRIAGKGGKTKFTIENATRTRIVLADTK 55
 
Name Accession Description Interval E-value
KH-I_PNO1_rpt1 cd22391
first type I K homology (KH) RNA-binding domain found in partner of NOB1 (PNO1) and similar ...
 73-152 4.93e-57

first type I K homology (KH) RNA-binding domain found in partner of NOB1 (PNO1) and similar proteins; PNO1 is an RNA-binding protein that acts as a ribosome assembly factor and plays an important role in ribosome biogenesis. It positively regulates dimethylation of two adjacent adenosines in the loop of a conserved hairpin near the 3'-end of 18S rRNA. PNO1 contains two K-homology (KH) RNA-binding domains. The model corresponds to the first one. The KH1 domain is a divergent KH domain that lacks the RNA-binding GXXG motif.


Pssm-ID: 411819  Cd Length: 80  Bit Score: 175.03  E-value: 4.93e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1049480185  73 EETRKIPVPANRYTPLKENWMKIFTPIVEHLGLQIRFNLKSRNVEIRTCKETKDVSALTKAADFVKAFILGFQVEDALAL 152
Cdd:cd22391     1 PEFRKVPVPPHRYTPLKENWMKIYTPIVEHLKLQIRMNLKTRKVELRTSKETEDIGALQKAADFVKAFMLGFEVEDALAL 80
KH-I_PNO1_rpt2 cd22392
second type I K homology (KH) RNA-binding domain found in partner of NOB1 (PNO1) and similar ...
 154-208 2.44e-38

second type I K homology (KH) RNA-binding domain found in partner of NOB1 (PNO1) and similar proteins; PNO1 is an RNA-binding protein that acts as a ribosome assembly factor and plays an important role in ribosome biogenesis. It positively regulates dimethylation of two adjacent adenosines in the loop of a conserved hairpin near the 3'-end of 18S rRNA. PNO1 contains two K-homology (KH) RNA-binding domains. The model corresponds to the second one.


Pssm-ID: 411820  Cd Length: 96  Bit Score: 128.09  E-value: 2.44e-38
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1049480185 154 RLDDLFLESFEITDVKPLKGDHLSRAIGRIAGKGGKTKFTIENVTRTRIVLADVK 208
Cdd:cd22392     1 RLDDLYIESFEVKDVKTLKGDHLSRAIGRIAGKGGKTKFTIENATRTRIVLADTK 55
PRK13763 PRK13763
putative RNA-processing protein; Provisional
 99-203 2.80e-15

putative RNA-processing protein; Provisional


Pssm-ID: 237494 [Multi-domain]  Cd Length: 180  Bit Score: 70.67  E-value: 2.80e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1049480185  99 IVEHLGLQIRFNLKSRNVEIrTCKETKDVSALTKAADFVKAFILGFQVEDALALIRlDDLFLESFEITDVKPLKgDHLSR 178
Cdd:PRK13763   28 IEERTGVKLEIDSETGEVII-EPTDGEDPLAVLKARDIVKAIGRGFSPEKALRLLD-DDYVLEVIDLSDYGDSP-NALRR 104

                          90       100
                  ....*....|....*....|....*
gi 1049480185 179 AIGRIAGKGGKTKFTIENVTRTRIV 203
Cdd:PRK13763  105 IKGRIIGEGGKTRRIIEELTGVDIS 129
arCOG04150 TIGR03665
arCOG04150 universal archaeal KH domain protein; This family of proteins is universal among ...
 105-203 2.18e-14

arCOG04150 universal archaeal KH domain protein; This family of proteins is universal among the 41 archaeal genomes analyzed, and is not observed outside of the archaea. The proteins contain a single KH domain (pfam00013) which is likely to confer the ability to bind RNA.


Pssm-ID: 274711 [Multi-domain]  Cd Length: 172  Bit Score: 68.36  E-value: 2.18e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1049480185 105 LQIRFNLKSRNVEIRTCKETKDVSALTKAADFVKAFILGFQVEDALALIRlDDLFLESFEITDVKPLKgDHLSRAIGRIA 184
Cdd:TIGR03665  27 TGVKLDIDSETGEVKIEPEDEDPLAVMKAREVVKAIGRGFSPEKALKLLD-DDYMLEVIDLKEYGKSP-NALRRIKGRII 104

                          90
                  ....*....|....*....
gi 1049480185 185 GKGGKTKFTIENVTRTRIV 203
Cdd:TIGR03665 105 GEGGKTRRIIEELTGVSIS 123
 
Name Accession Description Interval E-value
KH-I_PNO1_rpt1 cd22391
first type I K homology (KH) RNA-binding domain found in partner of NOB1 (PNO1) and similar ...
 73-152 4.93e-57

first type I K homology (KH) RNA-binding domain found in partner of NOB1 (PNO1) and similar proteins; PNO1 is an RNA-binding protein that acts as a ribosome assembly factor and plays an important role in ribosome biogenesis. It positively regulates dimethylation of two adjacent adenosines in the loop of a conserved hairpin near the 3'-end of 18S rRNA. PNO1 contains two K-homology (KH) RNA-binding domains. The model corresponds to the first one. The KH1 domain is a divergent KH domain that lacks the RNA-binding GXXG motif.


Pssm-ID: 411819  Cd Length: 80  Bit Score: 175.03  E-value: 4.93e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1049480185  73 EETRKIPVPANRYTPLKENWMKIFTPIVEHLGLQIRFNLKSRNVEIRTCKETKDVSALTKAADFVKAFILGFQVEDALAL 152
Cdd:cd22391     1 PEFRKVPVPPHRYTPLKENWMKIYTPIVEHLKLQIRMNLKTRKVELRTSKETEDIGALQKAADFVKAFMLGFEVEDALAL 80
KH-I_PNO1_rpt2 cd22392
second type I K homology (KH) RNA-binding domain found in partner of NOB1 (PNO1) and similar ...
 154-208 2.44e-38

second type I K homology (KH) RNA-binding domain found in partner of NOB1 (PNO1) and similar proteins; PNO1 is an RNA-binding protein that acts as a ribosome assembly factor and plays an important role in ribosome biogenesis. It positively regulates dimethylation of two adjacent adenosines in the loop of a conserved hairpin near the 3'-end of 18S rRNA. PNO1 contains two K-homology (KH) RNA-binding domains. The model corresponds to the second one.


Pssm-ID: 411820  Cd Length: 96  Bit Score: 128.09  E-value: 2.44e-38
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1049480185 154 RLDDLFLESFEITDVKPLKGDHLSRAIGRIAGKGGKTKFTIENVTRTRIVLADVK 208
Cdd:cd22392     1 RLDDLYIESFEVKDVKTLKGDHLSRAIGRIAGKGGKTKFTIENATRTRIVLADTK 55
PRK13763 PRK13763
putative RNA-processing protein; Provisional
 99-203 2.80e-15

putative RNA-processing protein; Provisional


Pssm-ID: 237494 [Multi-domain]  Cd Length: 180  Bit Score: 70.67  E-value: 2.80e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1049480185  99 IVEHLGLQIRFNLKSRNVEIrTCKETKDVSALTKAADFVKAFILGFQVEDALALIRlDDLFLESFEITDVKPLKgDHLSR 178
Cdd:PRK13763   28 IEERTGVKLEIDSETGEVII-EPTDGEDPLAVLKARDIVKAIGRGFSPEKALRLLD-DDYVLEVIDLSDYGDSP-NALRR 104

                          90       100
                  ....*....|....*....|....*
gi 1049480185 179 AIGRIAGKGGKTKFTIENVTRTRIV 203
Cdd:PRK13763  105 IKGRIIGEGGKTRRIIEELTGVDIS 129
arCOG04150 TIGR03665
arCOG04150 universal archaeal KH domain protein; This family of proteins is universal among ...
 105-203 2.18e-14

arCOG04150 universal archaeal KH domain protein; This family of proteins is universal among the 41 archaeal genomes analyzed, and is not observed outside of the archaea. The proteins contain a single KH domain (pfam00013) which is likely to confer the ability to bind RNA.


Pssm-ID: 274711 [Multi-domain]  Cd Length: 172  Bit Score: 68.36  E-value: 2.18e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1049480185 105 LQIRFNLKSRNVEIRTCKETKDVSALTKAADFVKAFILGFQVEDALALIRlDDLFLESFEITDVKPLKgDHLSRAIGRIA 184
Cdd:TIGR03665  27 TGVKLDIDSETGEVKIEPEDEDPLAVMKAREVVKAIGRGFSPEKALKLLD-DDYMLEVIDLKEYGKSP-NALRRIKGRII 104

                          90
                  ....*....|....*....
gi 1049480185 185 GKGGKTKFTIENVTRTRIV 203
Cdd:TIGR03665 105 GEGGKTRRIIEELTGVSIS 123
KH-I_IGF2BP_rpt4 cd22403
fourth type I K homology (KH) RNA-binding domain found in the insulin-like growth factor 2 ...
 177-206 7.05e-03

fourth type I K homology (KH) RNA-binding domain found in the insulin-like growth factor 2 mRNA-binding protein (IGF2BP) family; The IGF2BP family includes three members: IGF2BP1/IMP-1/CRD-BP/VICKZ1, IGF2BP2/IMP-2/VICKZ2, and IGF2BP3/IMP-3/VICKZ3, which are RNA-binding factors that recruit target transcripts to cytoplasmic protein-RNA complexes (mRNPs). They function by binding to the 5' UTR of the insulin-like growth factor 2 (IGF2) mRNA and regulating IGF2 translation. IGF2BP proteins contain four K-homology (KH) RNA-binding domains which are important in RNA binding and are known to be involved in RNA synthesis and metabolism. The model corresponds to the fourth one.


Pssm-ID: 411831 [Multi-domain]  Cd Length: 66  Bit Score: 34.14  E-value: 7.05e-03
                          10        20        30
                  ....*....|....*....|....*....|
gi 1049480185 177 SRAIGRIAGKGGKTKFTIENVTRTRIVLAD 206
Cdd:cd22403     8 SSMVGRIIGKGGQNVRELQRLTGAIIKLPR 37
 
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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